HEADER PROTEIN FIBRIL 15-OCT-24 9DZ0 TITLE FKFGG(DPN)(DGL)(DPN)GG, A CYCLIC PEPTIDE WITH MIXED CHIRALITY COMPND MOL_ID: 1; COMPND 2 MOLECULE: FKFGG(DPN)(DGL)(DPN)GG; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: DMS IS A SOLVENT MOLECULE. IT IS NOT COVALENTLY LINKED COMPND 6 TO THE PEPTIDE. SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630 KEYWDS PEPTIDE WITH MIXED CHIRALITY, PROTEIN FIBRIL EXPDTA X-RAY DIFFRACTION AUTHOR M.R.SAWAYA,J.A.RASKATOV,A.HAZARI REVDAT 2 16-APR-25 9DZ0 1 JRNL REVDAT 1 26-MAR-25 9DZ0 0 JRNL AUTH A.HAZARI,M.R.SAWAYA,H.LEE,M.SAJIMON,H.KIM,W.A.GODDARD III, JRNL AUTH 2 D.EISENBERG,J.A.RASKATOV JRNL TITL FORMATION OF RIPPLED BETA-SHEETS FROM MIXED CHIRALITY LINEAR JRNL TITL 2 AND CYCLIC PEPTIDES-NEW STRUCTURAL MOTIFS BASED ON THE JRNL TITL 3 PAULING-COREY RIPPLED BETA-SHEET. JRNL REF CHEM SCI V. 16 5907 2025 JRNL REFN ISSN 2041-6520 JRNL PMID 40060095 JRNL DOI 10.1039/D4SC08079C REMARK 2 REMARK 2 RESOLUTION. 1.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0267 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 14.66 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 94.4 REMARK 3 NUMBER OF REFLECTIONS : 2926 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : FREE R-VALUE REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.129 REMARK 3 FREE R VALUE : 0.136 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.014 REMARK 3 FREE R VALUE TEST SET COUNT : 293 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 5 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.23 REMARK 3 REFLECTION IN BIN (WORKING SET) : 675 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 86.41 REMARK 3 BIN R VALUE (WORKING SET) : 0.1490 REMARK 3 BIN FREE R VALUE SET COUNT : 75 REMARK 3 BIN FREE R VALUE : 0.1500 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 78 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 4 REMARK 3 SOLVENT ATOMS : 13 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 11.15 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.06300 REMARK 3 B22 (A**2) : 0.95600 REMARK 3 B33 (A**2) : -1.03800 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.29400 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.035 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.030 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.985 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.981 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 85 ; 0.017 ; 0.012 REMARK 3 BOND LENGTHS OTHERS (A): 73 ; 0.180 ; 0.018 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 110 ; 1.998 ; 1.694 REMARK 3 BOND ANGLES OTHERS (DEGREES): 167 ; 6.519 ; 1.694 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 10 ; 4.795 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 2 ; 9.653 ;20.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 6 ; 6.740 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 6 ; 0.058 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 105 ; 0.024 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 31 ; 0.008 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 14 ; 0.172 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 16 ; 0.243 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 43 ; 0.227 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 5 ; 0.125 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 40 ; 0.501 ; 0.576 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 38 ; 0.495 ; 0.574 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 50 ; 0.688 ; 0.875 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 50 ; 0.683 ; 0.875 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 45 ; 1.730 ; 1.115 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 46 ; 1.743 ; 1.178 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 60 ; 2.347 ; 1.523 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 61 ; 2.352 ; 1.592 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 158 ; 4.604 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK BULK SOLVENT REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN USED IF PRESENT IN REMARK 3 THE INPUT FILE REMARK 4 REMARK 4 9DZ0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-OCT-24. REMARK 100 THE DEPOSITION ID IS D_1000289120. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-OCT-23 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 3-4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS-II REMARK 200 BEAMLINE : 17-ID-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979330 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS 20230630 REMARK 200 DATA SCALING SOFTWARE : XSCALE 20230630 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 2926 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.100 REMARK 200 RESOLUTION RANGE LOW (A) : 14.660 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.3 REMARK 200 DATA REDUNDANCY : 9.100 REMARK 200 R MERGE (I) : 0.11300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.13 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.35000 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: AB INITIO PHASING REMARK 200 SOFTWARE USED: SHELXD 2013/2 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 29.80 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.75 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: DIMETHYLSULFOXIDE AND WATER, BATCH REMARK 280 MODE, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 14.66000 REMARK 290 SMTRY3 2 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 -29.32000 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 29.32000 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 -58.64000 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 58.64000 REMARK 350 BIOMT3 5 0.000000 0.000000 1.000000 0.00000 DBREF 9DZ0 A 1 10 PDB 9DZ0 9DZ0 1 10 SEQRES 1 A 10 PHE LYS PHE GLY GLY DPN DGL DPN GLY GLY HET DPN A 6 20 HET DGL A 7 15 HET DPN A 8 20 HET DMS A 101 10 HETNAM DPN D-PHENYLALANINE HETNAM DGL D-GLUTAMIC ACID HETNAM DMS DIMETHYL SULFOXIDE FORMUL 1 DPN 2(C9 H11 N O2) FORMUL 1 DGL C5 H9 N O4 FORMUL 2 DMS C2 H6 O S FORMUL 3 HOH *13(H2 O) SHEET 1 AA1 2 LYS A 2 PHE A 3 0 SHEET 2 AA1 2 DPN A 6 DGL A 7 -1 O DPN A 6 N PHE A 3 LINK N PHE A 1 C GLY A 10 1555 1555 1.34 LINK C GLY A 5 N DPN A 6 1555 1555 1.33 LINK C DPN A 6 N DGL A 7 1555 1555 1.33 LINK C DGL A 7 N DPN A 8 1555 1555 1.33 LINK C DPN A 8 N GLY A 9 1555 1555 1.35 CRYST1 14.130 29.320 9.520 90.00 103.77 90.00 P 1 21 1 2 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 0.070771 0.000000 0.017344 0.00000 SCALE2 0.000000 0.034106 0.000000 0.00000 SCALE3 0.000000 0.000000 0.108150 0.00000 CONECT 1 141 CONECT 72 77 CONECT 77 72 78 88 CONECT 78 77 79 81 89 CONECT 79 78 80 97 CONECT 80 79 CONECT 81 78 82 90 91 CONECT 82 81 83 84 CONECT 83 82 85 92 CONECT 84 82 86 93 CONECT 85 83 87 94 CONECT 86 84 87 95 CONECT 87 85 86 96 CONECT 88 77 CONECT 89 78 CONECT 90 81 CONECT 91 81 CONECT 92 83 CONECT 93 84 CONECT 94 85 CONECT 95 86 CONECT 96 87 CONECT 97 79 98 106 CONECT 98 97 99 101 107 CONECT 99 98 100 112 CONECT 100 99 CONECT 101 98 102 108 109 CONECT 102 101 103 110 111 CONECT 103 102 104 105 CONECT 104 103 CONECT 105 103 CONECT 106 97 CONECT 107 98 CONECT 108 101 CONECT 109 101 CONECT 110 102 CONECT 111 102 CONECT 112 99 113 123 CONECT 113 112 114 116 124 CONECT 114 113 115 132 CONECT 115 114 CONECT 116 113 117 125 126 CONECT 117 116 118 119 CONECT 118 117 120 127 CONECT 119 117 121 128 CONECT 120 118 122 129 CONECT 121 119 122 130 CONECT 122 120 121 131 CONECT 123 112 CONECT 124 113 CONECT 125 116 CONECT 126 116 CONECT 127 118 CONECT 128 119 CONECT 129 120 CONECT 130 121 CONECT 131 122 CONECT 132 114 CONECT 141 1 CONECT 147 148 149 150 CONECT 148 147 CONECT 149 147 151 152 153 CONECT 150 147 154 155 156 CONECT 151 149 CONECT 152 149 CONECT 153 149 CONECT 154 150 CONECT 155 150 CONECT 156 150 MASTER 242 0 4 0 2 0 0 6 95 1 69 1 END