HEADER DE NOVO PROTEIN 16-NOV-16 5TXD
TITLE STRUCTURE OF AMYLOID-BETA DERIVED PEPTIDE - NKGAIF
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: AMYLOID BETA A4 PROTEIN;
COMPND 3 CHAIN: Z;
COMPND 4 FRAGMENT: UNP RESIDUES 698-703;
COMPND 5 SYNONYM: ABPP,APPI,APP,ALZHEIMER DISEASE AMYLOID PROTEIN,AMYLOID
COMPND 6 PRECURSOR PROTEIN,BETA-AMYLOID PRECURSOR PROTEIN,CEREBRAL VASCULAR
COMPND 7 AMYLOID PEPTIDE,CVAP,PREA4,PROTEASE NEXIN-II,PN-II;
COMPND 8 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 SYNTHETIC: YES;
SOURCE 3 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 4 ORGANISM_COMMON: HUMAN;
SOURCE 5 ORGANISM_TAXID: 9606;
SOURCE 6 OTHER_DETAILS: SYNTHESIZED
KEYWDS PROTEIN FIBRIL, DE NOVO PROTEIN
EXPDTA X-RAY DIFFRACTION
AUTHOR S.SANGWAN,M.R.SAWAYA,D.EISENBERG
REVDAT 4 03-APR-24 5TXD 1 REMARK
REVDAT 3 06-MAR-24 5TXD 1 COMPND
REVDAT 2 10-OCT-18 5TXD 1 COMPND JRNL
REVDAT 1 15-NOV-17 5TXD 0
JRNL AUTH T.D.DO,S.SANGWAN,N.E.C.DE ALMEIDA,A.I.ILITCHEV,M.GIAMMONA,
JRNL AUTH 2 M.R.SAWAYA,S.K.BURATTO,D.S.EISENBERG,M.T.BOWERS
JRNL TITL DISTAL AMYLOID BETA-PROTEIN FRAGMENTS TEMPLATE AMYLOID
JRNL TITL 2 ASSEMBLY.
JRNL REF PROTEIN SCI. V. 27 1181 2018
JRNL REFN ESSN 1469-896X
JRNL PMID 29349888
JRNL DOI 10.1002/PRO.3375
REMARK 2
REMARK 2 RESOLUTION. 1.45 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : PHENIX
REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN
REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE,
REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER,
REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY,
REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON,
REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI,
REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT
REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART
REMARK 3
REMARK 3 REFINEMENT TARGET : NULL
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.45
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.03
REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.440
REMARK 3 COMPLETENESS FOR RANGE (%) : 87.4
REMARK 3 NUMBER OF REFLECTIONS : 679
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 R VALUE (WORKING + TEST SET) : 0.176
REMARK 3 R VALUE (WORKING SET) : 0.174
REMARK 3 FREE R VALUE : 0.191
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 11.190
REMARK 3 FREE R VALUE TEST SET COUNT : 76
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS).
REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE
REMARK 3
REMARK 3 BULK SOLVENT MODELLING.
REMARK 3 METHOD USED : NULL
REMARK 3 SOLVENT RADIUS : 1.11
REMARK 3 SHRINKAGE RADIUS : 0.90
REMARK 3 K_SOL : NULL
REMARK 3 B_SOL : NULL
REMARK 3
REMARK 3 ERROR ESTIMATES.
REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.020
REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 16.800
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 7.46
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : NULL
REMARK 3 B22 (A**2) : NULL
REMARK 3 B33 (A**2) : NULL
REMARK 3 B12 (A**2) : NULL
REMARK 3 B13 (A**2) : NULL
REMARK 3 B23 (A**2) : NULL
REMARK 3
REMARK 3 TWINNING INFORMATION.
REMARK 3 FRACTION: NULL
REMARK 3 OPERATOR: NULL
REMARK 3
REMARK 3 DEVIATIONS FROM IDEAL VALUES.
REMARK 3 RMSD COUNT
REMARK 3 BOND : NULL NULL
REMARK 3 ANGLE : NULL NULL
REMARK 3 CHIRALITY : NULL NULL
REMARK 3 PLANARITY : NULL NULL
REMARK 3 DIHEDRAL : NULL NULL
REMARK 3
REMARK 3 TLS DETAILS
REMARK 3 NUMBER OF TLS GROUPS : NULL
REMARK 3
REMARK 3 NCS DETAILS
REMARK 3 NUMBER OF NCS GROUPS : NULL
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 5TXD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-NOV-16.
REMARK 100 THE DEPOSITION ID IS D_1000224982.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 07-DEC-14
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 5
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : APS
REMARK 200 BEAMLINE : 24-ID-E
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.9791
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS
REMARK 200 DATA SCALING SOFTWARE : XSCALE
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 679
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.450
REMARK 200 RESOLUTION RANGE LOW (A) : 26.030
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 87.4
REMARK 200 DATA REDUNDANCY : 2.300
REMARK 200 R MERGE (I) : 0.12900
REMARK 200 R SYM (I) : NULL
REMARK 200 FOR THE DATA SET : 6.8000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL
REMARK 200 COMPLETENESS FOR SHELL (%) : NULL
REMARK 200 DATA REDUNDANCY IN SHELL : NULL
REMARK 200 R MERGE FOR SHELL (I) : NULL
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 FOR SHELL : NULL
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: PHASER
REMARK 200 STARTING MODEL: 6 RESIDUE ALANINE BETA STRAND
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 13.45
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.42
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: RESERVOIR CONTAINED 20% PEG 3350, 0.2M
REMARK 280 POTASSIUM PHOSPHATE DIBASIC, PH 5, VAPOR DIFFUSION, HANGING DROP,
REMARK 280 TEMPERATURE 298K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -X,Y,-Z
REMARK 290 3555 X+1/2,Y+1/2,Z
REMARK 290 4555 -X+1/2,Y+1/2,-Z
REMARK 290
REMARK 290 WHERE NNN -> OPERATOR NUMBER
REMARK 290 MMM -> TRANSLATION VECTOR
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS
REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM
REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY
REMARK 290 RELATED MOLECULES.
REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000
REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 14.70100
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 2.41350
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 14.70100
REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 2.41350
REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000
REMARK 290
REMARK 290 REMARK: NULL
REMARK 300
REMARK 300 BIOMOLECULE: 1
REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM
REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN
REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON
REMARK 300 BURIED SURFACE AREA.
REMARK 300 REMARK: THE BIOLOGICAL ASSEMBLY IS A PAIR OF BETA SHEETS
REMARK 350
REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN
REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE
REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS
REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND
REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN.
REMARK 350
REMARK 350 BIOMOLECULE: 1
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: OCTAMERIC
REMARK 350 APPLY THE FOLLOWING TO CHAINS: Z
REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000
REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000
REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000
REMARK 350 APPLY THE FOLLOWING TO CHAINS: Z
REMARK 350 BIOMT1 2 1.000000 0.000000 0.000000 0.00000
REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 4.82700
REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000
REMARK 350 APPLY THE FOLLOWING TO CHAINS: Z
REMARK 350 BIOMT1 3 -1.000000 0.000000 0.000000 0.00000
REMARK 350 BIOMT2 3 0.000000 1.000000 0.000000 0.00000
REMARK 350 BIOMT3 3 0.000000 0.000000 -1.000000 0.00000
REMARK 350 APPLY THE FOLLOWING TO CHAINS: Z
REMARK 350 BIOMT1 4 -1.000000 0.000000 0.000000 0.00000
REMARK 350 BIOMT2 4 0.000000 1.000000 0.000000 4.82700
REMARK 350 BIOMT3 4 0.000000 0.000000 -1.000000 0.00000
REMARK 350 APPLY THE FOLLOWING TO CHAINS: Z
REMARK 350 BIOMT1 5 1.000000 0.000000 0.000000 14.70100
REMARK 350 BIOMT2 5 0.000000 1.000000 0.000000 2.41350
REMARK 350 BIOMT3 5 0.000000 0.000000 1.000000 0.00000
REMARK 350 APPLY THE FOLLOWING TO CHAINS: Z
REMARK 350 BIOMT1 6 1.000000 0.000000 0.000000 14.70100
REMARK 350 BIOMT2 6 0.000000 1.000000 0.000000 7.24050
REMARK 350 BIOMT3 6 0.000000 0.000000 1.000000 0.00000
REMARK 350 APPLY THE FOLLOWING TO CHAINS: Z
REMARK 350 BIOMT1 7 -1.000000 0.000000 0.000000 14.70100
REMARK 350 BIOMT2 7 0.000000 1.000000 0.000000 2.41350
REMARK 350 BIOMT3 7 0.000000 0.000000 -1.000000 0.00000
REMARK 350 APPLY THE FOLLOWING TO CHAINS: Z
REMARK 350 BIOMT1 8 -1.000000 0.000000 0.000000 14.70100
REMARK 350 BIOMT2 8 0.000000 1.000000 0.000000 7.24050
REMARK 350 BIOMT3 8 0.000000 0.000000 -1.000000 0.00000
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 Z 101
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 5TXH RELATED DB: PDB
REMARK 900 RELATED ID: 5TXD RELATED DB: PDB
DBREF 5TXD Z 1 6 UNP P05067 A4_HUMAN 698 703
SEQADV 5TXD PHE Z 6 UNP P05067 ILE 703 CONFLICT
SEQRES 1 Z 6 ASN LYS GLY ALA ILE PHE
HET PO4 Z 101 5
HETNAM PO4 PHOSPHATE ION
FORMUL 2 PO4 O4 P 3-
FORMUL 3 HOH *(H2 O)
SITE 1 AC1 4 ASN Z 1 LYS Z 2 PHE Z 6 HOH Z 201
CRYST1 29.402 4.827 26.612 90.00 102.04 90.00 C 1 2 1 4
ORIGX1 1.000000 0.000000 0.000000 0.00000
ORIGX2 0.000000 1.000000 0.000000 0.00000
ORIGX3 0.000000 0.000000 1.000000 0.00000
SCALE1 0.034011 0.000000 0.007252 0.00000
SCALE2 0.000000 0.207168 0.000000 0.00000
SCALE3 0.000000 0.000000 0.038422 0.00000
ATOM 1 N ASN Z 1 -8.220 -1.457 10.787 1.00 6.70 N
ATOM 2 CA ASN Z 1 -8.014 -2.133 9.508 1.00 5.69 C
ATOM 3 C ASN Z 1 -7.082 -1.378 8.586 1.00 5.45 C
ATOM 4 O ASN Z 1 -7.073 -0.155 8.564 1.00 6.38 O
ATOM 5 CB ASN Z 1 -9.351 -2.355 8.807 1.00 6.14 C
ATOM 6 CG ASN Z 1 -10.323 -3.117 9.672 1.00 7.80 C
ATOM 7 OD1 ASN Z 1 -9.932 -4.035 10.395 1.00 6.89 O
ATOM 8 ND2 ASN Z 1 -11.585 -2.725 9.631 1.00 7.52 N
ATOM 9 N LYS Z 2 -6.282 -2.121 7.836 1.00 5.68 N
ATOM 10 CA LYS Z 2 -5.319 -1.526 6.921 1.00 4.15 C
ATOM 11 C LYS Z 2 -5.261 -2.324 5.630 1.00 4.36 C
ATOM 12 O LYS Z 2 -5.369 -3.543 5.651 1.00 4.55 O
ATOM 13 CB LYS Z 2 -3.933 -1.459 7.562 1.00 3.95 C
ATOM 14 CG LYS Z 2 -3.920 -0.865 8.960 1.00 7.21 C
ATOM 15 CD LYS Z 2 -2.510 -0.817 9.525 1.00 7.88 C
ATOM 16 CE LYS Z 2 -1.690 0.282 8.860 1.00 10.92 C
ATOM 17 NZ LYS Z 2 -0.277 0.348 9.393 1.00 8.72 N
ATOM 18 N GLY Z 3 -5.090 -1.641 4.504 1.00 3.36 N
ATOM 19 CA GLY Z 3 -5.029 -2.326 3.229 1.00 3.35 C
ATOM 20 C GLY Z 3 -4.323 -1.539 2.147 1.00 2.13 C
ATOM 21 O GLY Z 3 -4.221 -0.316 2.214 1.00 2.67 O
ATOM 22 N ALA Z 4 -3.844 -2.256 1.139 1.00 3.47 N
ATOM 23 CA ALA Z 4 -3.235 -1.636 -0.024 1.00 3.48 C
ATOM 24 C ALA Z 4 -3.736 -2.312 -1.273 1.00 3.96 C
ATOM 25 O ALA Z 4 -3.857 -3.545 -1.307 1.00 5.79 O
ATOM 26 CB ALA Z 4 -1.739 -1.725 0.035 1.00 3.48 C
ATOM 27 N ILE Z 5 -4.040 -1.505 -2.282 1.00 3.15 N
ATOM 28 CA ILE Z 5 -4.428 -2.020 -3.582 1.00 4.23 C
ATOM 29 C ILE Z 5 -3.582 -1.317 -4.633 1.00 4.12 C
ATOM 30 O ILE Z 5 -3.572 -0.087 -4.702 1.00 4.16 O
ATOM 31 CB ILE Z 5 -5.922 -1.793 -3.888 1.00 3.32 C
ATOM 32 CG1 ILE Z 5 -6.821 -2.525 -2.876 1.00 3.99 C
ATOM 33 CG2 ILE Z 5 -6.222 -2.278 -5.297 1.00 4.17 C
ATOM 34 CD1 ILE Z 5 -6.980 -1.853 -1.502 1.00 4.25 C
ATOM 35 N PHE Z 6 -2.861 -2.087 -5.441 1.00 5.71 N
ATOM 36 CA PHE Z 6 -1.945 -1.490 -6.412 1.00 5.44 C
ATOM 37 C PHE Z 6 -1.594 -2.445 -7.538 1.00 7.01 C
ATOM 38 O PHE Z 6 -2.291 -3.448 -7.718 1.00 8.03 O
ATOM 39 CB PHE Z 6 -0.677 -1.016 -5.709 1.00 5.01 C
ATOM 40 CG PHE Z 6 0.032 -2.090 -4.930 1.00 4.75 C
ATOM 41 CD1 PHE Z 6 -0.414 -2.472 -3.670 1.00 4.10 C
ATOM 42 CD2 PHE Z 6 1.176 -2.688 -5.439 1.00 4.64 C
ATOM 43 CE1 PHE Z 6 0.245 -3.446 -2.948 1.00 3.78 C
ATOM 44 CE2 PHE Z 6 1.849 -3.660 -4.720 1.00 4.00 C
ATOM 45 CZ PHE Z 6 1.385 -4.043 -3.473 1.00 4.51 C
ATOM 46 OXT PHE Z 6 -0.626 -2.232 -8.289 1.00 8.38 O
TER 47 PHE Z 6
HETATM 48 P PO4 Z 101 -6.065 -0.390 13.382 1.00 29.08 P
HETATM 49 O1 PO4 Z 101 -5.821 -0.923 11.991 1.00 15.35 O
HETATM 50 O2 PO4 Z 101 -7.065 0.744 13.323 1.00 33.88 O
HETATM 51 O3 PO4 Z 101 -6.650 -1.476 14.271 1.00 21.93 O
HETATM 52 O4 PO4 Z 101 -4.759 0.128 13.933 1.00 28.21 O
HETATM 53 O HOH Z 201 -9.437 1.786 13.134 1.00 20.96 O
CONECT 48 49 50 51 52
CONECT 49 48
CONECT 50 48
CONECT 51 48
CONECT 52 48
MASTER 225 0 1 0 0 0 1 6 52 1 5 1
END