HEADER PROTEIN FIBRIL 27-DEC-14 4XFO
TITLE STRUCTURE OF AN AMYLOID-FORMING SEGMENT TAVVTN FROM HUMAN
TITLE 2 TRANSTHYRETIN
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: AMYLOID-FORMING PEPTIDE TAVVTN;
COMPND 3 CHAIN: A;
COMPND 4 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 SYNTHETIC: YES;
SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT;
SOURCE 4 ORGANISM_TAXID: 32630;
SOURCE 5 OTHER_DETAILS: THIS SEQUENCE CORRESPONDS TO A SEGMENT FROM HUMAN
SOURCE 6 TRANSTHYRETIN
KEYWDS AMYLOID, TRANSTHYRETIN, FIBRIL, PROTEIN FIBRIL
EXPDTA X-RAY DIFFRACTION
AUTHOR L.SAELICES,M.SAWAYA,D.CASCIO,D.S.EISENBERG
REVDAT 4 28-FEB-24 4XFO 1 JRNL REMARK
REVDAT 3 09-DEC-15 4XFO 1 JRNL
REVDAT 2 28-OCT-15 4XFO 1 JRNL
REVDAT 1 21-OCT-15 4XFO 0
JRNL AUTH L.SAELICES,L.M.JOHNSON,W.Y.LIANG,M.R.SAWAYA,D.CASCIO,
JRNL AUTH 2 P.RUCHALA,J.WHITELEGGE,L.JIANG,R.RIEK,D.S.EISENBERG
JRNL TITL UNCOVERING THE MECHANISM OF AGGREGATION OF HUMAN
JRNL TITL 2 TRANSTHYRETIN.
JRNL REF J.BIOL.CHEM. V. 290 28932 2015
JRNL REFN ESSN 1083-351X
JRNL PMID 26459562
JRNL DOI 10.1074/JBC.M115.659912
REMARK 2
REMARK 2 RESOLUTION. 1.35 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.9_1692)
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 : ML
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.35
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 16.01
REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.120
REMARK 3 COMPLETENESS FOR RANGE (%) : 91.9
REMARK 3 NUMBER OF REFLECTIONS : 624
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 R VALUE (WORKING + TEST SET) : 0.135
REMARK 3 R VALUE (WORKING SET) : 0.134
REMARK 3 FREE R VALUE : 0.148
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.100
REMARK 3 FREE R VALUE TEST SET COUNT : 63
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 : FLAT BULK SOLVENT MODEL
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) : 0.060
REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 13.920
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL
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 : 0.009 41
REMARK 3 ANGLE : 1.270 57
REMARK 3 CHIRALITY : 0.052 10
REMARK 3 PLANARITY : 0.004 7
REMARK 3 DIHEDRAL : 12.584 12
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 4XFO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-JAN-15.
REMARK 100 THE DEPOSITION ID IS D_1000205587.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 09-DEC-12
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 5.5
REMARK 200 NUMBER OF CRYSTALS USED : NULL
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) : 0.9792
REMARK 200 MONOCHROMATOR : SI (111)
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : PIXEL
REMARK 200 DETECTOR MANUFACTURER : PSI PILATUS 6M
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS
REMARK 200 DATA SCALING SOFTWARE : XSCALE
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 629
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.350
REMARK 200 RESOLUTION RANGE LOW (A) : 16.010
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 92.6
REMARK 200 DATA REDUNDANCY : 21.80
REMARK 200 R MERGE (I) : NULL
REMARK 200 R SYM (I) : NULL
REMARK 200 FOR THE DATA SET : 6.9300
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: NULL
REMARK 200 SOFTWARE USED: MOLREP
REMARK 200 STARTING MODEL: NULL
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 6.22
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.35
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M AMMONIUM SULFATE, 0.1 M BIS-TRIS
REMARK 280 PH 5.5, 25% W/V POLYETHYLENE GLYCOL 3,350, 25% GLYCEROL, VAPOR
REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 298K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,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
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 INDEFINITELY LONG BETA
REMARK 300 SHEETS CONSTRUCTED FROM CHAIN A AND UNIT CELL TRANSLATIONS ALONG
REMARK 300 THE "A" DIRECTION (THAT IS, THE "A" DIRECTION CORRESPONDS TO THE
REMARK 300 FIBER AXIS) (I.E. X,Y,Z; X+1,Y,Z; X+2,Y,Z; ETC.) TOGETHER WITH A
REMARK 300 COMPLEMENTARY SHEET FORMED FROM X,Y+1,Z AND ITS UNIT CELL
REMARK 300 TRANSLATIONS ALONG THE "A" DIRECTION (I.E. X+1,Y+1,Z; X+2,Y+1,Z; X+
REMARK 300 3,Y+1,Z;, ETC.)
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: TETRAMERIC
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A
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: A
REMARK 350 BIOMT1 2 1.000000 0.000000 0.000000 4.75000
REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000
REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A
REMARK 350 BIOMT1 3 1.000000 0.000000 0.000000 9.50000
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: A
REMARK 350 BIOMT1 4 1.000000 0.000000 0.000000 14.25000
REMARK 350 BIOMT2 4 0.000000 1.000000 0.000000 0.00000
REMARK 350 BIOMT3 4 0.000000 0.000000 1.000000 0.00000
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 4XFN RELATED DB: PDB
DBREF 4XFO A 1 6 PDB 4XFO 4XFO 1 6
SEQRES 1 A 6 THR ALA VAL VAL THR ASN
CRYST1 4.750 10.660 16.390 77.64 87.81 77.61 P 1 1
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 0.210526 -0.046264 0.001755 0.00000
SCALE2 0.000000 0.096047 -0.020718 0.00000
SCALE3 0.000000 0.000000 0.062462 0.00000
ATOM 1 N THR A 1 0.496 -0.528 -2.304 1.00 1.55 N
ATOM 2 CA THR A 1 0.217 -0.538 -3.735 1.00 1.55 C
ATOM 3 C THR A 1 0.863 -1.737 -4.414 1.00 2.55 C
ATOM 4 O THR A 1 2.075 -1.899 -4.378 1.00 1.94 O
ATOM 5 CB THR A 1 0.711 0.769 -4.396 1.00 2.85 C
ATOM 6 OG1 THR A 1 0.144 1.886 -3.696 1.00 3.35 O
ATOM 7 CG2 THR A 1 0.300 0.824 -5.868 1.00 3.18 C
ATOM 8 N ALA A 2 0.030 -2.576 -5.023 1.00 1.18 N
ATOM 9 CA ALA A 2 0.499 -3.729 -5.770 1.00 1.03 C
ATOM 10 C ALA A 2 -0.111 -3.669 -7.153 1.00 1.24 C
ATOM 11 O ALA A 2 -1.334 -3.531 -7.295 1.00 2.05 O
ATOM 12 CB ALA A 2 0.118 -5.041 -5.070 1.00 1.74 C
ATOM 13 N VAL A 3 0.743 -3.766 -8.169 1.00 0.47 N
ATOM 14 CA VAL A 3 0.322 -3.667 -9.556 1.00 0.39 C
ATOM 15 C VAL A 3 0.951 -4.820 -10.318 1.00 0.52 C
ATOM 16 O VAL A 3 2.171 -4.950 -10.363 1.00 0.52 O
ATOM 17 CB VAL A 3 0.735 -2.306 -10.193 1.00 0.47 C
ATOM 18 CG1 VAL A 3 0.224 -2.207 -11.635 1.00 0.54 C
ATOM 19 CG2 VAL A 3 0.247 -1.129 -9.327 1.00 0.79 C
ATOM 20 N VAL A 4 0.107 -5.666 -10.903 1.00 0.34 N
ATOM 21 CA VAL A 4 0.571 -6.889 -11.538 1.00 0.39 C
ATOM 22 C VAL A 4 -0.018 -7.055 -12.916 1.00 0.53 C
ATOM 23 O VAL A 4 -1.225 -6.906 -13.093 1.00 0.46 O
ATOM 24 CB VAL A 4 0.191 -8.153 -10.703 1.00 0.70 C
ATOM 25 CG1 VAL A 4 0.590 -9.437 -11.437 1.00 1.04 C
ATOM 26 CG2 VAL A 4 0.831 -8.093 -9.328 1.00 1.15 C
ATOM 27 N THR A 5 0.842 -7.375 -13.880 1.00 0.32 N
ATOM 28 CA THR A 5 0.433 -7.881 -15.191 1.00 0.72 C
ATOM 29 C THR A 5 1.026 -9.269 -15.339 1.00 0.93 C
ATOM 30 O THR A 5 2.207 -9.472 -15.092 1.00 1.03 O
ATOM 31 CB THR A 5 0.898 -6.972 -16.337 1.00 1.15 C
ATOM 32 OG1 THR A 5 0.038 -5.829 -16.389 1.00 2.12 O
ATOM 33 CG2 THR A 5 0.820 -7.688 -17.673 1.00 1.44 C
ATOM 34 N ASN A 6 0.174 -10.225 -15.693 1.00 0.89 N
ATOM 35 CA ASN A 6 0.565 -11.615 -15.856 1.00 1.76 C
ATOM 36 C ASN A 6 -0.257 -12.201 -17.006 1.00 2.47 C
ATOM 37 O ASN A 6 -0.042 -13.334 -17.424 1.00 3.59 O
ATOM 38 CB ASN A 6 0.341 -12.389 -14.553 1.00 1.49 C
ATOM 39 CG ASN A 6 0.960 -13.790 -14.556 1.00 1.48 C
ATOM 40 OD1 ASN A 6 2.141 -13.976 -14.857 1.00 2.17 O
ATOM 41 ND2 ASN A 6 0.156 -14.780 -14.180 1.00 1.46 N
ATOM 42 OXT ASN A 6 -1.156 -11.510 -17.524 1.00 3.92 O
TER 43 ASN A 6
MASTER 197 0 0 0 0 0 0 6 42 1 0 1
END