HEADER PROTEIN FIBRIL 18-JUN-22 8DDG
TITLE FYF PEPTIDE FORMS A STANDARD BETA-SHEET
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: PHE-TYR-PHE;
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
KEYWDS RIPPLED BETA-SHEET, RACEMIC PEPTIDE, PROTEIN FIBRIL
EXPDTA ELECTRON CRYSTALLOGRAPHY
AUTHOR M.R.SAWAYA,A.HAZARI,D.E.EISENBERG,N.W.VLAHAKIS
REVDAT 2 22-MAY-24 8DDG 1 REMARK
REVDAT 1 28-SEP-22 8DDG 0
JRNL AUTH A.HAZARI,M.R.SAWAYA,N.VLAHAKIS,T.C.JOHNSTONE,D.BOYER,
JRNL AUTH 2 J.RODRIGUEZ,D.EISENBERG,J.A.RASKATOV
JRNL TITL THE RIPPLED BETA-SHEET LAYER CONFIGURATION-A NOVEL
JRNL TITL 2 SUPRAMOLECULAR ARCHITECTURE BASED ON PREDICTIONS BY PAULING
JRNL TITL 3 AND COREY.
JRNL REF CHEM SCI V. 13 8947 2022
JRNL REFN ISSN 2041-6520
JRNL PMID 36091211
JRNL DOI 10.1039/D2SC02531K
REMARK 2
REMARK 2 RESOLUTION. 0.90 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 0.90
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 5.78
REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.410
REMARK 3 COMPLETENESS FOR RANGE (%) : 71.2
REMARK 3 NUMBER OF REFLECTIONS : 1232
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 R VALUE (WORKING + TEST SET) : 0.170
REMARK 3 R VALUE (WORKING SET) : 0.169
REMARK 3 FREE R VALUE : 0.185
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.090
REMARK 3 FREE R VALUE TEST SET COUNT : 112
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 5.7800 - 0.9000 0.71 1120 112 0.1692 0.1851
REMARK 3
REMARK 3 BULK SOLVENT MODELLING.
REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL
REMARK 3 SOLVENT RADIUS : 1.10
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) : 0.075
REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.609
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 6.87
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 3.26
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 : 0.020 37
REMARK 3 ANGLE : 1.254 49
REMARK 3 CHIRALITY : 0.090 3
REMARK 3 PLANARITY : 0.008 6
REMARK 3 DIHEDRAL : 19.201 4
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 8DDG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-JUN-22.
REMARK 100 THE DEPOSITION ID IS D_1000266472.
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 : 14-DEC-21
REMARK 240 TEMPERATURE (KELVIN) : NULL
REMARK 240 PH : NULL
REMARK 240 NUMBER OF CRYSTALS USED : NULL
REMARK 240 MICROSCOPE MODEL : FEI TECNAI F30
REMARK 240 DETECTOR TYPE : TVIPS TEMCAM-F416 (4K X 4K)
REMARK 240 ACCELERATION VOLTAGE (KV) : 300
REMARK 240 NUMBER OF UNIQUE REFLECTIONS : 1237
REMARK 240 RESOLUTION RANGE HIGH (A) : 0.900
REMARK 240 RESOLUTION RANGE LOW (A) : 18.920
REMARK 240 DATA SCALING SOFTWARE : XSCALE
REMARK 240 COMPLETENESS FOR RANGE (%) : 71.0
REMARK 240 DATA REDUNDANCY : 4.834
REMARK 240 IN THE HIGHEST RESOLUTION SHELL
REMARK 240 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) :0.90
REMARK 240 HIGHEST RESOLUTION SHELL, RANGE LOW (A) :1.00
REMARK 240 COMPLETENESS FOR SHELL (%) : 72.2
REMARK 240 DATA REDUNDANCY IN SHELL : 4.94
REMARK 240 R MERGE FOR SHELL (I) : 0.32200
REMARK 240 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS
REMARK 240 SOFTWARE USED : SHELXD
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 11.57000
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 2.42000
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 11.57000
REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 2.42000
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: PENTAMERIC
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 0.00000
REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 -4.84000
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 0.00000
REMARK 350 BIOMT2 3 0.000000 1.000000 0.000000 4.84000
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 0.00000
REMARK 350 BIOMT2 4 0.000000 1.000000 0.000000 -9.68000
REMARK 350 BIOMT3 4 0.000000 0.000000 1.000000 0.00000
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A
REMARK 350 BIOMT1 5 1.000000 0.000000 0.000000 0.00000
REMARK 350 BIOMT2 5 0.000000 1.000000 0.000000 9.68000
REMARK 350 BIOMT3 5 0.000000 0.000000 1.000000 0.00000
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 8DDH RELATED DB: PDB
REMARK 900 RELATED ID: 8DDF RELATED DB: PDB
DBREF 8DDG A 67 69 PDB 8DDG 8DDG 67 69
SEQRES 1 A 3 PHE TYR PHE
CRYST1 23.140 4.840 19.790 90.00 107.05 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 0.043215 0.000000 0.013252 0.00000
SCALE2 0.000000 0.206612 0.000000 0.00000
SCALE3 0.000000 0.000000 0.052853 0.00000
ATOM 1 N PHE A 67 11.803 3.940 5.910 1.00 3.25 N
ANISOU 1 N PHE A 67 220 226 790 13 -82 11 N
ATOM 2 CA PHE A 67 10.566 4.721 5.737 1.00 2.88 C
ANISOU 2 CA PHE A 67 174 204 718 20 -65 -103 C
ATOM 3 C PHE A 67 9.411 3.846 6.057 1.00 2.56 C
ANISOU 3 C PHE A 67 153 163 656 10 -75 -2 C
ATOM 4 O PHE A 67 9.529 2.642 6.197 1.00 3.33 O
ANISOU 4 O PHE A 67 213 328 724 -62 -58 30 O
ATOM 5 CB PHE A 67 10.427 5.204 4.302 1.00 3.09 C
ANISOU 5 CB PHE A 67 205 312 658 -15 -89 -113 C
ATOM 6 CG PHE A 67 10.166 4.124 3.321 1.00 2.90 C
ANISOU 6 CG PHE A 67 212 268 621 78 -36 -21 C
ATOM 7 CD1 PHE A 67 8.883 3.631 3.108 1.00 2.85 C
ANISOU 7 CD1 PHE A 67 227 309 547 38 -58 -225 C
ATOM 8 CD2 PHE A 67 11.199 3.609 2.587 1.00 3.20 C
ANISOU 8 CD2 PHE A 67 182 436 597 35 -65 79 C
ATOM 9 CE1 PHE A 67 8.652 2.623 2.204 1.00 3.12 C
ANISOU 9 CE1 PHE A 67 322 401 461 11 -133 -66 C
ATOM 10 CE2 PHE A 67 10.968 2.625 1.669 1.00 3.67 C
ANISOU 10 CE2 PHE A 67 365 454 576 215 21 123 C
ATOM 11 CZ PHE A 67 9.689 2.132 1.473 1.00 3.61 C
ANISOU 11 CZ PHE A 67 424 456 492 143 -126 172 C
ATOM 12 H1 PHE A 67 12.498 4.417 5.622 1.00 3.98 H
ATOM 13 H2 PHE A 67 11.747 3.186 5.440 1.00 3.98 H
ATOM 14 H3 PHE A 67 11.914 3.746 6.771 1.00 3.98 H
ATOM 15 HA PHE A 67 10.582 5.499 6.315 1.00 3.54 H
ATOM 16 HB2 PHE A 67 9.687 5.829 4.256 1.00 3.79 H
ATOM 17 HB3 PHE A 67 11.251 5.645 4.042 1.00 3.79 H
ATOM 18 HD1 PHE A 67 8.170 3.990 3.584 1.00 3.50 H
ATOM 19 HD2 PHE A 67 12.062 3.931 2.713 1.00 3.92 H
ATOM 20 HE1 PHE A 67 7.795 2.279 2.092 1.00 3.82 H
ATOM 21 HE2 PHE A 67 11.675 2.283 1.172 1.00 4.48 H
ATOM 22 HZ PHE A 67 9.539 1.465 0.842 1.00 4.41 H
ATOM 23 N TYR A 68 8.259 4.466 6.125 1.00 3.11 N
ANISOU 23 N TYR A 68 194 216 772 4 -9 -28 N
ATOM 24 CA TYR A 68 7.048 3.684 6.112 1.00 2.82 C
ANISOU 24 CA TYR A 68 189 163 721 17 -75 -43 C
ATOM 25 C TYR A 68 5.952 4.579 5.613 1.00 3.52 C
ANISOU 25 C TYR A 68 218 398 722 68 -84 -9 C
ATOM 26 O TYR A 68 6.110 5.793 5.505 1.00 2.69 O
ANISOU 26 O TYR A 68 183 191 648 -3 -47 -82 O
ATOM 27 CB TYR A 68 6.708 3.153 7.483 1.00 2.58 C
ANISOU 27 CB TYR A 68 166 154 659 6 -4 -78 C
ATOM 28 CG TYR A 68 6.178 4.139 8.455 1.00 2.67 C
ANISOU 28 CG TYR A 68 181 275 557 -74 -11 20 C
ATOM 29 CD1 TYR A 68 7.012 5.066 9.063 1.00 2.98 C
ANISOU 29 CD1 TYR A 68 170 486 477 9 -113 -30 C
ATOM 30 CD2 TYR A 68 4.852 4.116 8.811 1.00 3.48 C
ANISOU 30 CD2 TYR A 68 213 510 601 -118 1 -102 C
ATOM 31 CE1 TYR A 68 6.529 5.935 9.982 1.00 3.02 C
ANISOU 31 CE1 TYR A 68 242 432 473 -63 -93 70 C
ATOM 32 CE2 TYR A 68 4.366 4.973 9.714 1.00 4.15 C
ANISOU 32 CE2 TYR A 68 265 707 604 -116 7 -235 C
ATOM 33 CZ TYR A 68 5.201 5.890 10.300 1.00 3.31 C
ANISOU 33 CZ TYR A 68 263 444 550 -105 23 -43 C
ATOM 34 OH TYR A 68 4.695 6.750 11.224 1.00 3.65 O
ANISOU 34 OH TYR A 68 379 433 576 -12 42 7 O
ATOM 35 H TYR A 68 8.154 5.318 6.177 1.00 3.81 H
ATOM 36 HA TYR A 68 7.154 2.927 5.516 1.00 3.47 H
ATOM 37 HB2 TYR A 68 6.034 2.462 7.381 1.00 3.17 H
ATOM 38 HB3 TYR A 68 7.514 2.776 7.870 1.00 3.17 H
ATOM 39 HD1 TYR A 68 7.914 5.090 8.837 1.00 3.66 H
ATOM 40 HD2 TYR A 68 4.283 3.494 8.417 1.00 4.26 H
ATOM 41 HE1 TYR A 68 7.092 6.553 10.390 1.00 3.70 H
ATOM 42 HE2 TYR A 68 3.465 4.948 9.945 1.00 5.06 H
ATOM 43 HH TYR A 68 5.235 6.839 11.861 1.00 4.46 H
ATOM 44 N PHE A 69 4.838 3.960 5.312 1.00 2.91 N
ANISOU 44 N PHE A 69 192 176 737 1 -57 -61 N
ATOM 45 CA PHE A 69 3.692 4.732 4.967 1.00 4.02 C
ANISOU 45 CA PHE A 69 222 479 824 3 -51 -131 C
ATOM 46 C PHE A 69 2.463 3.944 5.270 1.00 3.53 C
ANISOU 46 C PHE A 69 222 288 830 18 -36 -150 C
ATOM 47 O PHE A 69 1.404 4.347 4.819 1.00 4.56 O
ANISOU 47 O PHE A 69 281 603 849 99 -113 -193 O
ATOM 48 CB PHE A 69 3.735 5.159 3.519 1.00 3.67 C
ANISOU 48 CB PHE A 69 238 402 754 9 -19 -326 C
ATOM 49 CG PHE A 69 3.787 4.040 2.536 1.00 3.00 C
ANISOU 49 CG PHE A 69 188 242 712 20 -41 -40 C
ATOM 50 CD1 PHE A 69 2.636 3.446 2.077 1.00 2.61 C
ANISOU 50 CD1 PHE A 69 183 223 584 -13 -95 -53 C
ATOM 51 CD2 PHE A 69 4.989 3.614 2.033 1.00 2.91 C
ANISOU 51 CD2 PHE A 69 184 258 663 -31 17 77 C
ATOM 52 CE1 PHE A 69 2.687 2.453 1.148 1.00 2.87 C
ANISOU 52 CE1 PHE A 69 195 299 596 -34 -118 39 C
ATOM 53 CE2 PHE A 69 5.037 2.619 1.101 1.00 3.58 C
ANISOU 53 CE2 PHE A 69 219 414 729 -77 -48 100 C
ATOM 54 CZ PHE A 69 3.878 2.034 0.656 1.00 3.50 C
ANISOU 54 CZ PHE A 69 246 468 618 -136 -103 20 C
ATOM 55 OXT PHE A 69 2.523 2.943 5.983 1.00 4.40 O
ANISOU 55 OXT PHE A 69 221 696 756 124 -8 15 O
ATOM 56 H PHE A 69 4.730 3.107 5.302 1.00 3.57 H
ATOM 57 HA PHE A 69 3.671 5.552 5.485 1.00 4.90 H
ATOM 58 HB2 PHE A 69 2.939 5.678 3.327 1.00 4.48 H
ATOM 59 HB3 PHE A 69 4.527 5.703 3.382 1.00 4.48 H
ATOM 60 HD1 PHE A 69 1.812 3.726 2.406 1.00 3.21 H
ATOM 61 HD2 PHE A 69 5.778 4.008 2.329 1.00 3.57 H
ATOM 62 HE1 PHE A 69 1.899 2.059 0.849 1.00 3.52 H
ATOM 63 HE2 PHE A 69 5.858 2.337 0.766 1.00 4.38 H
ATOM 64 HZ PHE A 69 3.910 1.355 0.022 1.00 4.28 H
TER 65 PHE A 69
MASTER 179 0 0 0 0 0 0 6 35 1 0 1
END