HEADER PROTEIN FIBRIL 29-JAN-25 9N35 TITLE MIXTURE OF L-PEPTIDE FVGGVV AND D-PEPTIDE MVGGVV FORMS RIPPLED SHEETS COMPND MOL_ID: 1; COMPND 2 MOLECULE: FVGGVV; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: MVGGVV; COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630; SOURCE 5 MOL_ID: 2; SOURCE 6 SYNTHETIC: YES; SOURCE 7 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 8 ORGANISM_TAXID: 32630 KEYWDS RIPPLED SHEET, MIXED CHIRALITY, PROTEIN FIBRIL EXPDTA X-RAY DIFFRACTION AUTHOR M.R.SAWAYA,J.A.RASKATOV,A.HAZARI REVDAT 2 09-APR-25 9N35 1 JRNL REVDAT 1 26-MAR-25 9N35 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 : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 11.37 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 92.7 REMARK 3 NUMBER OF REFLECTIONS : 2935 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.166 REMARK 3 R VALUE (WORKING SET) : 0.163 REMARK 3 FREE R VALUE : 0.188 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 327 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) : 748 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 83.52 REMARK 3 BIN R VALUE (WORKING SET) : 0.2030 REMARK 3 BIN FREE R VALUE SET COUNT : 83 REMARK 3 BIN FREE R VALUE : 0.1740 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 79 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 40 REMARK 3 SOLVENT ATOMS : 3 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 7.96 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.10000 REMARK 3 B22 (A**2) : 0.97000 REMARK 3 B33 (A**2) : -0.85000 REMARK 3 B12 (A**2) : 0.08000 REMARK 3 B13 (A**2) : -0.37000 REMARK 3 B23 (A**2) : -0.02000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.049 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.045 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 : 0.968 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.956 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 114 ; 0.016 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 92 ; 0.033 ; 0.017 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 164 ; 1.983 ; 1.609 REMARK 3 BOND ANGLES OTHERS (DEGREES): 209 ; 2.176 ; 1.631 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 10 ; 3.851 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 1 ; 9.802 ;20.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 4 ; 5.635 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 8 ; 0.088 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 93 ; 0.013 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 15 ; 0.034 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL 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): 46 ; 0.911 ; 0.579 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 46 ; 0.914 ; 0.578 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 54 ; 0.924 ; 0.870 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 55 ; 0.919 ; 0.874 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 68 ; 2.667 ; 0.987 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 66 ; 2.707 ; 0.984 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 108 ; 3.294 ; 1.483 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 97 ; 1.673 ;10.768 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 83 ; 1.164 ; 9.023 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 206 ;14.828 ; 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 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 ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 9N35 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-JAN-25. REMARK 100 THE DEPOSITION ID IS D_1000292395. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-JUN-24 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 3 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 VERSION JUN 30, 2024 REMARK 200 BUILT=20240723 REMARK 200 DATA SCALING SOFTWARE : XSCALE VERSION JUN 30, 2024 REMARK 200 BUILT=20240723 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 3263 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.100 REMARK 200 RESOLUTION RANGE LOW (A) : 11.370 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.7 REMARK 200 DATA REDUNDANCY : 4.200 REMARK 200 R MERGE (I) : 0.13000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.4600 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) : 0.61800 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: SHELXT VERSION 2018/2 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 37.36 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.96 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: HEXAFLUOROISOPROPANOL, WATER, PH 3, REMARK 280 BATCH MODE, 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 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 470 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 1770 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -2.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 DBREF 9N35 A 35 40 PDB 9N35 9N35 35 40 DBREF 9N35 B 35 40 PDB 9N35 9N35 35 40 SEQRES 1 A 6 PHE VAL GLY GLY VAL VAL SEQRES 1 B 6 MED DVA GLY GLY DVA DVA HET MED B 35 19 HET DVA B 36 16 HET DVA B 39 16 HET DVA B 40 17 HET CFH A 101 11 HET CFH A 102 11 HET CFH B 101 11 HET CFH B 102 11 HETNAM MED D-METHIONINE HETNAM DVA D-VALINE HETNAM CFH 1,1,1,3,3,3-HEXAFLUOROPROPAN-2-OL FORMUL 2 MED C5 H11 N O2 S FORMUL 2 DVA 3(C5 H11 N O2) FORMUL 3 CFH 4(C3 H2 F6 O) FORMUL 7 HOH *3(H2 O) LINK C MED B 35 N DVA B 36 1555 1555 1.31 LINK C DVA B 36 N GLY B 37 1555 1555 1.31 LINK C GLY B 38 N DVA B 39 1555 1555 1.33 LINK C DVA B 39 N DVA B 40 1555 1555 1.32 CRYST1 20.920 11.500 9.390 97.22 90.77 94.60 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 0.047801 0.003843 0.001139 0.00000 SCALE2 0.000000 0.087237 0.011181 0.00000 SCALE3 0.000000 0.000000 0.107377 0.00000 CONECT 87 88 95 96 CONECT 88 87 89 91 98 CONECT 89 88 90 106 CONECT 90 89 CONECT 91 88 92 99 100 CONECT 92 91 93 101 102 CONECT 93 92 94 CONECT 94 93 103 104 105 CONECT 95 87 CONECT 96 87 CONECT 98 88 CONECT 99 91 CONECT 100 91 CONECT 101 92 CONECT 102 92 CONECT 103 94 CONECT 104 94 CONECT 105 94 CONECT 106 89 107 113 CONECT 107 106 108 111 114 CONECT 108 107 109 110 115 CONECT 109 108 116 117 118 CONECT 110 108 119 120 121 CONECT 111 107 112 122 CONECT 112 111 CONECT 113 106 CONECT 114 107 CONECT 115 108 CONECT 116 109 CONECT 117 109 CONECT 118 109 CONECT 119 110 CONECT 120 110 CONECT 121 110 CONECT 122 111 CONECT 131 136 CONECT 136 131 137 143 CONECT 137 136 138 141 144 CONECT 138 137 139 140 145 CONECT 139 138 146 147 148 CONECT 140 138 149 150 151 CONECT 141 137 142 152 CONECT 142 141 CONECT 143 136 CONECT 144 137 CONECT 145 138 CONECT 146 139 CONECT 147 139 CONECT 148 139 CONECT 149 140 CONECT 150 140 CONECT 151 140 CONECT 152 141 153 160 CONECT 153 152 154 157 161 CONECT 154 153 155 156 162 CONECT 155 154 163 164 165 CONECT 156 154 166 167 168 CONECT 157 153 158 159 CONECT 158 157 CONECT 159 157 CONECT 160 152 CONECT 161 153 CONECT 162 154 CONECT 163 155 CONECT 164 155 CONECT 165 155 CONECT 166 156 CONECT 167 156 CONECT 168 156 CONECT 170 171 CONECT 171 170 172 173 174 CONECT 172 171 CONECT 173 171 CONECT 174 171 175 176 180 CONECT 175 174 CONECT 176 174 177 178 179 CONECT 177 176 CONECT 178 176 CONECT 179 176 CONECT 180 174 CONECT 181 182 CONECT 182 181 183 184 185 CONECT 183 182 CONECT 184 182 CONECT 185 182 186 187 191 CONECT 186 185 CONECT 187 185 188 189 190 CONECT 188 187 CONECT 189 187 CONECT 190 187 CONECT 191 185 CONECT 192 193 CONECT 193 192 194 195 196 CONECT 194 193 CONECT 195 193 CONECT 196 193 197 198 202 CONECT 197 196 CONECT 198 196 199 200 201 CONECT 199 198 CONECT 200 198 CONECT 201 198 CONECT 202 196 CONECT 203 204 CONECT 204 203 205 206 207 CONECT 205 204 CONECT 206 204 CONECT 207 204 208 209 213 CONECT 208 207 CONECT 209 207 210 211 212 CONECT 210 209 CONECT 211 209 CONECT 212 209 CONECT 213 207 MASTER 229 0 8 0 0 0 0 6 122 2 113 2 END