HEADER ANTIBIOTIC 12-JUL-19 6PSL TITLE STRUCTURE OF A N-ME-D-GLN4,D-AZA-THR8,ARG10-TEIXOBACTIN ANALOGUE COMPND MOL_ID: 1; COMPND 2 MOLECULE: TEIXOBACTIN ANALOGUE; 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 ANTIBIOTIC, TEIXOBACTIN, AZATEIXOBACTIN EXPDTA X-RAY DIFFRACTION AUTHOR J.S.NOWICK,H.YANG,A.PISHENKO,X.LI REVDAT 4 15-NOV-23 6PSL 1 ATOM REVDAT 3 15-SEP-21 6PSL 1 LINK REVDAT 2 19-FEB-20 6PSL 1 JRNL REVDAT 1 27-NOV-19 6PSL 0 JRNL AUTH H.YANG,A.V.PISHENKO,X.LI,J.S.NOWICK JRNL TITL DESIGN, SYNTHESIS, AND STUDY OF LACTAM AND RING-EXPANDED JRNL TITL 2 ANALOGUES OF TEIXOBACTIN. JRNL REF J.ORG.CHEM. V. 85 1331 2020 JRNL REFN ISSN 0022-3263 JRNL PMID 31746604 JRNL DOI 10.1021/ACS.JOC.9B02631 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.13_2998 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 15.28 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 535 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.092 REMARK 3 FREE R VALUE : 0.117 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL 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 0.0000 - 2.1000 0.00 0 0 0.1200 0.1900 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 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) : 0.174 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 6.205 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 8.89 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 8.89 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 : 0.003 90 REMARK 3 ANGLE : 1.116 118 REMARK 3 CHIRALITY : 0.069 16 REMARK 3 PLANARITY : 0.002 13 REMARK 3 DIHEDRAL : 19.302 40 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 6PSL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-SEP-19. REMARK 100 THE DEPOSITION ID IS D_1000242938. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-APR-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.00 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 8.2.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.77 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 535 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 15.280 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 45.70 REMARK 200 R MERGE (I) : 0.05300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 78.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.35 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 33.40 REMARK 200 R MERGE FOR SHELL (I) : 0.06600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 52.70 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): NULL REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.43 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.16 M CACL2, 0.1 M HEPES NA PH 7.00, REMARK 280 24% PEG 400, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 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+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 21.55200 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 10.77600 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 10.77600 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 21.55200 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: 1030 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 2320 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -27.0 KCAL/MOL 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 BIOMT1 2 -0.500000 0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 0.866025 0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 32.32800 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 Q3S A 8 -9.45 110.95 REMARK 500 ARG A 10 -73.97 -106.09 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 CL A 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Ligand residues HJV A 4 through REMARK 800 ILE A 6 bound to SER A 3 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Ligand residues Q3S A 8 through REMARK 800 ALA A 9 bound to SER A 7 DBREF 6PSL A 1 11 PDB 6PSL 6PSL 1 11 SEQRES 1 A 11 ZAE ILE SER HJV 28J ILE SER Q3S ALA ARG ILE HET ZAE A 1 24 HET HJV A 4 20 HET 28J A 5 18 HET Q3S A 8 14 HET CL A 101 1 HETNAM ZAE N-METHYL-D-PHENYLALANINE HETNAM HJV N~2~-METHYL-D-GLUTAMINE HETNAM 28J D-ALLOISOLEUCINE HETNAM Q3S (2R,3S)-2,3-DIAMINOBUTANOIC ACID HETNAM CL CHLORIDE ION FORMUL 1 ZAE C10 H13 N O2 FORMUL 1 HJV C6 H12 N2 O3 FORMUL 1 28J C6 H13 N O2 FORMUL 1 Q3S C4 H10 N2 O2 FORMUL 2 CL CL 1- FORMUL 3 HOH *4(H2 O) LINK C ZAE A 1 N ILE A 2 1555 1555 1.33 LINK C SER A 3 N HJV A 4 1555 1555 1.33 LINK C HJV A 4 N 28J A 5 1555 1555 1.33 LINK C 28J A 5 N ILE A 6 1555 1555 1.33 LINK C SER A 7 N Q3S A 8 1555 1555 1.33 LINK C Q3S A 8 N ALA A 9 1555 1555 1.33 LINK N2 Q3S A 8 C ILE A 11 1555 1555 1.43 SITE 1 AC1 7 ZAE A 1 ILE A 6 SER A 7 Q3S A 8 SITE 2 AC1 7 ALA A 9 ARG A 10 ILE A 11 SITE 1 AC2 10 ZAE A 1 ILE A 2 SER A 3 SER A 7 SITE 2 AC2 10 Q3S A 8 ALA A 9 ARG A 10 CL A 101 SITE 3 AC2 10 HOH A 202 HOH A 204 SITE 1 AC3 8 HJV A 4 ILE A 6 SER A 7 ARG A 10 SITE 2 AC3 8 CL A 101 HOH A 202 HOH A 203 HOH A 204 CRYST1 20.024 20.024 32.328 90.00 90.00 120.00 P 32 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 0.049940 0.028833 0.000000 0.00000 SCALE2 0.000000 0.057666 0.000000 0.00000 SCALE3 0.000000 0.000000 0.030933 0.00000 CONECT 1 2 12 13 CONECT 2 1 3 5 14 CONECT 3 2 4 25 CONECT 4 3 CONECT 5 2 6 15 16 CONECT 6 5 7 8 CONECT 7 6 9 17 CONECT 8 6 10 18 CONECT 9 7 11 19 CONECT 10 8 11 20 CONECT 11 9 10 21 CONECT 12 1 22 23 24 CONECT 13 1 CONECT 14 2 CONECT 15 5 CONECT 16 5 CONECT 17 7 CONECT 18 8 CONECT 19 9 CONECT 20 10 CONECT 21 11 CONECT 22 12 CONECT 23 12 CONECT 24 12 CONECT 25 3 CONECT 46 56 CONECT 55 56 65 66 67 CONECT 56 46 55 57 CONECT 57 56 58 63 68 CONECT 58 57 59 69 70 CONECT 59 58 60 71 72 CONECT 60 59 61 62 CONECT 61 60 73 74 CONECT 62 60 CONECT 63 57 64 75 CONECT 64 63 CONECT 65 55 CONECT 66 55 CONECT 67 55 CONECT 68 57 CONECT 69 58 CONECT 70 58 CONECT 71 59 CONECT 72 59 CONECT 73 61 CONECT 74 61 CONECT 75 63 76 CONECT 76 75 77 81 83 CONECT 77 76 78 79 84 CONECT 78 77 85 86 87 CONECT 79 77 80 88 89 CONECT 80 79 90 91 92 CONECT 81 76 82 93 CONECT 82 81 CONECT 83 76 CONECT 84 77 CONECT 85 78 CONECT 86 78 CONECT 87 78 CONECT 88 79 CONECT 89 79 CONECT 90 80 CONECT 91 80 CONECT 92 80 CONECT 93 81 CONECT 114 123 CONECT 123 114 124 130 CONECT 124 123 125 128 131 CONECT 125 124 126 137 CONECT 126 125 CONECT 127 128 132 133 134 CONECT 128 124 127 129 135 CONECT 129 128 136 173 CONECT 130 123 CONECT 131 124 CONECT 132 127 CONECT 133 127 CONECT 134 127 CONECT 135 128 CONECT 136 129 CONECT 137 125 CONECT 173 129 MASTER 237 0 5 0 0 0 7 6 94 1 82 1 END