PDB Short entry for 1YM3 HEADER LYASE 20-JAN-05 1YM3 TITLE CRYSTAL STRUCTURE OF CARBONIC ANHYDRASE RV3588C FROM MYCOBACTERIUM TITLE 2 TUBERCULOSIS COMPND MOL_ID: 1; COMPND 2 MOLECULE: CARBONIC ANHYDRASE (CARBONATE DEHYDRATASE) (CARBONIC COMPND 3 DEHYDRATASE); COMPND 4 CHAIN: A; COMPND 5 EC: 4.2.1.1; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTERIUM TUBERCULOSIS; SOURCE 3 ORGANISM_TAXID: 83332; SOURCE 4 STRAIN: H37RV; SOURCE 5 GENE: RV3588C; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21-AI; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PCRT7 KEYWDS ZN PROTEIN, STRUCTURAL PROTEOMICS IN EUROPE, SPINE, STRUCTURAL KEYWDS 2 GENOMICS, LYASE EXPDTA X-RAY DIFFRACTION AUTHOR A.S.COVARRUBIAS,A.M.LARSSON,M.HOGBOM,J.LINDBERG,T.BERGFORS, AUTHOR 2 C.BJORKELID,S.L.MOWBRAY,T.UNGE,T.A.JONES,STRUCTURAL PROTEOMICS IN AUTHOR 3 EUROPE (SPINE) REVDAT 7 23-AUG-23 1YM3 1 REMARK SEQADV LINK REVDAT 6 07-MAR-18 1YM3 1 REMARK REVDAT 5 13-JUL-11 1YM3 1 VERSN REVDAT 4 24-FEB-09 1YM3 1 VERSN REVDAT 3 24-MAY-05 1YM3 1 JRNL REVDAT 2 15-MAR-05 1YM3 1 EXPDTA REVDAT 1 08-MAR-05 1YM3 0 JRNL AUTH A.SUAREZ COVARRUBIAS,A.M.LARSSON,M.HOGBOM,J.LINDBERG, JRNL AUTH 2 T.BERGFORS,C.BJORKELID,S.L.MOWBRAY,T.UNGE,T.A.JONES JRNL TITL STRUCTURE AND FUNCTION OF CARBONIC ANHYDRASES FROM JRNL TITL 2 MYCOBACTERIUM TUBERCULOSIS. JRNL REF J.BIOL.CHEM. V. 280 18782 2005 JRNL REFN ISSN 0021-9258 JRNL PMID 15753099 JRNL DOI 10.1074/JBC.M414348200 REMARK 2 REMARK 2 RESOLUTION. 1.75 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.1.24 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.20 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 82.9 REMARK 3 NUMBER OF REFLECTIONS : 13934 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) : 0.181 REMARK 3 R VALUE (WORKING SET) : 0.179 REMARK 3 FREE R VALUE : 0.229 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 734 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) : 1.75 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.79 REMARK 3 REFLECTION IN BIN (WORKING SET) : 956 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.1860 REMARK 3 BIN FREE R VALUE SET COUNT : 59 REMARK 3 BIN FREE R VALUE : 0.2380 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1435 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 2 REMARK 3 SOLVENT ATOMS : 130 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.21 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.36000 REMARK 3 B22 (A**2) : 0.36000 REMARK 3 B33 (A**2) : -0.71000 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): 0.154 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.146 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.085 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.595 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.963 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.943 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1468 ; 0.016 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 1385 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1994 ; 1.484 ; 1.946 REMARK 3 BOND ANGLES OTHERS (DEGREES): 3186 ; 0.874 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 193 ; 5.556 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 234 ; 0.090 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1678 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 300 ; 0.009 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 288 ; 0.208 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 1551 ; 0.229 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): 828 ; 0.080 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 69 ; 0.184 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 1 ; 0.007 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 20 ; 0.619 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 66 ; 0.322 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 18 ; 0.176 ; 0.200 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): 956 ; 0.980 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1532 ; 1.753 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 512 ; 2.682 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 462 ; 4.272 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL 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 : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 4 A 206 REMARK 3 ORIGIN FOR THE GROUP (A): 20.0998 22.5969 21.0858 REMARK 3 T TENSOR REMARK 3 T11: 0.0381 T22: 0.0095 REMARK 3 T33: 0.0326 T12: -0.0001 REMARK 3 T13: -0.0093 T23: -0.0022 REMARK 3 L TENSOR REMARK 3 L11: 0.5139 L22: 0.8383 REMARK 3 L33: 0.9139 L12: 0.1853 REMARK 3 L13: 0.1750 L23: 0.3555 REMARK 3 S TENSOR REMARK 3 S11: 0.0211 S12: -0.0526 S13: -0.0233 REMARK 3 S21: -0.0872 S22: -0.0219 S23: 0.0198 REMARK 3 S31: 0.0856 S32: -0.0211 S33: 0.0009 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 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 1YM3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-FEB-05. REMARK 100 THE DEPOSITION ID IS D_1000031674. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-MAY-04 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : MAX II REMARK 200 BEAMLINE : I711 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.085 REMARK 200 MONOCHROMATOR : SINGLE ASYMMETRICALLY CUT REMARK 200 SI(111) CRYSTAL WITH HORIZONTAL REMARK 200 DIFFRACTION PLANE. THE CRYSTAL REMARK 200 IS BENDABLE FOR HORIZONTAL REMARK 200 FOCUSING. REMARK 200 OPTICS : VERTICALLY FOCUSING CYLINDRICAL REMARK 200 MIRROR 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 : 13934 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.750 REMARK 200 RESOLUTION RANGE LOW (A) : 26.200 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 83.3 REMARK 200 DATA REDUNDANCY : 4.700 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.04400 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 23.3500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.75 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.81 REMARK 200 COMPLETENESS FOR SHELL (%) : 80.1 REMARK 200 DATA REDUNDANCY IN SHELL : 4.40 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.29800 REMARK 200 <I/SIGMA(I)> FOR SHELL : 5.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: PDB ENTRY 1I6O AND 1DDZ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 34.70 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.90 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MGCL2, PEG 400, HEPES, PH 7.0, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 293.0K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 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+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 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 52.09600 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 28.18850 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 28.18850 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 26.04800 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 28.18850 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 28.18850 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 78.14400 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 28.18850 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 28.18850 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 26.04800 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 28.18850 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 28.18850 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 78.14400 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 52.09600 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 300 REMARK: THE SECOND PART OF THE BIOLOGICAL ASSEMBLY IS GENERATED REMARK 300 BY THE TWO FOLD AXIS: -Y, -X, 1/2-Z 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,PQS REMARK 350 TOTAL BURIED SURFACE AREA: 3500 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15730 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -37.0 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 0.000000 -1.000000 0.000000 56.37700 REMARK 350 BIOMT2 2 -1.000000 0.000000 0.000000 56.37700 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 52.09600 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 A 313 LIES ON A SPECIAL POSITION. REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A -7 REMARK 465 ALA A -6 REMARK 465 HIS A -5 REMARK 465 HIS A -4 REMARK 465 HIS A -3 REMARK 465 HIS A -2 REMARK 465 HIS A -1 REMARK 465 HIS A 0 REMARK 465 GLY A 1 REMARK 465 PRO A 2 REMARK 465 ASN A 3 REMARK 465 VAL A 32 REMARK 465 ASP A 33 REMARK 465 HIS A 34 REMARK 465 ARG A 35 REMARK 465 ALA A 36 REMARK 465 GLY A 37 REMARK 465 LEU A 38 REMARK 465 ALA A 39 REMARK 465 ALA A 40 REMARK 465 GLY A 41 REMARK 465 VAL A 207 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 OE1 GLU A 173 O HOH A 399 2.06 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 OD1 ASP A 80 OD2 ASP A 80 8665 1.49 REMARK 500 CG ASP A 80 OD1 ASP A 80 8665 2.01 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 SER A 147 -8.26 -143.79 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 301 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 51 SG REMARK 620 2 ASP A 53 OD1 98.7 REMARK 620 3 HIS A 104 NE2 119.1 90.8 REMARK 620 4 CYS A 107 SG 112.1 123.2 111.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 302 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 199 O REMARK 620 2 HIS A 199 ND1 82.9 REMARK 620 3 HOH A 303 O 82.9 86.6 REMARK 620 4 HOH A 305 O 93.1 174.8 96.2 REMARK 620 5 HOH A 307 O 172.7 96.6 89.8 87.7 REMARK 620 6 HOH A 315 O 94.7 91.8 177.3 85.2 92.6 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 ZN A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 302 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: RV3588 RELATED DB: TARGETDB DBREF 1YM3 A 2 207 UNP O53573 O53573_MYCTU 2 207 SEQADV 1YM3 MET A -7 UNP O53573 CLONING ARTIFACT SEQADV 1YM3 ALA A -6 UNP O53573 CLONING ARTIFACT SEQADV 1YM3 HIS A -5 UNP O53573 CLONING ARTIFACT SEQADV 1YM3 HIS A -4 UNP O53573 CLONING ARTIFACT SEQADV 1YM3 HIS A -3 UNP O53573 CLONING ARTIFACT SEQADV 1YM3 HIS A -2 UNP O53573 CLONING ARTIFACT SEQADV 1YM3 HIS A -1 UNP O53573 CLONING ARTIFACT SEQADV 1YM3 HIS A 0 UNP O53573 CLONING ARTIFACT SEQADV 1YM3 GLY A 1 UNP O53573 CLONING ARTIFACT SEQRES 1 A 215 MET ALA HIS HIS HIS HIS HIS HIS GLY PRO ASN THR ASN SEQRES 2 A 215 PRO VAL ALA ALA TRP LYS ALA LEU LYS GLU GLY ASN GLU SEQRES 3 A 215 ARG PHE VAL ALA GLY ARG PRO GLN HIS PRO SER GLN SER SEQRES 4 A 215 VAL ASP HIS ARG ALA GLY LEU ALA ALA GLY GLN LYS PRO SEQRES 5 A 215 THR ALA VAL ILE PHE GLY CYS ALA ASP SER ARG VAL ALA SEQRES 6 A 215 ALA GLU ILE ILE PHE ASP GLN GLY LEU GLY ASP MET PHE SEQRES 7 A 215 VAL VAL ARG THR ALA GLY HIS VAL ILE ASP SER ALA VAL SEQRES 8 A 215 LEU GLY SER ILE GLU TYR ALA VAL THR VAL LEU ASN VAL SEQRES 9 A 215 PRO LEU ILE VAL VAL LEU GLY HIS ASP SER CYS GLY ALA SEQRES 10 A 215 VAL ASN ALA ALA LEU ALA ALA ILE ASN ASP GLY THR LEU SEQRES 11 A 215 PRO GLY GLY TYR VAL ARG ASP VAL VAL GLU ARG VAL ALA SEQRES 12 A 215 PRO SER VAL LEU LEU GLY ARG ARG ASP GLY LEU SER ARG SEQRES 13 A 215 VAL ASP GLU PHE GLU GLN ARG HIS VAL HIS GLU THR VAL SEQRES 14 A 215 ALA ILE LEU MET ALA ARG SER SER ALA ILE SER GLU ARG SEQRES 15 A 215 ILE ALA GLY GLY SER LEU ALA ILE VAL GLY VAL THR TYR SEQRES 16 A 215 GLN LEU ASP ASP GLY ARG ALA VAL LEU ARG ASP HIS ILE SEQRES 17 A 215 GLY ASN ILE GLY GLU GLU VAL HET ZN A 301 1 HET MG A 302 1 HETNAM ZN ZINC ION HETNAM MG MAGNESIUM ION FORMUL 2 ZN ZN 2+ FORMUL 3 MG MG 2+ FORMUL 4 HOH *130(H2 O) HELIX 1 1 ASN A 5 GLY A 23 1 19 HELIX 2 2 HIS A 27 SER A 31 5 5 HELIX 3 3 ALA A 57 PHE A 62 1 6 HELIX 4 4 ALA A 75 VAL A 78 5 4 HELIX 5 5 ASP A 80 VAL A 93 1 14 HELIX 6 6 CYS A 107 GLY A 120 1 14 HELIX 7 7 TYR A 126 ASP A 144 1 19 HELIX 8 8 ARG A 148 SER A 168 1 21 HELIX 9 9 SER A 168 GLY A 177 1 10 SHEET 1 A 5 MET A 69 THR A 74 0 SHEET 2 A 5 ALA A 46 CYS A 51 1 N ILE A 48 O VAL A 72 SHEET 3 A 5 LEU A 98 HIS A 104 1 O VAL A 100 N PHE A 49 SHEET 4 A 5 ALA A 181 TYR A 187 1 O VAL A 185 N GLY A 103 SHEET 5 A 5 VAL A 195 ILE A 200 -1 O VAL A 195 N THR A 186 LINK SG CYS A 51 ZN ZN A 301 1555 1555 2.37 LINK OD1 ASP A 53 ZN ZN A 301 1555 1555 2.10 LINK NE2 HIS A 104 ZN ZN A 301 1555 1555 2.05 LINK SG CYS A 107 ZN ZN A 301 1555 1555 2.30 LINK O HIS A 199 MG MG A 302 1555 1555 2.04 LINK ND1 HIS A 199 MG MG A 302 1555 1555 2.27 LINK MG MG A 302 O HOH A 303 1555 1555 2.07 LINK MG MG A 302 O HOH A 305 1555 1555 2.05 LINK MG MG A 302 O HOH A 307 1555 1555 2.08 LINK MG MG A 302 O HOH A 315 1555 1555 2.13 SITE 1 AC1 4 CYS A 51 ASP A 53 HIS A 104 CYS A 107 SITE 1 AC2 5 HIS A 199 HOH A 303 HOH A 305 HOH A 307 SITE 2 AC2 5 HOH A 315 CRYST1 56.377 56.377 104.192 90.00 90.00 90.00 P 41 21 2 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 0.017738 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017738 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009598 0.00000