HEADER ANTIBIOTIC 18-MAY-20 7C4U TITLE MICROED STRUCTURE OF ORTHORHOMBIC VANCOMYCIN AT 1.2 A RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: VANCOMYCIN; COMPND 3 CHAIN: A, B SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: AMYCOLATOPSIS ORIENTALIS; SOURCE 3 ORGANISM_TAXID: 31958 KEYWDS MICROED, VANCOMYCIN, SUPERBACTERIA, ANTIBIOTIC EXPDTA ELECTRON CRYSTALLOGRAPHY AUTHOR Q.FAN,H.ZHOU,X.LI,J.WANG REVDAT 4 17-MAR-21 7C4U 1 JRNL REVDAT 3 26-AUG-20 7C4U 1 REMARK REVDAT 2 19-AUG-20 7C4U 1 REMARK REVDAT 1 12-AUG-20 7C4U 0 JRNL AUTH Q.FAN,L.LI,H.XUE,H.ZHOU,L.ZHAO,J.LIU,J.MAO,S.WU,S.ZHANG, JRNL AUTH 2 C.WU,X.LI,X.ZHOU,J.WANG JRNL TITL PRECISE CONTROL OVER KINETICS OF MOLECULAR ASSEMBLY: JRNL TITL 2 PRODUCTION OF PARTICLES WITH TUNABLE SIZES AND CRYSTALLINE JRNL TITL 3 FORMS. JRNL REF ANGEW.CHEM.INT.ED.ENGL. V. 59 15141 2020 JRNL REFN ESSN 1521-3773 JRNL PMID 32432368 JRNL DOI 10.1002/ANIE.202003922 REMARK 2 REMARK 2 RESOLUTION. 1.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.15_3459 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 7.57 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 75.2 REMARK 3 NUMBER OF REFLECTIONS : 6839 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.203 REMARK 3 R VALUE (WORKING SET) : 0.202 REMARK 3 FREE R VALUE : 0.216 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 342 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 7.5709 - 1.5097 0.75 3295 174 0.1905 0.1998 REMARK 3 2 1.5097 - 1.2000 0.76 3202 168 0.2408 0.2740 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) : 0.110 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.000 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 11.43 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL 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 7C4U COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 21-MAY-20. REMARK 100 THE DEPOSITION ID IS D_1300017030. REMARK 240 REMARK 240 EXPERIMENTAL DETAILS REMARK 240 RECONSTRUCTION METHOD : CRYSTALLOGRAPHY REMARK 240 SAMPLE TYPE : 3D ARRAY REMARK 240 SPECIMEN TYPE : NULL REMARK 240 DATA ACQUISITION REMARK 240 DATE OF DATA COLLECTION : 01-JUN-19 REMARK 240 TEMPERATURE (KELVIN) : NULL REMARK 240 PH : NULL REMARK 240 NUMBER OF CRYSTALS USED : NULL REMARK 240 MICROSCOPE MODEL : FEI TECNAI F20 REMARK 240 DETECTOR TYPE : GATAN ULTRASCAN 4000 (4K X 4K) REMARK 240 ACCELERATION VOLTAGE (KV) : 200 REMARK 240 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 240 RESOLUTION RANGE HIGH (A) : NULL REMARK 240 RESOLUTION RANGE LOW (A) : NULL REMARK 240 DATA SCALING SOFTWARE : NULL REMARK 240 COMPLETENESS FOR RANGE (%) : NULL REMARK 240 DATA REDUNDANCY : NULL REMARK 240 IN THE HIGHEST RESOLUTION SHELL REMARK 240 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) :1.20 REMARK 240 HIGHEST RESOLUTION SHELL, RANGE LOW (A) :1.30 REMARK 240 COMPLETENESS FOR SHELL (%) : 75.6 REMARK 240 DATA REDUNDANCY IN SHELL : 7.45 REMARK 240 R MERGE FOR SHELL (I) : 0.74000 REMARK 240 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 240 SOFTWARE USED : NULL REMARK 240 STARTING MODEL : NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 2 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 X,-Y,-Z REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 -X,-Y+1/2,Z+1/2 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 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 16.51000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 20.86000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 16.51000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 20.86000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 TOTAL BURIED SURFACE AREA: 300 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 1400 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -7.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C 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 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 200 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 1410 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 2.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, D 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 VANCOMYCIN IS A TRICYCLIC GLYCOPEPTIDE. THE SCAFFOLD IS REMARK 400 A HEPTAPEPTIDE WITH THE CONFIGURATION D-D-L-D-D-L-L. IT IS REMARK 400 FURTHER GLYCOSYLATED BY A DISACCHARIDE MADE OF D-GLUCOSE REMARK 400 AND VANCOSAMINE. REMARK 400 HERE, VANCOMYCIN IS REPRESENTED BY GROUPING TOUGHER THE REMARK 400 SEQUENCE (SEQRES) AND THE TWO LIGANDS (HET) BGC AND RER. REMARK 400 REMARK 400 THE VANCOMYCIN IS GLYCOPEPTIDE, A MEMBER OF ANTIBIOTIC CLASS. REMARK 400 REMARK 400 GROUP: 1 REMARK 400 NAME: VANCOMYCIN REMARK 400 CHAIN: A, B, C, D REMARK 400 COMPONENT_1: PEPTIDE LIKE POLYMER REMARK 400 COMPONENT_2: RESIDUE BGC REMARK 400 COMPONENT_3: RESIDUE RER REMARK 400 DESCRIPTION: VANCOMYCIN IS A TRICYCLIC GLYCOPEPTIDE, GLYCOSYLATED REMARK 400 BY A DISACCHARIDE (RESIDUES 8 AND 9) ON RESIDUE 4. REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 CZ OMZ A 2 C5 GHP A 4 2.13 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 ASN B 3 -144.77 177.98 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-30288 RELATED DB: EMDB REMARK 900 MICROED STRUCTURE OF ORTHORHOMBIC VANCOMYCIN AT 1.2 A RESOLUTION DBREF 7C4U A 1 7 PDB 7C4U 7C4U 1 7 DBREF 7C4U B 1 7 PDB 7C4U 7C4U 1 7 SEQRES 1 A 7 MLU OMZ ASN GHP GHP OMY 3FG SEQRES 1 B 7 MLU OMZ ASN GHP GHP OMY 3FG HET MLU A 1 9 HET OMZ A 2 14 HET GHP A 4 11 HET GHP A 5 11 HET OMY A 6 14 HET 3FG A 7 13 HET MLU B 1 9 HET OMZ B 2 14 HET GHP B 4 11 HET GHP B 5 11 HET OMY B 6 14 HET 3FG B 7 13 HET BGC C 1 11 HET RER C 2 10 HET BGC D 1 11 HET RER D 2 10 HET CL A 101 1 HETNAM MLU N-METHYL-D-LEUCINE HETNAM OMZ (BETAR)-3-CHLORO-BETA-HYDROXY-D-TYROSINE HETNAM GHP (2R)-AMINO(4-HYDROXYPHENYL)ETHANOIC ACID HETNAM OMY (BETAR)-3-CHLORO-BETA-HYDROXY-L-TYROSINE HETNAM 3FG (2S)-AMINO(3,5-DIHYDROXYPHENYL)ETHANOIC ACID HETNAM BGC BETA-D-GLUCOPYRANOSE HETNAM RER VANCOSAMINE HETNAM CL CHLORIDE ION HETSYN BGC BETA-D-GLUCOSE; D-GLUCOSE; GLUCOSE HETSYN RER (1R,3S,4S,5S)-3-AMINO-2,3,6-TRIDEOXY-3-METHYL-ALPHA-L- HETSYN 2 RER ARABINO-HEXOPYRANOSE FORMUL 1 MLU 2(C7 H15 N O2) FORMUL 1 OMZ 2(C9 H10 CL N O4) FORMUL 1 GHP 4(C8 H9 N O3) FORMUL 1 OMY 2(C9 H10 CL N O4) FORMUL 1 3FG 2(C8 H9 N O4) FORMUL 3 BGC 2(C6 H12 O6) FORMUL 3 RER 2(C7 H15 N O3) FORMUL 5 CL CL 1- FORMUL 6 HOH *50(H2 O) LINK C MLU A 1 N OMZ A 2 1555 1555 1.32 LINK C OMZ A 2 N ASN A 3 1555 1555 1.32 LINK OH OMZ A 2 C5 GHP A 4 1555 1555 1.37 LINK C ASN A 3 N GHP A 4 1555 1555 1.32 LINK C GHP A 4 N GHP A 5 1555 1555 1.31 LINK C3 GHP A 4 OCZ OMY A 6 1555 1555 1.37 LINK O4 GHP A 4 C1 BGC C 1 1555 1555 1.37 LINK C GHP A 5 N OMY A 6 1555 1555 1.33 LINK C3 GHP A 5 CG1 3FG A 7 1555 1555 1.49 LINK C OMY A 6 N 3FG A 7 1555 1555 1.32 LINK C MLU B 1 N OMZ B 2 1555 1555 1.32 LINK C OMZ B 2 N ASN B 3 1555 1555 1.31 LINK OH OMZ B 2 C5 GHP B 4 1555 1555 1.37 LINK C ASN B 3 N GHP B 4 1555 1555 1.31 LINK C GHP B 4 N GHP B 5 1555 1555 1.31 LINK C3 GHP B 4 OCZ OMY B 6 1555 1555 1.37 LINK O4 GHP B 4 C1 BGC D 1 1555 1555 1.38 LINK C GHP B 5 N OMY B 6 1555 1555 1.32 LINK C3 GHP B 5 CG1 3FG B 7 1555 1555 1.49 LINK C OMY B 6 N 3FG B 7 1555 1555 1.31 LINK O2 BGC C 1 C1 RER C 2 1555 1555 1.37 LINK O2 BGC D 1 C1 RER D 2 1555 1555 1.37 CISPEP 1 GHP A 5 OMY A 6 0 4.80 CISPEP 2 GHP B 5 OMY B 6 0 -5.84 CRYST1 20.060 33.020 41.720 90.00 90.00 90.00 P 2 21 21 8 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 0.049850 0.000000 0.000000 0.00000 SCALE2 0.000000 0.030285 0.000000 0.00000 SCALE3 0.000000 0.000000 0.023969 0.00000 HETATM 1 N MLU A 1 -3.746 -7.259 12.032 1.00 9.70 N HETATM 2 CN MLU A 1 -3.225 -7.333 10.656 1.00 10.49 C HETATM 3 CA MLU A 1 -3.772 -5.861 12.458 1.00 9.07 C HETATM 4 C MLU A 1 -4.454 -4.990 11.433 1.00 7.97 C HETATM 5 O MLU A 1 -5.713 -5.138 11.277 1.00 8.90 O HETATM 6 CB MLU A 1 -4.599 -5.785 13.711 1.00 12.33 C HETATM 7 CG MLU A 1 -4.189 -4.571 14.510 1.00 26.77 C HETATM 8 CD1 MLU A 1 -5.343 -4.225 15.439 1.00 25.77 C HETATM 9 CD2 MLU A 1 -2.995 -4.983 15.363 1.00 32.72 C HETATM 10 N OMZ A 2 -3.734 -4.126 10.744 1.00 7.60 N HETATM 11 CA OMZ A 2 -4.329 -3.324 9.734 1.00 9.50 C HETATM 12 C OMZ A 2 -3.814 -1.899 9.793 1.00 11.62 C HETATM 13 O OMZ A 2 -4.214 -1.156 8.845 1.00 11.37 O HETATM 14 CB OMZ A 2 -4.012 -3.895 8.347 1.00 9.47 C HETATM 15 OC OMZ A 2 -4.359 -5.224 8.235 1.00 9.00 O HETATM 16 CG OMZ A 2 -2.561 -3.698 8.066 1.00 8.45 C HETATM 17 CD1 OMZ A 2 -2.146 -2.714 7.205 1.00 8.23 C HETATM 18 CD2 OMZ A 2 -1.633 -4.529 8.676 1.00 9.87 C HETATM 19 CE1 OMZ A 2 -0.812 -2.551 6.966 1.00 8.81 C HETATM 20 CL OMZ A 2 -0.296 -1.314 5.916 1.00 16.54 CL HETATM 21 CE2 OMZ A 2 -0.296 -4.355 8.437 1.00 7.78 C HETATM 22 CZ OMZ A 2 0.121 -3.340 7.578 1.00 8.01 C HETATM 23 OH OMZ A 2 1.428 -3.161 7.349 1.00 8.25 O