HEADER ANTIBIOTIC 23-JUL-97 1SHO TITLE CRYSTAL STRUCTURE OF VANCOMYCIN AT ATOMIC RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: VANCOMYCIN; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: AMYCOLATOPSIS ORIENTALIS; SOURCE 4 ORGANISM_TAXID: 31958 KEYWDS GLYCOPEPTIDE, ANTIBIOTIC EXPDTA X-RAY DIFFRACTION AUTHOR G.M.SHELDRICK REVDAT 5 29-JUL-20 1SHO 1 COMPND REMARK SEQRES HETNAM REVDAT 5 2 1 LINK SITE ATOM REVDAT 4 27-JUL-11 1SHO 1 REMARK REVDAT 3 13-JUL-11 1SHO 1 VERSN REVDAT 2 24-FEB-09 1SHO 1 VERSN REVDAT 1 24-DEC-97 1SHO 0 JRNL AUTH M.SCHAFER,T.R.SCHNEIDER,G.M.SHELDRICK JRNL TITL CRYSTAL STRUCTURE OF VANCOMYCIN. JRNL REF STRUCTURE V. 4 1509 1996 JRNL REFN ISSN 0969-2126 JRNL PMID 8994975 JRNL DOI 10.1016/S0969-2126(96)00156-6 REMARK 2 REMARK 2 RESOLUTION. 1.09 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL-96 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.09 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 70.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL 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) : 0.105 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) : 11867 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)) : 0.104 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)) : 11394 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 160 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 48 REMARK 3 SOLVENT ATOMS : 108 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 314.50 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 155.00 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 2 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 2867 REMARK 3 NUMBER OF RESTRAINTS : 3022 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.024 REMARK 3 ANGLE DISTANCES (A) : 0.000 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.022 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.057 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.093 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.000 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.041 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.003 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.017 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.104 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 : NULL REMARK 3 SPECIAL CASE: ENGH AND HUBER RESTRAINT DISTANCES FOR ACETATE AND REMARK 3 FOR THE TWO DISORDERED SUGARS REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1SHO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000176377. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-AUG-95 REMARK 200 TEMPERATURE (KELVIN) : 125 REMARK 200 PH : 5.8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : EMBL/DESY, HAMBURG REMARK 200 BEAMLINE : BW7B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.862 REMARK 200 MONOCHROMATOR : GE(111) REMARK 200 OPTICS : BENT CRYSTAL MONOCHROMATOR REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11867 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.090 REMARK 200 RESOLUTION RANGE LOW (A) : 70.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 13.90 REMARK 200 R MERGE (I) : 0.05800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 27.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.09 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.17 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.80 REMARK 200 R MERGE FOR SHELL (I) : 0.08300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 19.70 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: AB INITIO REMARK 200 SOFTWARE USED: SHELX-96 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.61 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.90 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 5.8 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-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 32.91500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 14.24000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 14.24000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 49.37250 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 14.24000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 14.24000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 16.45750 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 14.24000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 14.24000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 49.37250 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 14.24000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 14.24000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 16.45750 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 32.91500 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 730 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 1650 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -5.2 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A2035 LIES ON A SPECIAL POSITION. REMARK 375 HOH B2016 LIES ON A SPECIAL POSITION. REMARK 375 HOH B2017 LIES ON A SPECIAL POSITION. 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: 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 A 3 -69.71 -101.95 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1AA5 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF VANCOMYCIN REMARK 900 RELATED ID: 1C0Q RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF VANCOMYCIN COMPLEXED WITH 2-ACETOXY-D- REMARK 900 PROPANOIC ACID REMARK 900 RELATED ID: 1C0R RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF VANCOMYCIN WITH D-LACTIC ACID REMARK 900 RELATED ID: 1FVM RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF VANCOMYCIN COMPLEXED WITH DI-ACETYL-LYS-D-ALA- REMARK 900 D-ALA REMARK 900 RELATED ID: 1GAC RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF A82846B COMPLEXED WITH ITS CELL WALL REMARK 900 PENTAPEPTIDE FRAGMENT REMARK 900 RELATED ID: 1GHG RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF VANCOMYCIN AGLYCON REMARK 900 RELATED ID: 1PN3 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF TDP-EPI-VANCOSAMINYLTRANSFERASE GTFA COMPLEXD REMARK 900 WITH TDP AND DESVANCOSAMINYL VANCOMYCIN REMARK 900 RELATED ID: 1PNV RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF TDP-EPI-VANCOSAMINYLTRANSFERASE GTFA COMPLEXED REMARK 900 WITH TDP AND VANCOMYCIN REMARK 900 RELATED ID: 1QD8 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF VANCOMYCIN COMPLEXED WITH N-ACETYL GLYCIN REMARK 900 RELATED ID: 1RRV RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF TDP-VANCOSAMINYLTRANSFERASE GTFD COMPLEXED REMARK 900 WITH TDP AND DESVANCOSAMINYL VANCOMYCIN. DBREF 1SHO A 1 7 NOR NOR00681 NOR00681 1 7 DBREF 1SHO B 1 7 NOR NOR00681 NOR00681 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 11 HET BGC D 1 12 HET RER D 2 10 HET ACT B 10 4 HET CL B 11 1 HET CL B 12 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 ACT ACETATE ION HETNAM CL CHLORIDE ION HETSYN RER VANCOSAMINE 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 ACT C2 H3 O2 1- FORMUL 6 CL 2(CL 1-) FORMUL 8 HOH *108(H2 O) LINK C MLU A 1 N OMZ A 2 1555 1555 1.34 LINK C OMZ A 2 N ASN A 3 1555 1555 1.31 LINK OH OMZ A 2 C5 GHP A 4 1555 1555 1.39 LINK C ASN A 3 N GHP A 4 1555 1555 1.33 LINK C GHP A 4 N GHP A 5 1555 1555 1.33 LINK C3 GHP A 4 OCZ OMY A 6 1555 1555 1.40 LINK O4 GHP A 4 C1 BGC C 1 1555 1555 1.39 LINK C GHP A 5 N OMY A 6 1555 1555 1.32 LINK C3 GHP A 5 CG1 3FG A 7 1555 1555 1.50 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 1.38 LINK C ASN B 3 N GHP B 4 1555 1555 1.32 LINK C GHP B 4 N GHP B 5 1555 1555 1.33 LINK C3 GHP B 4 OCZ OMY B 6 1555 1555 1.42 LINK O4 GHP B 4 C1 BGC D 1 1555 1555 1.37 LINK C GHP B 5 N OMY B 6 1555 1555 1.34 LINK C3 GHP B 5 CG1 3FG B 7 1555 1555 1.47 LINK C OMY B 6 N 3FG B 7 1555 1555 1.33 LINK O2 BGC C 1 C1 RER C 2 1555 1555 1.44 LINK O2 BGC D 1 C1 RER D 2 1555 1555 1.43 CISPEP 1 GHP A 5 OMY A 6 0 5.48 CISPEP 2 GHP B 5 OMY B 6 0 18.56 CRYST1 28.480 28.480 65.830 90.00 90.00 90.00 P 43 21 2 16 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 0.035112 0.000000 0.000000 0.00000 SCALE2 0.000000 0.035112 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015191 0.00000 MASTER 270 0 19 0 0 0 0 6 0 0 0 2 END