HEADER ANTIBIOTIC 11-FEB-20 6Y13 TITLE BICYCLIC STAPLED PEPTIDE BP70 AT 1.1 ANGSTROM RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: BP70; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: BICYCLIC STAPLED PEPTIDE BP70 SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630 KEYWDS ANTIMICROBIAL, BICYCLIC, LECTIN, ANTIBIOTIC EXPDTA X-RAY DIFFRACTION AUTHOR S.BAERISWYL,A.STOCKER,J.-L.REYMOND REVDAT 4 01-FEB-23 6Y13 1 COMPND SOURCE JRNL REMARK REVDAT 4 2 1 DBREF SEQRES HELIX LINK REVDAT 4 3 1 SITE ATOM REVDAT 3 02-FEB-22 6Y13 1 JRNL REMARK REVDAT 2 03-MAR-21 6Y13 1 TITLE COMPND JRNL REVDAT 1 17-FEB-21 6Y13 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.V1 REMARK 2 REMARK 2 RESOLUTION. 1.11 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) : 1.11 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.16 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.6 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) : 4332 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 : 105 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 0 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 : 946 REMARK 3 NUMBER OF RESTRAINTS : 1190 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.021 REMARK 3 ANGLE DISTANCES (A) : 0.049 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.319 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.116 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.108 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.081 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.000 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.080 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.000 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228 REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH AND HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6Y13 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_1292106685. 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 : 6.50 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) : 0.8000 REMARK 200 MONOCHROMATOR : BARTELS MONOCHROMATOR REMARK 200 OPTICS : COLLIMATING MIRROR (M1), BARTELS REMARK 200 MONOCHROMATOR (DCCM), TOROIDAL REMARK 200 MIRROR (M2) 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 : 7887 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.112 REMARK 200 RESOLUTION RANGE LOW (A) : 26.160 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.7 REMARK 200 DATA REDUNDANCY : 6.200 REMARK 200 R MERGE (I) : 0.35400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 2.6700 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.11 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.12 REMARK 200 COMPLETENESS FOR SHELL (%) : 67.2 REMARK 200 DATA REDUNDANCY IN SHELL : 3.40 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.790 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.7.16 REMARK 200 STARTING MODEL: XXXX REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.76 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.44 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.6 M AMMONIUM SULFATE, 0.1 M MES REMARK 280 MONOHYDRATE PH 6.5, 10% V/V 1,4-DIOXANE, 2% V/V GLYCEROL, PH REMARK 280 6.50, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 3 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z REMARK 290 6555 -X,-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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 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 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: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 TYR A 105 CB - CG - CD1 ANGL. DEV. = -5.7 DEGREES REMARK 500 DAB A 106 CA - C - N ANGL. DEV. = 16.7 DEGREES REMARK 500 ARG A 109 CD - NE - CZ ANGL. DEV. = 8.9 DEGREES REMARK 500 ARG A 109 NE - CZ - NH1 ANGL. DEV. = -4.7 DEGREES REMARK 500 CYS A 110 CA - CB - SG ANGL. DEV. = 8.4 DEGREES REMARK 500 TYR A 111 CB - CG - CD2 ANGL. DEV. = 4.0 DEGREES REMARK 500 REMARK 500 REMARK: NULL 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 residues ORN A 3 and NLE A 4 DBREF 6Y13 A 101 113 PDB 6Y13 6Y13 101 113 SEQRES 1 A 13 O65 HIS ORN NLE TYR DAB CYS ILE ARG CYS TYR ALA NH2 HET O65 A 101 20 HET ORN A 103 19 HET NLE A 104 19 HET DAB A 106 16 HET NH2 A 113 3 HETNAM O65 3,5-BIS(HYDROXYMETHYL)-4-METHYL-BENZALDEHYDE HETNAM ORN L-ORNITHINE HETNAM NLE NORLEUCINE HETNAM DAB 2,4-DIAMINOBUTYRIC ACID HETNAM NH2 AMINO GROUP FORMUL 1 O65 C10 H12 O4 FORMUL 1 ORN C5 H12 N2 O2 FORMUL 1 NLE C6 H13 N O2 FORMUL 1 DAB C4 H10 N2 O2 FORMUL 1 NH2 H2 N HELIX 1 AA1 ORN A 103 ALA A 112 1 10 LINK CAJ O65 A 101 N HIS A 102 1555 1555 1.23 LINK CAM O65 A 101 SG CYS A 107 1555 1555 1.81 LINK CAH O65 A 101 SG CYS A 110 1555 1555 1.65 LINK C HIS A 102 N ORN A 103 1555 1555 1.35 LINK C ORN A 103 N NLE A 104 1555 1555 1.29 LINK C NLE A 104 N TYR A 105 1555 1555 1.38 LINK C TYR A 105 N DAB A 106 1555 1555 1.34 LINK C DAB A 106 N CYS A 107 1555 1555 1.25 LINK C ALA A 112 N NH2 A 113 1555 1555 1.36 SITE 1 AC1 5 HIS A 102 ORN A 103 DAB A 106 CYS A 107 SITE 2 AC1 5 CYS A 110 SITE 1 AC2 7 HIS A 102 TYR A 105 DAB A 106 CYS A 107 SITE 2 AC2 7 ILE A 108 ALA A 112 O65 A 101 CRYST1 26.856 26.856 26.156 90.00 90.00 120.00 P 3 2 1 6 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 0.037236 0.021498 0.000000 0.00000 SCALE2 0.000000 0.042996 0.000000 0.00000 SCALE3 0.000000 0.000000 0.038232 0.00000 HETATM 1 CAA O65 A 101 2.310 -16.190 -22.115 1.00 8.99 C ANISOU 1 CAA O65 A 101 829 1919 668 169 -341 737 C HETATM 2 CAB O65 A 101 3.120 -15.415 -21.118 1.00 9.36 C ANISOU 2 CAB O65 A 101 817 1741 999 -67 -94 385 C HETATM 3 CAC O65 A 101 3.950 -14.433 -21.646 1.00 9.26 C ANISOU 3 CAC O65 A 101 155 1710 1653 370 -118 923 C HETATM 4 CAD O65 A 101 4.651 -13.585 -20.797 1.00 9.45 C ANISOU 4 CAD O65 A 101 457 920 2213 651 185 193 C HETATM 5 CAE O65 A 101 4.523 -13.719 -19.419 1.00 12.88 C ANISOU 5 CAE O65 A 101 1332 1349 2212 -142 484 -339 C HETATM 6 CAF O65 A 101 3.692 -14.701 -18.891 1.00 9.26 C ANISOU 6 CAF O65 A 101 1491 681 1345 206 -231 -114 C HETATM 7 CAG O65 A 101 2.991 -15.549 -19.740 1.00 12.29 C ANISOU 7 CAG O65 A 101 2524 1189 957 -694 515 -215 C HETATM 8 CAH O65 A 101 2.105 -16.685 -18.998 1.00 10.34 C ANISOU 8 CAH O65 A 101 1005 1326 1596 -242 553 113 C HETATM 9 CAJ O65 A 101 5.271 -12.787 -18.443 1.00 19.95 C ANISOU 9 CAJ O65 A 101 3386 1661 2533 -1041 -763 279 C HETATM 10 CAM O65 A 101 4.373 -14.118 -23.137 1.00 14.07 C ANISOU 10 CAM O65 A 101 1149 2138 2060 -561 1109 173 C HETATM 11 H1 O65 A 101 1.855 -16.908 -21.669 1.00 13.49 H HETATM 12 H2 O65 A 101 2.892 -16.550 -22.789 1.00 13.49 H HETATM 13 H3 O65 A 101 1.666 -15.609 -22.525 1.00 13.49 H HETATM 14 H4 O65 A 101 5.207 -12.928 -21.150 1.00 11.34 H HETATM 15 H5 O65 A 101 3.606 -14.791 -17.969 1.00 11.11 H HETATM 16 H6 O65 A 101 1.350 -16.901 -19.568 1.00 12.40 H HETATM 17 H7 O65 A 101 1.750 -16.305 -18.179 1.00 12.40 H HETATM 18 H9 O65 A 101 3.587 -14.024 -23.697 1.00 16.89 H HETATM 19 O3 O65 A 101 5.545 -13.466 -17.394 1.00 21.57 O ANISOU 19 O3 O65 A 101 5995 679 1520 137 330 -610 O HETATM 20 H10 O65 A 101 4.881 -13.292 -23.175 1.00 16.89 H