HEADER ANTIBIOTIC 13-OCT-16 5M2H TITLE CRYSTAL STRUCTURE OF VANCOMYCIN-ZN(II)-CITRATE COMPLEX 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 VANCOMYCIN, ZINC, GLYCOPEPTIDE, ANTIBIOTIC EXPDTA X-RAY DIFFRACTION AUTHOR A.ZARKAN,H.-R.MACKLYNE,D.Y.CHIRGADZE,A.D.BOND,A.R.HESKETH,H.-J.HONG REVDAT 5 29-JUL-20 5M2H 1 COMPND REMARK HETNAM LINK REVDAT 5 2 1 SITE ATOM REVDAT 4 10-JUL-19 5M2H 1 REMARK REVDAT 3 24-APR-19 5M2H 1 REMARK SEQRES REVDAT 2 13-JUN-18 5M2H 1 DBREF REVDAT 1 19-JUL-17 5M2H 0 JRNL AUTH A.ZARKAN,H.R.MACKLYNE,D.Y.CHIRGADZE,A.D.BOND,A.R.HESKETH, JRNL AUTH 2 H.J.HONG JRNL TITL ZN(II) MEDIATES VANCOMYCIN POLYMERIZATION AND POTENTIATES JRNL TITL 2 ITS ANTIBIOTIC ACTIVITY AGAINST RESISTANT BACTERIA. JRNL REF SCI REP V. 7 4893 2017 JRNL REFN ESSN 2045-2322 JRNL PMID 28687742 JRNL DOI 10.1038/S41598-017-04868-2 REMARK 2 REMARK 2 RESOLUTION. 0.95 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0135 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 0.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.31 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 3 NUMBER OF REFLECTIONS : 17433 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.106 REMARK 3 R VALUE (WORKING SET) : 0.105 REMARK 3 FREE R VALUE : 0.118 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1939 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 0.95 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 0.98 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1063 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 81.63 REMARK 3 BIN R VALUE (WORKING SET) : 0.0980 REMARK 3 BIN FREE R VALUE SET COUNT : 119 REMARK 3 BIN FREE R VALUE : 0.1130 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 : 86 REMARK 3 SOLVENT ATOMS : 74 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 5.92 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.02000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : -0.02000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.015 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.016 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.007 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 0.261 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.975 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.973 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 260 ; 0.042 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): 181 ; 0.010 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 341 ; 2.738 ; 2.832 REMARK 3 BOND ANGLES OTHERS (DEGREES): 403 ; 4.925 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 8 ;14.756 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 2 ;31.787 ;30.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 2 ; 6.751 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 38 ; 0.220 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 216 ; 0.041 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 52 ; 0.009 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 54 ; 0.596 ; 0.403 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 53 ; 0.588 ; 0.400 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 52 ; 0.613 ; 0.582 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 53 ; 0.608 ; 0.583 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 206 ; 0.908 ; 0.517 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 206 ; 0.911 ; 0.516 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 290 ; 1.038 ; 0.758 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 373 ; 2.247 ; 6.389 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 325 ; 1.321 ; 4.975 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 440 ; 6.937 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 9 ;31.706 ; 5.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 491 ; 5.603 ; 5.000 REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 5M2H COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 14-OCT-16. REMARK 100 THE DEPOSITION ID IS D_1200001791. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-OCT-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I04-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.92819 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 S 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19399 REMARK 200 RESOLUTION RANGE HIGH (A) : 0.950 REMARK 200 RESOLUTION RANGE LOW (A) : 37.310 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 200 DATA REDUNDANCY : 9.900 REMARK 200 R MERGE (I) : 0.05200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 30.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 0.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 90.5 REMARK 200 DATA REDUNDANCY IN SHELL : 5.30 REMARK 200 R MERGE FOR SHELL (I) : 0.08500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 11.70 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 62.89 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.31 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M DI-AMMONIUM HYDROGEN CITRATE REMARK 280 SALT AND 20% (W/V) PEG 3350, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 2 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,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z REMARK 290 7555 -X+1/2,Y+1/2,-Z REMARK 290 8555 X+1/2,-Y+1/2,-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 -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 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 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 1.000000 0.000000 0.000000 24.51900 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 28.74050 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 24.51900 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 28.74050 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 24.51900 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 28.74050 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 24.51900 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 28.74050 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 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 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 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 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 B 202 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: 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 O HOH B 203 O HOH B 210 1.48 REMARK 500 O HOH A 207 O HOH A 227 1.81 REMARK 500 O HOH A 201 O HOH A 235 1.82 REMARK 500 O HOH B 225 O HOH B 229 1.89 REMARK 500 O HOH B 210 O HOH B 225 1.95 REMARK 500 O HOH A 226 O HOH A 228 2.00 REMARK 500 OD1 ASN B 3 O HOH B 201 2.01 REMARK 500 O HOH A 230 O HOH A 235 2.19 REMARK 500 REMARK 500 REMARK: NULL 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 234 O HOH A 234 3654 1.83 REMARK 500 O HOH A 203 O HOH A 203 3654 1.92 REMARK 500 O HOH B 204 O HOH B 204 4543 2.00 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 ASN B 3 CG ASN B 3 OD1 0.155 REMARK 500 ASN B 3 CG ASN B 3 ND2 -0.161 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 MLU B 1 -12.04 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 245 DISTANCE = 6.12 ANGSTROMS REMARK 525 HOH B 229 DISTANCE = 6.21 ANGSTROMS REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 P6G B 103 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 103 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CIT A 104 O2 REMARK 620 2 CIT A 104 O7 82.0 REMARK 620 3 CIT A 104 O6 98.9 76.3 REMARK 620 4 CIT A 105 O5 93.9 104.7 167.2 REMARK 620 5 CIT A 105 O7 165.0 91.5 92.7 74.5 REMARK 620 6 HOH A 217 O 92.1 161.8 87.7 92.9 97.9 REMARK 620 N 1 2 3 4 5 DBREF 5M2H A 1 7 NOR 5M2H 5M2H 1 7 DBREF 5M2H B 1 7 NOR 5M2H 5M2H 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 ZN A 103 1 HET CIT A 104 13 HET CIT A 105 13 HET P6G B 103 17 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 ZN ZINC ION HETNAM CIT CITRIC ACID HETNAM P6G HEXAETHYLENE GLYCOL HETSYN RER VANCOSAMINE HETSYN P6G POLYETHYLENE GLYCOL PEG400 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 ZN ZN 2+ FORMUL 6 CIT 2(C6 H8 O7) FORMUL 8 P6G C12 H26 O7 FORMUL 9 HOH *74(H2 O) LINK C MLU A 1 N OMZ A 2 1555 1555 1.36 LINK C OMZ A 2 N ASN A 3 1555 1555 1.38 LINK OH OMZ A 2 C5 GHP A 4 1555 1555 1.42 LINK C ASN A 3 N GHP A 4 1555 1555 1.36 LINK C GHP A 4 N GHP A 5 1555 1555 1.36 LINK C3 GHP A 4 OCZ OMY A 6 1555 1555 1.40 LINK O4 GHP A 4 C1 BGC C 1 1555 1555 1.43 LINK C GHP A 5 N OMY A 6 1555 1555 1.35 LINK C3 GHP A 5 CG1 3FG A 7 1555 1555 1.53 LINK C OMY A 6 N 3FG A 7 1555 1555 1.35 LINK C MLU B 1 N OMZ B 2 1555 1555 1.45 LINK C OMZ B 2 N ASN B 3 1555 1555 1.37 LINK OH OMZ B 2 C5 GHP B 4 1555 1555 1.41 LINK C ASN B 3 N GHP B 4 1555 1555 1.36 LINK C GHP B 4 N GHP B 5 1555 1555 1.35 LINK C3 GHP B 4 OCZ OMY B 6 1555 1555 1.40 LINK O4 GHP B 4 C1 BGC D 1 1555 1555 1.43 LINK C GHP B 5 N OMY B 6 1555 1555 1.35 LINK C3 GHP B 5 CG1 3FG B 7 1555 1555 1.53 LINK C OMY B 6 N 3FG B 7 1555 1555 1.37 LINK O2 BGC C 1 C1 RER C 2 1555 1555 1.43 LINK O2 BGC D 1 C1 RER D 2 1555 1555 1.45 LINK ZN ZN A 103 O2 CIT A 104 1555 1555 2.06 LINK ZN ZN A 103 O7 CIT A 104 1555 1555 2.27 LINK ZN ZN A 103 O6 CIT A 104 1555 1555 2.06 LINK ZN ZN A 103 O5 CIT A 105 1555 1555 2.01 LINK ZN ZN A 103 O7 CIT A 105 1555 1555 2.23 LINK ZN ZN A 103 O HOH A 217 1555 1555 2.12 CISPEP 1 GHP A 5 OMY A 6 0 11.96 CISPEP 2 GHP B 5 OMY B 6 0 9.56 CRYST1 49.038 57.481 21.638 90.00 90.00 90.00 C 2 2 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 0.020392 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017397 0.000000 0.00000 SCALE3 0.000000 0.000000 0.046215 0.00000 HETATM 1 N MLU A 1 21.747 -22.265 -0.108 1.00 6.36 N ANISOU 1 N MLU A 1 665 1021 731 272 -137 -307 N HETATM 2 CN MLU A 1 22.605 -21.095 -0.564 1.00 9.64 C ANISOU 2 CN MLU A 1 828 1210 1624 181 -294 -527 C HETATM 3 CA MLU A 1 21.140 -22.959 -1.265 1.00 5.28 C ANISOU 3 CA MLU A 1 505 887 611 35 0 29 C HETATM 4 C MLU A 1 22.268 -23.395 -2.217 1.00 5.06 C ANISOU 4 C MLU A 1 622 690 608 162 -18 36 C HETATM 5 O MLU A 1 23.113 -24.185 -1.778 1.00 6.62 O ANISOU 5 O MLU A 1 966 934 615 378 26 146 O HETATM 6 CB MLU A 1 20.456 -24.351 -0.890 1.00 9.21 C ANISOU 6 CB MLU A 1 900 1391 1209 -266 -63 193 C HETATM 7 CG MLU A 1 19.263 -24.463 0.024 1.00 9.33 C ANISOU 7 CG MLU A 1 1238 1133 1173 55 108 -166 C HETATM 8 CD1 MLU A 1 19.006 -25.950 0.326 1.00 13.75 C ANISOU 8 CD1 MLU A 1 1636 1400 2186 -319 416 172 C HETATM 9 CD2 MLU A 1 18.055 -23.790 -0.559 1.00 10.10 C ANISOU 9 CD2 MLU A 1 1227 1264 1347 -58 14 -173 C HETATM 10 N OMZ A 2 22.217 -22.934 -3.500 1.00 4.45 N ANISOU 10 N OMZ A 2 577 613 501 123 -3 53 N HETATM 11 CA OMZ A 2 23.224 -23.393 -4.435 1.00 4.34 C ANISOU 11 CA OMZ A 2 546 610 493 212 -11 38 C HETATM 12 C OMZ A 2 22.671 -23.904 -5.758 1.00 4.40 C ANISOU 12 C OMZ A 2 515 583 572 207 -2 64 C HETATM 13 O OMZ A 2 23.464 -24.427 -6.579 1.00 5.33 O ANISOU 13 O OMZ A 2 626 798 598 224 42 -39 O HETATM 14 CB OMZ A 2 24.380 -22.343 -4.687 1.00 5.16 C ANISOU 14 CB OMZ A 2 558 847 554 181 -63 43 C HETATM 15 OC OMZ A 2 24.861 -21.913 -3.422 1.00 6.24 O ANISOU 15 OC OMZ A 2 719 1006 643 170 -278 62 O HETATM 16 CG OMZ A 2 23.880 -21.167 -5.537 1.00 4.19 C ANISOU 16 CG OMZ A 2 375 696 521 39 -45 30 C HETATM 17 CD1 OMZ A 2 24.029 -21.221 -6.932 1.00 4.32 C ANISOU 17 CD1 OMZ A 2 359 723 557 83 -23 58 C HETATM 18 CD2 OMZ A 2 23.192 -20.062 -4.960 1.00 4.42 C ANISOU 18 CD2 OMZ A 2 497 655 527 9 -89 53 C HETATM 19 CE1 OMZ A 2 23.442 -20.251 -7.752 1.00 4.31 C ANISOU 19 CE1 OMZ A 2 390 701 546 -84 -33 93 C HETATM 20 CL OMZ A 2 23.614 -20.348 -9.475 1.00 5.16 CL ANISOU 20 CL OMZ A 2 596 832 530 -86 17 56 CL HETATM 21 CE2 OMZ A 2 22.580 -19.110 -5.779 1.00 4.06 C ANISOU 21 CE2 OMZ A 2 465 546 532 9 -57 65 C HETATM 22 CZ OMZ A 2 22.676 -19.210 -7.184 1.00 3.81 C ANISOU 22 CZ OMZ A 2 386 508 552 -92 -115 103 C HETATM 23 OH OMZ A 2 22.013 -18.287 -7.970 1.00 4.35 O ANISOU 23 OH OMZ A 2 482 561 606 -139 -178 102 O