HEADER ANTIBIOTIC 17-APR-13 4K7T TITLE STRUCTURE OF THE TERNARY COMPLEX OF BACITRACIN, ZINC, AND GERANYL- TITLE 2 PYROPHOSPHATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: BACITRACIN A2; COMPND 3 CHAIN: A SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS SUBTILIS; SOURCE 3 ORGANISM_TAXID: 1423 KEYWDS ANTIBIOTIC, BACITRACIN, CELL-WALL BIOSYNTHESIS INHIBITOR, KEYWDS 2 UNDECAPRENYL-PYROPHOSPHATE EXPDTA X-RAY DIFFRACTION AUTHOR N.J.ECONOMOU,P.J.LOLL REVDAT 3 16-OCT-13 4K7T 1 REMARK SITE REVDAT 2 18-SEP-13 4K7T 1 JRNL REVDAT 1 14-AUG-13 4K7T 0 JRNL AUTH N.J.ECONOMOU,S.COCKLIN,P.J.LOLL JRNL TITL HIGH-RESOLUTION CRYSTAL STRUCTURE REVEALS MOLECULAR DETAILS JRNL TITL 2 OF TARGET RECOGNITION BY BACITRACIN. JRNL REF PROC.NATL.ACAD.SCI.USA V. 110 14207 2013 JRNL REFN ISSN 0027-8424 JRNL PMID 23940351 JRNL DOI 10.1073/PNAS.1308268110 REMARK 2 REMARK 2 RESOLUTION. 1.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8.1_1168) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VICENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE- REMARK 3 : KUNSTLEVE,LI-WEI HUNG,ROBERT IMMORMINO, REMARK 3 : TOM IOERGER,AIRLIE MCCOY,ERIK MCKEE,NIGEL REMARK 3 : MORIARTY,REETAL PAI,RANDY READ,JANE REMARK 3 : RICHARDSON,DAVID RICHARDSON,TOD ROMO,JIM REMARK 3 : SACCHETTINI,NICHOLAS SAUTER,JACOB SMITH, REMARK 3 : LAURENT STORONI,TOM TERWILLIGER,PETER REMARK 3 : ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 12.01 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.220 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 4983 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.128 REMARK 3 R VALUE (WORKING SET) : 0.127 REMARK 3 FREE R VALUE : 0.149 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.620 REMARK 3 FREE R VALUE TEST SET COUNT : 438 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 12.0061 - 1.5856 1.00 3007 151 0.1304 0.1545 REMARK 3 2 1.5856 - 1.2590 1.00 2991 171 0.1128 0.1339 REMARK 3 3 1.2590 - 1.1000 1.00 3044 116 0.1376 0.1633 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL 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) : 0.080 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.110 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 11.55 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 12.66 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 : 0.008 121 REMARK 3 ANGLE : 2.051 164 REMARK 3 CHIRALITY : 0.120 16 REMARK 3 PLANARITY : 0.005 19 REMARK 3 DIHEDRAL : 15.381 39 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 4K7T COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-MAY-13. REMARK 100 THE RCSB ID CODE IS RCSB078999. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X6A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL REMARK 200 WAVELENGTH OR RANGE (A) : 0.98 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : SI(111) REMARK 200 REMARK 200 DETECTOR TYPE : AREA DETECTOR REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 270 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 4983 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.100 REMARK 200 RESOLUTION RANGE LOW (A) : 12.005 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 10.600 REMARK 200 R MERGE (I) : 0.09200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.6900 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) : 1.16 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.66900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.100 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 (%): 40.35 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.06 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG-2000 IN 0.1 M SODIUM ACETATE REMARK 280 PH 6.5, MICROBATCH UNDER OIL, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 62 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 -X,-Y,Z REMARK 290 5555 Y,-X+Y,Z+2/3 REMARK 290 6555 X-Y,X,Z+1/3 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 10.74667 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 5.37333 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 10.74667 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 5.37333 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 400 REMARK 400 COMPOUND REMARK 400 ILE-1 AND CYS-2 HAVE UNDERGONE A CONDENSATION REACTION TO PRODUCE A REMARK 400 THIAZOLINE RING REMARK 400 REMARK 400 THE BACITRACIN A1 IS CYCLIC PEPTIDE, A MEMBER OF ANTIBIOTIC CLASS. REMARK 400 REMARK 400 GROUP: 1 REMARK 400 NAME: BACITRACIN A1 REMARK 400 CHAIN: A REMARK 400 COMPONENT_1: PEPTIDE LIKE POLYMER REMARK 400 DESCRIPTION: NULL 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 ILE A 1 O REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 219 O HOH A 217 5554 1.88 REMARK 500 O HOH A 217 O HOH A 217 4565 2.09 REMARK 500 REMARK 500 REMARK: NULL 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 CYS A 2 6.76 124.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 102 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GPP A 101 O1B REMARK 620 2 GPP A 101 O1A 95.3 REMARK 620 3 DGL A 4 OE1 96.2 83.5 REMARK 620 4 HOH A 201 O 90.7 172.5 91.4 REMARK 620 5 ILE A 1 N 98.0 88.8 164.4 94.8 REMARK 620 6 CYS A 2 N 172.4 90.2 89.6 84.3 76.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 103 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ILE A 8 O REMARK 620 2 ILE A 5 O 93.5 REMARK 620 3 GPP A 101 O2B 103.5 163.0 REMARK 620 4 DAS A 11 OD2 98.9 97.8 80.8 REMARK 620 5 GPP A 101 O2A 112.7 81.2 91.1 148.4 REMARK 620 6 GPP A 101 O3A 86.3 128.6 52.9 133.1 52.5 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GPP A 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 103 DBREF 4K7T A 1 12 NOR NOR00018 NOR00018 1 12 SEQRES 1 A 12 ILE CYS LEU DGL ILE LYS ORD ILE DPN HIS DAS ASN HET DGL A 4 15 HET ORD A 7 18 HET DPN A 9 20 HET DAS A 11 12 HET GPP A 101 36 HET ZN A 102 1 HET NA A 103 1 HETNAM DGL D-GLUTAMIC ACID HETNAM ORD D-ORNITHINE HETNAM DPN D-PHENYLALANINE HETNAM DAS D-ASPARTIC ACID HETNAM GPP GERANYL DIPHOSPHATE HETNAM ZN ZINC ION HETNAM NA SODIUM ION FORMUL 1 DGL C5 H9 N O4 FORMUL 1 ORD C5 H12 N2 O2 FORMUL 1 DPN C9 H11 N O2 FORMUL 1 DAS C4 H7 N O4 FORMUL 2 GPP C10 H20 O7 P2 FORMUL 3 ZN ZN 2+ FORMUL 4 NA NA 1+ FORMUL 5 HOH *20(H2 O) LINK C LEU A 3 N DGL A 4 1555 1555 1.33 LINK C DGL A 4 N ILE A 5 1555 1555 1.33 LINK C ORD A 7 N ILE A 8 1555 1555 1.33 LINK C ILE A 8 N DPN A 9 1555 1555 1.33 LINK C DPN A 9 N HIS A 10 1555 1555 1.32 LINK C HIS A 10 N DAS A 11 1555 1555 1.33 LINK C DAS A 11 N ASN A 12 1555 1555 1.33 LINK O1B GPP A 101 ZN ZN A 102 1555 1555 2.01 LINK O1A GPP A 101 ZN ZN A 102 1555 1555 2.08 LINK OE1 DGL A 4 ZN ZN A 102 1555 1555 2.10 LINK ZN ZN A 102 O HOH A 201 1555 1555 2.12 LINK N ILE A 1 ZN ZN A 102 1555 1555 2.14 LINK N CYS A 2 ZN ZN A 102 1555 1555 2.18 LINK O ILE A 8 NA NA A 103 1555 1555 2.23 LINK O ILE A 5 NA NA A 103 1555 1555 2.30 LINK O2B GPP A 101 NA NA A 103 1555 1555 2.36 LINK OD2 DAS A 11 NA NA A 103 1555 1555 2.39 LINK O2A GPP A 101 NA NA A 103 1555 1555 2.42 LINK O3A GPP A 101 NA NA A 103 1555 1555 3.10 LINK C ILE A 1 SG CYS A 2 1555 1555 1.75 LINK C LYS A 6 N ORD A 7 1555 1555 1.33 LINK NZ LYS A 6 C ASN A 12 1555 1555 1.35 LINK C ILE A 1 N CYS A 2 1555 1555 1.30 SITE 1 AC1 14 ILE A 1 CYS A 2 LEU A 3 DGL A 4 SITE 2 AC1 14 ILE A 5 ILE A 8 DPN A 9 HIS A 10 SITE 3 AC1 14 DAS A 11 ASN A 12 ZN A 102 NA A 103 SITE 4 AC1 14 HOH A 201 HOH A 206 SITE 1 AC2 6 ILE A 1 CYS A 2 LEU A 3 DGL A 4 SITE 2 AC2 6 GPP A 101 HOH A 201 SITE 1 AC3 5 ILE A 5 LYS A 6 ILE A 8 DAS A 11 SITE 2 AC3 5 GPP A 101 CRYST1 35.980 35.980 16.120 90.00 90.00 120.00 P 62 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 0.027793 0.016046 0.000000 0.00000 SCALE2 0.000000 0.032093 0.000000 0.00000 SCALE3 0.000000 0.000000 0.062035 0.00000