HEADER ANTIBIOTIC 11-FEB-20 6Y14 TITLE BICYCLIC PEPTIDE BP65 CRYSTALLIZED AS RACEMIC MIXTURE AT 0.9 ANGSTROM TITLE 2 RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: BP65; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: ANTIMICROBIAL BICYCLIC STAPLED PEPTIDE BP65, COMPND 6 CRYSTALLIZED AS RACEMATE WITH ITS D-ENANTIOMER BP69 SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630 KEYWDS ANTIMICROBIAL, BICYCLIC, STAPLED, ANTIBIOTIC EXPDTA X-RAY DIFFRACTION AUTHOR S.BAERISWYL,A.STOCKER,J.-L.REYMOND REVDAT 5 01-FEB-23 6Y14 1 COMPND SOURCE JRNL REMARK REVDAT 5 2 1 DBREF SEQRES HELIX LINK REVDAT 5 3 1 SITE ATOM REVDAT 4 02-FEB-22 6Y14 1 JRNL REVDAT 3 04-AUG-21 6Y14 1 JRNL REVDAT 2 03-MAR-21 6Y14 1 JRNL REVDAT 1 17-FEB-21 6Y14 0 JRNL AUTH S.BAERISWYL,H.PERSONNE,I.DI BONAVENTURA,T.KOHLER, JRNL AUTH 2 C.VAN DELDEN,A.STOCKER,S.JAVOR,J.L.REYMOND JRNL TITL A MIXED CHIRALITY ALPHA-HELIX IN A STAPLED BICYCLIC AND A JRNL TITL 2 LINEAR ANTIMICROBIAL PEPTIDE REVEALED BY X-RAY JRNL TITL 3 CRYSTALLOGRAPHY. JRNL REF RSC CHEM BIOL V. 2 1608 2021 JRNL REFN ESSN 2633-0679 JRNL PMID 34977576 JRNL DOI 10.1039/D1CB00124H REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH S.BAERISWYL,H.PERSONNE,I.DI BONAVENTURA,T.KOHLER, REMARK 1 AUTH 2 C.VAN DELDEN,A.STOCKER,S.JAVOR,J.L.REYMOND REMARK 1 TITL A MIXED CHIRALITY ALPHA-HELIX IN A STAPLED BICYCLIC AND A REMARK 1 TITL 2 LINEAR ANTIMICROBIAL PEPTIDE REVEALED BY X-RAY REMARK 1 TITL 3 CRYSTALLOGRAPHY. REMARK 1 REF RSC CHEM BIOL V. 2 1608 2021 REMARK 1 REFN ESSN 2633-0679 REMARK 1 PMID 34977576 REMARK 1 DOI 10.1039/D1CB00124H REMARK 1 REFERENCE 2 REMARK 1 AUTH S.BAERISWYL,H.PERSONNE,I.DI BONAVENTURA,T.KOHLER, REMARK 1 AUTH 2 C.VAN DELDEN,A.STOCKER,S.JAVOR,J.L.REYMOND REMARK 1 TITL A MIXED CHIRALITY ALPHA-HELIX IN A STAPLED BICYCLIC AND A REMARK 1 TITL 2 LINEAR ANTIMICROBIAL PEPTIDE REVEALED BY X-RAY REMARK 1 TITL 3 CRYSTALLOGRAPHY. REMARK 1 REF RSC CHEM BIOL V. 2 1608 2021 REMARK 1 REFN ESSN 2633-0679 REMARK 1 PMID 34977576 REMARK 1 DOI 10.1039/D1CB00124H REMARK 1 REFERENCE 3 REMARK 1 AUTH H.PERSONNE,S.BAERISWYL,I.DI BONAVENTURA,T.KOHLER, REMARK 1 AUTH 2 C.VAN DELDEN,A.STOCKER,S.JAVOR,J.-L.REYMOND REMARK 1 TITL MIXED CHIRALITY ALPHA-HELIX IN A STAPLED BICYCLIC AND A REMARK 1 TITL 2 LINEAR ANTIMICROBIAL PEPTIDE REVEALED BY X-RAY REMARK 1 TITL 3 CRYSTALLOGRAPHY REMARK 1 REF CHEMRXIV 2021 REMARK 1 REFN ISSN 2573-2293 REMARK 1 DOI 10.26434/CHEMRXIV.14052293.V3 REMARK 2 REMARK 2 RESOLUTION. 0.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELX REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 0.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.70 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 87.7 REMARK 3 CROSS-VALIDATION METHOD : FREE R-VALUE REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : NULL REMARK 3 FREE R VALUE (NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : NULL REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : NULL REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE (F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 194 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 26 REMARK 3 SOLVENT ATOMS : 13 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : NULL REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : NULL REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : NULL REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : NULL REMARK 3 NUMBER OF RESTRAINTS : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 ANGLE DISTANCES (A) : 0.822 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.005 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 94.00 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 1.000 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.128 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.000 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.022 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.000 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: NULL REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : NULL REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6Y14 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 21-FEB-20. REMARK 100 THE DEPOSITION ID IS D_1292106627. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-DEC-17 REMARK 200 TEMPERATURE (KELVIN) : 100.000 REMARK 200 PH : 5.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06DA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.8 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 29455 REMARK 200 RESOLUTION RANGE HIGH (A) : 0.900 REMARK 200 RESOLUTION RANGE LOW (A) : 27.700 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 87.7 REMARK 200 DATA REDUNDANCY : 1.760 REMARK 200 R MERGE (I) : 0.16500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 4.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 0.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 0.92 REMARK 200 COMPLETENESS FOR SHELL (%) : 84.7 REMARK 200 DATA REDUNDANCY IN SHELL : 1.76 REMARK 200 R MERGE FOR SHELL (I) : 0.24700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: AB INITIO PHASING REMARK 200 SOFTWARE USED: SHELX REMARK 200 STARTING MODEL: NONE REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.06 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.88 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M SODIUM CITRATE TRIBASIC REMARK 280 DIHYDRATE PH 5.6, 35% V/V TERT-BUTANOL, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 291K 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 2555 -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 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 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 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 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS A 109 CD CE NZ REMARK 470 LYS B 109 CD CE NZ REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue O65 A 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CIT A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CIT B 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-peptide LEU B 12 and NH2 B REMARK 800 13 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-peptide O65 B 101 and CYS B REMARK 800 10 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-peptide O65 B 101 and CYS B REMARK 800 7 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-peptide O65 B 101 and LYS B REMARK 800 2 DBREF 6Y14 A 101 113 PDB 6Y14 6Y14 101 113 DBREF 6Y14 B 101 113 PDB 6Y14 6Y14 101 113 SEQRES 1 A 13 O65 LYS LYS LEU LEU LYS CYS LEU LYS CYS LEU LEU NH2 SEQRES 1 B 13 O65 LYS LYS LEU LEU LYS CYS LEU LYS CYS LEU LEU NH2 HET O65 A 101 20 HET NH2 A 113 3 HET O65 B 101 20 HET NH2 B 113 3 HET CIT A 201 18 HET CIT B 201 18 HETNAM O65 3,5-BIS(HYDROXYMETHYL)-4-METHYL-BENZALDEHYDE HETNAM NH2 AMINO GROUP HETNAM CIT CITRIC ACID FORMUL 1 O65 2(C10 H12 O4) FORMUL 1 NH2 2(H2 N) FORMUL 3 CIT 2(C6 H8 O7) FORMUL 5 HOH *13(H2 O) HELIX 1 AA1 LYS A 103 LEU A 112 1 10 HELIX 2 AA2 LYS B 103 LEU B 112 1 10 LINK CAJ O65 A 101 N LYS A 102 1555 1555 1.34 LINK CAH O65 A 101 SG CYS A 107 1555 1555 1.81 LINK CAM O65 A 101 SG CYS A 110 1555 1555 1.80 LINK C LEU A 112 N NH2 A 113 1555 1555 1.27 LINK CAJ O65 B 101 N LYS B 102 1555 1555 1.39 LINK CAH O65 B 101 SG CYS B 107 1555 1555 1.83 LINK CAM O65 B 101 SG CYS B 110 1555 1555 1.84 LINK C LEU B 112 N NH2 B 113 1555 1555 1.27 SITE 1 AC1 8 LYS A 102 LYS A 103 LYS A 106 CYS A 107 SITE 2 AC1 8 CYS A 110 LEU A 111 O65 B 101 CIT A 201 SITE 1 AC2 9 LYS A 102 LYS A 103 O65 A 101 HOH A 303 SITE 2 AC2 9 HOH A 304 HOH A 308 LYS B 102 CIT B 201 SITE 3 AC2 9 HOH A 302 SITE 1 AC3 7 LYS A 102 LYS B 102 LYS B 103 LYS B 106 SITE 2 AC3 7 O65 B 101 CIT A 201 HOH B 302 SITE 1 AC4 6 LEU B 104 LEU B 105 LEU B 108 LYS B 109 SITE 2 AC4 6 CYS B 110 LEU B 111 SITE 1 AC5 11 O65 A 101 LYS B 102 LYS B 103 LYS B 106 SITE 2 AC5 11 CYS B 107 LEU B 108 LYS B 109 LEU B 111 SITE 3 AC5 11 LEU B 112 CIT B 201 HOH B 301 SITE 1 AC6 11 O65 A 101 LYS B 102 LYS B 103 LEU B 104 SITE 2 AC6 11 LEU B 105 LYS B 106 LEU B 108 LYS B 109 SITE 3 AC6 11 CYS B 110 LEU B 111 CIT B 201 SITE 1 AC7 11 LYS A 102 O65 A 101 LYS B 103 LYS B 106 SITE 2 AC7 11 CYS B 107 CYS B 110 CIT A 201 CIT B 201 SITE 3 AC7 11 HOH B 301 HOH B 303 HOH B 304 CRYST1 16.482 26.209 29.909 111.28 92.26 101.96 P -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 0.060672 0.012852 0.007862 0.00000 SCALE2 0.000000 0.039001 0.016004 0.00000 SCALE3 0.000000 0.000000 0.036168 0.00000 HETATM 1 CAA O65 A 101 -0.081 7.248 4.192 1.00 3.95 C ANISOU 1 CAA O65 A 101 270 455 696 54 -110 98 C HETATM 2 CAB O65 A 101 1.233 7.182 4.937 1.00 3.95 C ANISOU 2 CAB O65 A 101 293 322 527 -27 -124 40 C HETATM 3 CAC O65 A 101 1.279 7.150 6.316 1.00 3.95 C ANISOU 3 CAC O65 A 101 228 281 551 -29 -30 -110 C HETATM 4 CAD O65 A 101 2.486 7.040 7.015 1.00 3.95 C ANISOU 4 CAD O65 A 101 246 241 458 28 -68 -64 C HETATM 5 CAE O65 A 101 3.693 7.034 6.275 1.00 3.95 C ANISOU 5 CAE O65 A 101 190 317 469 9 -75 -1 C HETATM 6 CAF O65 A 101 3.635 7.055 4.919 1.00 3.95 C ANISOU 6 CAF O65 A 101 309 319 450 -2 -4 49 C HETATM 7 CAG O65 A 101 2.476 7.048 4.225 1.00 3.95 C ANISOU 7 CAG O65 A 101 232 435 487 -57 -59 63 C HETATM 8 CAH O65 A 101 2.558 6.904 2.711 1.00 3.95 C ANISOU 8 CAH O65 A 101 330 437 498 -72 -138 166 C HETATM 9 CAJ O65 A 101 5.010 7.038 7.038 1.00 3.95 C ANISOU 9 CAJ O65 A 101 170 531 457 2 -83 129 C HETATM 10 CAM O65 A 101 0.038 7.416 7.157 1.00 3.95 C ANISOU 10 CAM O65 A 101 239 541 806 -5 50 -140 C HETATM 11 OAK O65 A 101 5.132 6.405 8.081 1.00 3.95 O ANISOU 11 OAK O65 A 101 293 599 503 -199 -203 188 O HETATM 12 H1 O65 A 101 -0.690 6.603 4.559 1.00 3.95 H HETATM 13 H2 O65 A 101 0.068 7.055 3.263 1.00 3.95 H HETATM 14 H3 O65 A 101 -0.455 8.128 4.280 1.00 3.95 H HETATM 15 H4 O65 A 101 2.495 6.972 7.942 1.00 3.95 H HETATM 16 H5 O65 A 101 4.435 7.075 4.444 1.00 3.95 H HETATM 17 H6 O65 A 101 3.406 7.269 2.410 1.00 3.95 H HETATM 18 H7 O65 A 101 1.852 7.435 2.310 1.00 3.95 H HETATM 19 H9 O65 A 101 0.328 7.496 8.080 1.00 3.95 H HETATM 20 H10 O65 A 101 -0.307 8.283 6.894 1.00 3.95 H