HEADER PROTEIN FIBRIL 29-MAY-21 7N2I
TITLE MICROED STRUCTURE OF HUMAN LECT2 (45-53) PHASED BY ARCIMBOLDO-BORGES
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: LECT2;
COMPND 3 CHAIN: A;
COMPND 4 FRAGMENT: RESIDUES 45-53;
COMPND 5 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 SYNTHETIC: YES;
SOURCE 3 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 4 ORGANISM_TAXID: 9606
KEYWDS MICROED, AMYLOID, LECT2, PROTEIN FIBRIL
EXPDTA ELECTRON CRYSTALLOGRAPHY
AUTHOR L.S.RICHARDS,M.D.FLORES,C.T.ZEE,C.GLYNN,M.GALLAGHER-JONES,M.R.SAWAYA
REVDAT 3 22-MAY-24 7N2I 1 REMARK
REVDAT 2 10-MAY-23 7N2I 1 JRNL
REVDAT 1 01-JUN-22 7N2I 0
JRNL AUTH L.S.RICHARDS,M.D.FLORES,C.MILLAN,C.GLYNN,C.T.ZEE,M.R.SAWAYA,
JRNL AUTH 2 M.GALLAGHER-JONES,R.J.BORGES,I.USON,J.A.RODRIGUEZ
JRNL TITL FRAGMENT-BASED AB INITIO PHASING OF PEPTIDIC NANOCRYSTALS BY
JRNL TITL 2 MICROED.
JRNL REF ACS BIO MED CHEM AU V. 3 201 2023
JRNL REFN ESSN 2694-2437
JRNL PMID 37096030
JRNL DOI 10.1021/ACSBIOMEDCHEMAU.2C00082
REMARK 2
REMARK 2 RESOLUTION. 1.40 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 : ML
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.40
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 7.75
REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.400
REMARK 3 COMPLETENESS FOR RANGE (%) : 81.2
REMARK 3 NUMBER OF REFLECTIONS : 985
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 R VALUE (WORKING + TEST SET) : 0.194
REMARK 3 R VALUE (WORKING SET) : 0.194
REMARK 3 FREE R VALUE : 0.192
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.040
REMARK 3 FREE R VALUE TEST SET COUNT : 89
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS).
REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE
REMARK 3 1 7.7540 - 2.9695 0.77 103 11 0.1354 0.1280
REMARK 3 2 2.9695 - 2.3794 0.77 75 7 0.1834 0.1803
REMARK 3 3 2.3794 - 2.0853 0.80 101 10 0.1996 0.1673
REMARK 3 4 2.0853 - 1.8977 0.81 94 9 0.2001 0.2017
REMARK 3 5 1.8977 - 1.7634 0.80 81 8 0.2457 0.1272
REMARK 3 6 1.7634 - 1.6605 0.84 79 8 0.2201 0.3715
REMARK 3 7 1.6605 - 1.5781 0.78 72 7 0.2465 0.2548
REMARK 3 8 1.5781 - 1.5099 0.88 99 10 0.2217 0.2996
REMARK 3 9 1.5099 - 1.4522 0.84 95 10 0.2414 0.1986
REMARK 3 10 1.4522 - 1.4024 0.85 97 9 0.2652 0.4549
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) : 0.130
REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.650
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 15.81
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 8.78
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 7N2I COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-JUN-21.
REMARK 100 THE DEPOSITION ID IS D_1000254609.
REMARK 240
REMARK 240 EXPERIMENTAL DETAILS
REMARK 240 RECONSTRUCTION METHOD : CRYSTALLOGRAPHY
REMARK 240 SAMPLE TYPE : 3D ARRAY
REMARK 240 SPECIMEN TYPE : NULL
REMARK 240 DATA ACQUISITION
REMARK 240 DATE OF DATA COLLECTION : NULL
REMARK 240 TEMPERATURE (KELVIN) : NULL
REMARK 240 PH : NULL
REMARK 240 NUMBER OF CRYSTALS USED : NULL
REMARK 240 MICROSCOPE MODEL : FEI TALOS ARCTICA
REMARK 240 DETECTOR TYPE : TVIPS TEMCAM-F416 (4K X 4K)
REMARK 240 ACCELERATION VOLTAGE (KV) : 200
REMARK 240 NUMBER OF UNIQUE REFLECTIONS : 986
REMARK 240 RESOLUTION RANGE HIGH (A) : 1.400
REMARK 240 RESOLUTION RANGE LOW (A) : 7.754
REMARK 240 DATA SCALING SOFTWARE : XSCALE
REMARK 240 COMPLETENESS FOR RANGE (%) : 80.0
REMARK 240 DATA REDUNDANCY : 4.218
REMARK 240 IN THE HIGHEST RESOLUTION SHELL
REMARK 240 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) :1.40
REMARK 240 HIGHEST RESOLUTION SHELL, RANGE LOW (A) :1.48
REMARK 240 COMPLETENESS FOR SHELL (%) : 82.8
REMARK 240 DATA REDUNDANCY IN SHELL : 4.17
REMARK 240 R MERGE FOR SHELL (I) : 0.38500
REMARK 240 METHOD USED TO DETERMINE THE STRUCTURE: NULL
REMARK 240 SOFTWARE USED : NULL
REMARK 240 STARTING MODEL : NULL
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 29.20000
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 2.36500
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 29.20000
REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 2.36500
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 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: MONOMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 1220 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL
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 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: TORSION ANGLES
REMARK 500
REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS:
REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2)
REMARK 500
REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI-
REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400
REMARK 500
REMARK 500 M RES CSSEQI PSI PHI
REMARK 500 ALA A 5 56.62 -145.68
REMARK 500
REMARK 500 REMARK: NULL
DBREF 7N2I A 0 8 PDB 7N2I 7N2I 0 8
SEQRES 1 A 9 GLY SER THR VAL TYR ALA PRO PHE THR
FORMUL 2 HOH *2(H2 O)
CRYST1 58.400 4.730 19.630 90.00 105.01 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 0.017123 0.000000 0.004590 0.00000
SCALE2 0.000000 0.211416 0.000000 0.00000
SCALE3 0.000000 0.000000 0.052741 0.00000
ATOM 1 N GLY A 0 26.606 3.420 4.944 1.00 17.40 N
ATOM 2 CA GLY A 0 25.680 3.579 6.048 1.00 13.53 C
ATOM 3 C GLY A 0 24.611 2.507 6.061 1.00 9.49 C
ATOM 4 O GLY A 0 24.436 1.777 5.091 1.00 14.50 O
ATOM 5 N SER A 1 23.900 2.405 7.174 1.00 9.09 N
ATOM 6 CA SER A 1 22.770 1.498 7.263 1.00 6.71 C
ATOM 7 C SER A 1 21.495 2.223 6.868 1.00 5.68 C
ATOM 8 O SER A 1 21.431 3.446 6.835 1.00 6.97 O
ATOM 9 CB SER A 1 22.640 0.931 8.674 1.00 10.35 C
ATOM 10 OG SER A 1 23.807 0.214 9.030 1.00 10.87 O
ATOM 11 N THR A 2 20.472 1.448 6.570 1.00 6.39 N
ATOM 12 CA THR A 2 19.253 1.994 6.017 1.00 5.89 C
ATOM 13 C THR A 2 18.078 1.290 6.661 1.00 6.11 C
ATOM 14 O THR A 2 18.082 0.067 6.803 1.00 6.07 O
ATOM 15 CB THR A 2 19.199 1.731 4.506 1.00 8.91 C
ATOM 16 OG1 THR A 2 20.373 2.268 3.884 1.00 10.62 O
ATOM 17 CG2 THR A 2 17.968 2.356 3.890 1.00 9.10 C
ATOM 18 N VAL A 3 17.080 2.066 7.061 1.00 6.44 N
ATOM 19 CA VAL A 3 15.739 1.552 7.271 1.00 4.92 C
ATOM 20 C VAL A 3 14.894 2.140 6.162 1.00 4.88 C
ATOM 21 O VAL A 3 14.752 3.364 6.067 1.00 5.53 O
ATOM 22 CB VAL A 3 15.186 1.912 8.653 1.00 5.32 C
ATOM 23 CG1 VAL A 3 13.693 1.598 8.719 1.00 6.64 C
ATOM 24 CG2 VAL A 3 15.948 1.149 9.725 1.00 5.37 C
ATOM 25 N TYR A 4 14.396 1.285 5.294 1.00 5.33 N
ATOM 26 CA TYR A 4 13.564 1.697 4.181 1.00 4.07 C
ATOM 27 C TYR A 4 12.164 1.251 4.547 1.00 4.54 C
ATOM 28 O TYR A 4 11.860 0.055 4.500 1.00 4.61 O
ATOM 29 CB TYR A 4 14.026 1.006 2.907 1.00 6.66 C
ATOM 30 CG TYR A 4 13.195 1.352 1.701 1.00 5.78 C
ATOM 31 CD1 TYR A 4 13.546 2.405 0.876 1.00 7.04 C
ATOM 32 CD2 TYR A 4 12.060 0.628 1.384 1.00 6.40 C
ATOM 33 CE1 TYR A 4 12.799 2.713 -0.230 1.00 6.27 C
ATOM 34 CE2 TYR A 4 11.299 0.939 0.278 1.00 8.08 C
ATOM 35 CZ TYR A 4 11.668 1.988 -0.519 1.00 9.14 C
ATOM 36 OH TYR A 4 10.909 2.298 -1.621 1.00 9.33 O
ATOM 37 N ALA A 5 11.329 2.195 4.931 1.00 5.25 N
ATOM 38 CA ALA A 5 10.005 1.805 5.369 1.00 4.19 C
ATOM 39 C ALA A 5 8.974 2.852 4.979 1.00 3.96 C
ATOM 40 O ALA A 5 8.249 3.349 5.847 1.00 5.30 O
ATOM 41 CB ALA A 5 10.004 1.594 6.879 1.00 4.55 C
ATOM 42 N PRO A 6 8.854 3.191 3.696 1.00 6.32 N
ATOM 43 CA PRO A 6 7.727 4.027 3.279 1.00 4.06 C
ATOM 44 C PRO A 6 6.441 3.306 3.620 1.00 4.35 C
ATOM 45 O PRO A 6 6.356 2.082 3.547 1.00 4.89 O
ATOM 46 CB PRO A 6 7.909 4.131 1.765 1.00 6.70 C
ATOM 47 CG PRO A 6 8.585 2.862 1.402 1.00 5.20 C
ATOM 48 CD PRO A 6 9.543 2.609 2.534 1.00 5.92 C
ATOM 49 N PHE A 7 5.431 4.064 4.009 1.00 6.10 N
ATOM 50 CA PHE A 7 4.224 3.384 4.421 1.00 6.14 C
ATOM 51 C PHE A 7 2.996 4.209 4.106 1.00 8.04 C
ATOM 52 O PHE A 7 3.073 5.409 3.841 1.00 7.03 O
ATOM 53 CB PHE A 7 4.272 2.963 5.888 1.00 7.89 C
ATOM 54 CG PHE A 7 4.344 4.099 6.874 1.00 8.64 C
ATOM 55 CD1 PHE A 7 3.188 4.616 7.439 1.00 9.74 C
ATOM 56 CD2 PHE A 7 5.567 4.593 7.296 1.00 8.41 C
ATOM 57 CE1 PHE A 7 3.249 5.631 8.373 1.00 8.14 C
ATOM 58 CE2 PHE A 7 5.633 5.614 8.230 1.00 7.87 C
ATOM 59 CZ PHE A 7 4.475 6.124 8.775 1.00 8.52 C
ATOM 60 N THR A 8 1.860 3.522 4.105 1.00 10.75 N
ATOM 61 CA THR A 8 0.557 4.153 4.058 1.00 16.25 C
ATOM 62 C THR A 8 -0.311 3.374 5.031 1.00 20.10 C
ATOM 63 O THR A 8 0.118 2.338 5.543 1.00 18.08 O
ATOM 64 CB THR A 8 -0.084 4.082 2.657 1.00 22.95 C
ATOM 65 OG1 THR A 8 -0.391 2.720 2.339 1.00 24.81 O
ATOM 66 CG2 THR A 8 0.848 4.652 1.596 1.00 24.19 C
ATOM 67 OXT THR A 8 -1.441 3.752 5.332 1.00 21.92 O
TER 68 THR A 8
HETATM 69 O HOH A 101 20.665 3.540 1.987 1.00 13.76 O
HETATM 70 O HOH A 102 4.629 1.501 1.407 1.00 11.55 O
MASTER 191 0 0 0 0 0 0 6 69 1 0 1
END