HEADER HYDROLASE 30-JUN-14 4QRA TITLE STRUCTURE AND SPECIFICITY OF L-D-TRANSPEPTIDASE FROM MYCOBACTERIUM TITLE 2 TUBERCULOSIS AND ANTIBIOTIC RESISTANCE: CALCIUM BINDING PROMOTES TITLE 3 DIMER FORMATION CAVEAT 4QRA C-N BOND BETWEEN A TRP 112 AND A SER 113 IS OUTSIDE ACCEPTED CAVEAT 2 4QRA RANGE COMPND MOL_ID: 1; COMPND 2 MOLECULE: L,D-TRANSPEPTIDASE LDTB; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTERIUM TUBERCULOSIS; SOURCE 3 ORGANISM_TAXID: 83332; SOURCE 4 STRAIN: H37RV; SOURCE 5 GENE: LDTB, RV2518C, RVBD_2518C; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21DE3; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: E.COLI BL21DE3/PET28B; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28B KEYWDS STRUCTURAL GENOMICS, ENZYME FUNCTION INITIATIVE, CENTER FOR KEYWDS 2 STRUCTURAL GENOMICS OF INFECTIOUS DISEASES, CSGID, L-D- KEYWDS 3 TRANSPEPTIDASE; D-D-TRANSPEPTIDASE; SINGLE ANOMALOUS DIFFRACTION; KEYWDS 4 IMIPENEM; MEROPENEM;, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR K.GOKULAN,K.I.VARUGHESE REVDAT 3 28-FEB-24 4QRA 1 REMARK LINK REVDAT 2 24-AUG-16 4QRA 1 AUTHOR REVDAT 1 23-DEC-15 4QRA 0 JRNL AUTH K.GOKULAN,S.KHARE,C.E.CERNIGLIA,S.L.FOLEY,K.I.VARUGHESE JRNL TITL STRUCTURE AND SPECIFICITY OF L-D-TRANSPEPTIDASE FROM JRNL TITL 2 MYCOBACTERIUM TUBERCULOSIS AND ANTIBIOTIC RESISTANCE: JRNL TITL 3 CALCIUM BINDING PROMOTES DIMER FORMATION JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.29 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0029 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) : 2.29 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.86 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 97.5 REMARK 3 NUMBER OF REFLECTIONS : 37354 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) : 0.184 REMARK 3 R VALUE (WORKING SET) : 0.182 REMARK 3 FREE R VALUE : 0.226 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1964 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) : 2.29 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.35 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2656 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 94.91 REMARK 3 BIN R VALUE (WORKING SET) : 0.2070 REMARK 3 BIN FREE R VALUE SET COUNT : 139 REMARK 3 BIN FREE R VALUE : 0.2830 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5046 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 297 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 41.56 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.67000 REMARK 3 B22 (A**2) : -1.57000 REMARK 3 B33 (A**2) : 0.91000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.28000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.248 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.201 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.122 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 9.388 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.948 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.926 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5187 ; 0.018 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 4735 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7100 ; 1.843 ; 1.922 REMARK 3 BOND ANGLES OTHERS (DEGREES): 10860 ; 0.931 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 663 ; 8.033 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 232 ;31.914 ;24.138 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 742 ;14.690 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 31 ;17.301 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 790 ; 0.126 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 6036 ; 0.009 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 1211 ; 0.001 ; 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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 : 2 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 64 A 408 REMARK 3 ORIGIN FOR THE GROUP (A): -39.8928 -3.1446 -36.9757 REMARK 3 T TENSOR REMARK 3 T11: 0.0435 T22: 0.0349 REMARK 3 T33: 0.0216 T12: -0.0020 REMARK 3 T13: 0.0101 T23: -0.0001 REMARK 3 L TENSOR REMARK 3 L11: 0.2428 L22: 1.1037 REMARK 3 L33: 0.2818 L12: -0.1994 REMARK 3 L13: -0.0693 L23: -0.1984 REMARK 3 S TENSOR REMARK 3 S11: 0.0095 S12: -0.0694 S13: -0.0112 REMARK 3 S21: -0.1188 S22: -0.0305 S23: 0.0540 REMARK 3 S31: 0.1018 S32: 0.0146 S33: 0.0210 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 65 B 408 REMARK 3 RESIDUE RANGE : A 501 A 501 REMARK 3 ORIGIN FOR THE GROUP (A): -39.9036 -29.6968 -8.3427 REMARK 3 T TENSOR REMARK 3 T11: 0.0400 T22: 0.0388 REMARK 3 T33: 0.0195 T12: 0.0083 REMARK 3 T13: -0.0062 T23: -0.0002 REMARK 3 L TENSOR REMARK 3 L11: 0.2119 L22: 1.1251 REMARK 3 L33: 0.2736 L12: 0.0769 REMARK 3 L13: 0.0778 L23: -0.1750 REMARK 3 S TENSOR REMARK 3 S11: 0.0057 S12: 0.0787 S13: -0.0001 REMARK 3 S21: 0.0992 S22: -0.0318 S23: 0.0281 REMARK 3 S31: -0.0961 S32: 0.0118 S33: 0.0261 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK 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 4QRA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-JUL-14. REMARK 100 THE DEPOSITION ID IS D_1000086413. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-APR-12 REMARK 200 TEMPERATURE (KELVIN) : 120 REMARK 200 PH : 5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL9-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 37534 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.290 REMARK 200 RESOLUTION RANGE LOW (A) : 34.860 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.4 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.05720 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.2100 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MLPHARE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.14 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.01 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.02 M CALCIUM CHLORIDE, 0.1 M SODIUM REMARK 280 ACETATE BUFFER (PH 4.6 TO 5), AND 30% METHYL-2,4-PENTANEDIOL (V/ REMARK 280 V), VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 289K, PH 5 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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+1/2,Y+1/2,Z REMARK 290 4555 -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 56.87900 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 44.06600 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 56.87900 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 44.06600 REMARK 290 SMTRY3 4 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 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 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 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 LEU A 57 REMARK 465 LEU A 58 REMARK 465 VAL A 59 REMARK 465 PRO A 60 REMARK 465 LYS A 61 REMARK 465 LEU A 62 REMARK 465 THR A 63 REMARK 465 ASN A 127 REMARK 465 ALA A 128 REMARK 465 THR A 129 REMARK 465 ALA A 130 REMARK 465 LEU A 131 REMARK 465 GLY A 132 REMARK 465 LEU A 133 REMARK 465 GLY A 134 REMARK 465 GLY A 135 REMARK 465 ALA A 136 REMARK 465 ALA A 137 REMARK 465 LEU B 57 REMARK 465 LEU B 58 REMARK 465 VAL B 59 REMARK 465 PRO B 60 REMARK 465 LYS B 61 REMARK 465 LEU B 62 REMARK 465 THR B 63 REMARK 465 ALA B 64 REMARK 465 ASN B 127 REMARK 465 ALA B 128 REMARK 465 THR B 129 REMARK 465 ALA B 130 REMARK 465 LEU B 131 REMARK 465 GLY B 132 REMARK 465 LEU B 133 REMARK 465 GLY B 134 REMARK 465 GLY B 135 REMARK 465 ALA B 136 REMARK 465 ALA B 137 REMARK 465 THR B 138 REMARK 465 ARG B 139 REMARK 465 GLN B 140 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 CG2 VAL B 101 OE2 GLU B 116 1.64 REMARK 500 O TRP A 112 N SER A 113 1.76 REMARK 500 CB ARG B 104 CZ2 TRP B 112 1.86 REMARK 500 O GLY B 98 CD PRO B 100 1.91 REMARK 500 O GLY A 103 N LEU A 105 1.97 REMARK 500 O HOH B 625 O HOH B 638 2.10 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 TRP A 112 C SER A 113 N -0.381 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES 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,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) 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 ATM2 ATM3 REMARK 500 TRP A 112 CA - C - N ANGL. DEV. = 14.3 DEGREES REMARK 500 TRP A 112 O - C - N ANGL. DEV. = -15.3 DEGREES REMARK 500 PRO B 100 C - N - CD ANGL. DEV. = -35.8 DEGREES REMARK 500 ASP B 373 CB - CG - OD1 ANGL. DEV. = 6.0 DEGREES 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 ALA A 84 108.29 153.21 REMARK 500 ALA A 89 156.58 94.77 REMARK 500 ALA A 90 64.63 60.94 REMARK 500 ASN A 95 -23.77 147.60 REMARK 500 ASN A 97 -80.23 134.10 REMARK 500 ARG A 99 2.08 82.67 REMARK 500 ALA A 102 -166.54 -77.98 REMARK 500 ARG A 104 29.56 -14.95 REMARK 500 LEU A 105 -178.92 78.41 REMARK 500 PRO A 107 -179.76 -53.88 REMARK 500 ASP A 108 -26.70 -143.41 REMARK 500 LEU A 110 17.84 96.15 REMARK 500 ARG A 111 144.33 -177.73 REMARK 500 ASN A 121 70.10 65.97 REMARK 500 ASN A 227 58.91 -95.62 REMARK 500 MET A 280 -166.38 -105.91 REMARK 500 HIS A 347 -44.92 -137.85 REMARK 500 ASP B 85 75.33 -152.06 REMARK 500 VAL B 87 135.17 75.33 REMARK 500 LEU B 88 116.32 169.45 REMARK 500 ALA B 89 31.80 -141.14 REMARK 500 VAL B 94 -139.98 -116.43 REMARK 500 ASP B 96 121.30 145.76 REMARK 500 VAL B 101 -92.19 -102.05 REMARK 500 ALA B 102 -79.15 132.25 REMARK 500 ASP B 108 -40.59 138.27 REMARK 500 ASN B 121 -80.36 -39.03 REMARK 500 ASN B 204 -169.91 -162.37 REMARK 500 ASN B 227 59.09 -99.98 REMARK 500 ASN B 313 56.05 -97.37 REMARK 500 HIS B 347 -43.71 -137.81 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 LEU A 88 ALA A 89 61.35 REMARK 500 VAL A 94 ASN A 95 54.91 REMARK 500 VAL A 101 ALA A 102 -149.85 REMARK 500 PRO B 100 VAL B 101 -140.27 REMARK 500 ASN B 121 ARG B 122 -41.77 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 CA A 501 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LEU A 151 O REMARK 620 2 HOH A 624 O 88.3 REMARK 620 3 HOH A 625 O 90.3 75.4 REMARK 620 4 LEU B 151 O 163.0 105.6 83.8 REMARK 620 5 HOH B 525 O 80.9 145.2 71.8 82.1 REMARK 620 6 HOH B 526 O 83.2 143.7 139.6 90.9 67.8 REMARK 620 7 HOH B 527 O 105.7 72.5 143.4 88.2 142.2 76.0 REMARK 620 N 1 2 3 4 5 6 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 501 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4QR7 RELATED DB: PDB REMARK 900 RELATED ID: 4QRB RELATED DB: PDB DBREF 4QRA A 57 408 UNP I6Y9J2 I6Y9J2_MYCTU 57 408 DBREF 4QRA B 57 408 UNP I6Y9J2 I6Y9J2_MYCTU 57 408 SEQRES 1 A 352 LEU LEU VAL PRO LYS LEU THR ALA SER VAL THR ASP GLY SEQRES 2 A 352 ALA VAL GLY VAL THR VAL ASP ALA PRO VAL SER VAL THR SEQRES 3 A 352 ALA ALA ASP GLY VAL LEU ALA ALA VAL THR MET VAL ASN SEQRES 4 A 352 ASP ASN GLY ARG PRO VAL ALA GLY ARG LEU SER PRO ASP SEQRES 5 A 352 GLY LEU ARG TRP SER THR THR GLU GLN LEU GLY TYR ASN SEQRES 6 A 352 ARG ARG TYR THR LEU ASN ALA THR ALA LEU GLY LEU GLY SEQRES 7 A 352 GLY ALA ALA THR ARG GLN LEU THR PHE GLN THR SER SER SEQRES 8 A 352 PRO ALA HIS LEU THR MET PRO TYR VAL MET PRO GLY ASP SEQRES 9 A 352 GLY GLU VAL VAL GLY VAL GLY GLU PRO VAL ALA ILE ARG SEQRES 10 A 352 PHE ASP GLU ASN ILE ALA ASP ARG GLY ALA ALA GLU LYS SEQRES 11 A 352 ALA ILE LYS ILE THR THR ASN PRO PRO VAL GLU GLY ALA SEQRES 12 A 352 PHE TYR TRP LEU ASN ASN ARG GLU VAL ARG TRP ARG PRO SEQRES 13 A 352 GLU HIS PHE TRP LYS PRO GLY THR ALA VAL ASP VAL ALA SEQRES 14 A 352 VAL ASN THR TYR GLY VAL ASP LEU GLY GLU GLY MET PHE SEQRES 15 A 352 GLY GLU ASP ASN VAL GLN THR HIS PHE THR ILE GLY ASP SEQRES 16 A 352 GLU VAL ILE ALA THR ALA ASP ASP ASN THR LYS ILE LEU SEQRES 17 A 352 THR VAL ARG VAL ASN GLY GLU VAL VAL LYS SER MET PRO SEQRES 18 A 352 THR SER MET GLY LYS ASP SER THR PRO THR ALA ASN GLY SEQRES 19 A 352 ILE TYR ILE VAL GLY SER ARG TYR LYS HIS ILE ILE MET SEQRES 20 A 352 ASP SER SER THR TYR GLY VAL PRO VAL ASN SER PRO ASN SEQRES 21 A 352 GLY TYR ARG THR ASP VAL ASP TRP ALA THR GLN ILE SER SEQRES 22 A 352 TYR SER GLY VAL PHE VAL HIS SER ALA PRO TRP SER VAL SEQRES 23 A 352 GLY ALA GLN GLY HIS THR ASN THR SER HIS GLY CYS LEU SEQRES 24 A 352 ASN VAL SER PRO SER ASN ALA GLN TRP PHE TYR ASP HIS SEQRES 25 A 352 VAL LYS ARG GLY ASP ILE VAL GLU VAL VAL ASN THR VAL SEQRES 26 A 352 GLY GLY THR LEU PRO GLY ILE ASP GLY LEU GLY ASP TRP SEQRES 27 A 352 ASN ILE PRO TRP ASP GLN TRP ARG ALA GLY ASN ALA LYS SEQRES 28 A 352 ALA SEQRES 1 B 352 LEU LEU VAL PRO LYS LEU THR ALA SER VAL THR ASP GLY SEQRES 2 B 352 ALA VAL GLY VAL THR VAL ASP ALA PRO VAL SER VAL THR SEQRES 3 B 352 ALA ALA ASP GLY VAL LEU ALA ALA VAL THR MET VAL ASN SEQRES 4 B 352 ASP ASN GLY ARG PRO VAL ALA GLY ARG LEU SER PRO ASP SEQRES 5 B 352 GLY LEU ARG TRP SER THR THR GLU GLN LEU GLY TYR ASN SEQRES 6 B 352 ARG ARG TYR THR LEU ASN ALA THR ALA LEU GLY LEU GLY SEQRES 7 B 352 GLY ALA ALA THR ARG GLN LEU THR PHE GLN THR SER SER SEQRES 8 B 352 PRO ALA HIS LEU THR MET PRO TYR VAL MET PRO GLY ASP SEQRES 9 B 352 GLY GLU VAL VAL GLY VAL GLY GLU PRO VAL ALA ILE ARG SEQRES 10 B 352 PHE ASP GLU ASN ILE ALA ASP ARG GLY ALA ALA GLU LYS SEQRES 11 B 352 ALA ILE LYS ILE THR THR ASN PRO PRO VAL GLU GLY ALA SEQRES 12 B 352 PHE TYR TRP LEU ASN ASN ARG GLU VAL ARG TRP ARG PRO SEQRES 13 B 352 GLU HIS PHE TRP LYS PRO GLY THR ALA VAL ASP VAL ALA SEQRES 14 B 352 VAL ASN THR TYR GLY VAL ASP LEU GLY GLU GLY MET PHE SEQRES 15 B 352 GLY GLU ASP ASN VAL GLN THR HIS PHE THR ILE GLY ASP SEQRES 16 B 352 GLU VAL ILE ALA THR ALA ASP ASP ASN THR LYS ILE LEU SEQRES 17 B 352 THR VAL ARG VAL ASN GLY GLU VAL VAL LYS SER MET PRO SEQRES 18 B 352 THR SER MET GLY LYS ASP SER THR PRO THR ALA ASN GLY SEQRES 19 B 352 ILE TYR ILE VAL GLY SER ARG TYR LYS HIS ILE ILE MET SEQRES 20 B 352 ASP SER SER THR TYR GLY VAL PRO VAL ASN SER PRO ASN SEQRES 21 B 352 GLY TYR ARG THR ASP VAL ASP TRP ALA THR GLN ILE SER SEQRES 22 B 352 TYR SER GLY VAL PHE VAL HIS SER ALA PRO TRP SER VAL SEQRES 23 B 352 GLY ALA GLN GLY HIS THR ASN THR SER HIS GLY CYS LEU SEQRES 24 B 352 ASN VAL SER PRO SER ASN ALA GLN TRP PHE TYR ASP HIS SEQRES 25 B 352 VAL LYS ARG GLY ASP ILE VAL GLU VAL VAL ASN THR VAL SEQRES 26 B 352 GLY GLY THR LEU PRO GLY ILE ASP GLY LEU GLY ASP TRP SEQRES 27 B 352 ASN ILE PRO TRP ASP GLN TRP ARG ALA GLY ASN ALA LYS SEQRES 28 B 352 ALA HET CA A 501 1 HETNAM CA CALCIUM ION FORMUL 3 CA CA 2+ FORMUL 4 HOH *297(H2 O) HELIX 1 1 ASP A 180 ALA A 187 1 8 HELIX 2 2 SER A 306 GLY A 309 5 4 HELIX 3 3 PRO A 339 VAL A 342 5 4 HELIX 4 4 SER A 358 VAL A 369 1 12 HELIX 5 5 GLY A 392 ILE A 396 5 5 HELIX 6 6 PRO A 397 GLY A 404 1 8 HELIX 7 7 ASP B 180 ALA B 187 1 8 HELIX 8 8 SER B 306 GLY B 309 5 4 HELIX 9 9 PRO B 339 VAL B 342 5 4 HELIX 10 10 SER B 358 VAL B 369 1 12 HELIX 11 11 GLY B 392 ILE B 396 5 5 HELIX 12 12 PRO B 397 GLY B 404 1 8 SHEET 1 A 2 SER A 80 THR A 82 0 SHEET 2 A 2 ARG A 111 SER A 113 -1 O TRP A 112 N VAL A 81 SHEET 1 B 3 VAL A 94 ASN A 95 0 SHEET 2 B 3 ARG A 123 THR A 125 -1 O THR A 125 N VAL A 94 SHEET 3 B 3 THR A 142 GLN A 144 -1 O PHE A 143 N TYR A 124 SHEET 1 C 2 HIS A 150 THR A 152 0 SHEET 2 C 2 MET A 237 GLY A 239 1 O PHE A 238 N HIS A 150 SHEET 1 D 4 PRO A 154 MET A 157 0 SHEET 2 D 4 VAL A 170 PHE A 174 -1 O ARG A 173 N TYR A 155 SHEET 3 D 4 GLU A 207 PRO A 212 -1 O VAL A 208 N ILE A 172 SHEET 4 D 4 GLY A 198 TRP A 202 -1 N TYR A 201 O ARG A 209 SHEET 1 E 4 VAL A 163 VAL A 164 0 SHEET 2 E 4 VAL A 243 ILE A 249 1 O THR A 248 N VAL A 164 SHEET 3 E 4 ALA A 221 VAL A 226 -1 N VAL A 226 O VAL A 243 SHEET 4 E 4 ILE A 188 ASN A 193 -1 N THR A 191 O ASP A 223 SHEET 1 F 5 GLU A 271 PRO A 277 0 SHEET 2 F 5 ILE A 263 VAL A 268 -1 N LEU A 264 O MET A 276 SHEET 3 F 5 VAL A 253 ASP A 258 -1 N THR A 256 O THR A 265 SHEET 4 F 5 ILE A 374 VAL A 378 1 O GLU A 376 N ALA A 255 SHEET 5 F 5 GLY A 290 ILE A 293 -1 N TYR A 292 O VAL A 375 SHEET 1 G 4 ARG A 297 ASP A 304 0 SHEET 2 G 4 ARG A 319 GLN A 327 -1 O THR A 320 N MET A 303 SHEET 3 G 4 PHE A 334 SER A 337 -1 O VAL A 335 N THR A 326 SHEET 4 G 4 LEU A 355 VAL A 357 1 O LEU A 355 N PHE A 334 SHEET 1 H 3 SER B 80 THR B 82 0 SHEET 2 H 3 ARG B 111 THR B 114 -1 O TRP B 112 N VAL B 81 SHEET 3 H 3 ARG B 104 LEU B 105 -1 N LEU B 105 O SER B 113 SHEET 1 I 2 ARG B 123 TYR B 124 0 SHEET 2 I 2 PHE B 143 GLN B 144 -1 O PHE B 143 N TYR B 124 SHEET 1 J 2 HIS B 150 THR B 152 0 SHEET 2 J 2 MET B 237 GLY B 239 1 O PHE B 238 N THR B 152 SHEET 1 K 4 PRO B 154 MET B 157 0 SHEET 2 K 4 VAL B 170 PHE B 174 -1 O ARG B 173 N TYR B 155 SHEET 3 K 4 GLU B 207 PRO B 212 -1 O VAL B 208 N ILE B 172 SHEET 4 K 4 GLY B 198 TRP B 202 -1 N TYR B 201 O ARG B 209 SHEET 1 L 4 VAL B 163 VAL B 164 0 SHEET 2 L 4 VAL B 243 ILE B 249 1 O THR B 248 N VAL B 164 SHEET 3 L 4 ALA B 221 VAL B 226 -1 N VAL B 226 O VAL B 243 SHEET 4 L 4 ILE B 188 ASN B 193 -1 N THR B 191 O ASP B 223 SHEET 1 M 5 GLU B 271 PRO B 277 0 SHEET 2 M 5 ILE B 263 VAL B 268 -1 N LEU B 264 O MET B 276 SHEET 3 M 5 VAL B 253 ASP B 258 -1 N THR B 256 O THR B 265 SHEET 4 M 5 ILE B 374 VAL B 378 1 O GLU B 376 N ALA B 257 SHEET 5 M 5 GLY B 290 ILE B 293 -1 N TYR B 292 O VAL B 375 SHEET 1 N 4 ARG B 297 ASP B 304 0 SHEET 2 N 4 ARG B 319 GLN B 327 -1 O ALA B 325 N TYR B 298 SHEET 3 N 4 PHE B 334 SER B 337 -1 O VAL B 335 N THR B 326 SHEET 4 N 4 LEU B 355 VAL B 357 1 O LEU B 355 N PHE B 334 LINK O LEU A 151 CA CA A 501 1555 1555 2.37 LINK CA CA A 501 O HOH A 624 1555 1555 2.41 LINK CA CA A 501 O HOH A 625 1555 1555 2.48 LINK CA CA A 501 O LEU B 151 1555 1555 2.32 LINK CA CA A 501 O HOH B 525 1555 1555 2.37 LINK CA CA A 501 O HOH B 526 1555 1555 2.55 LINK CA CA A 501 O HOH B 527 1555 1555 2.42 CISPEP 1 ALA A 84 ASP A 85 0 13.81 CISPEP 2 ALA A 89 ALA A 90 0 8.56 CISPEP 3 ASN A 97 GLY A 98 0 -25.23 CISPEP 4 PRO A 107 ASP A 108 0 16.80 CISPEP 5 MET A 157 PRO A 158 0 -4.61 CISPEP 6 ASN A 193 PRO A 194 0 -1.39 CISPEP 7 GLY B 86 VAL B 87 0 -8.05 CISPEP 8 ASP B 96 ASN B 97 0 -2.65 CISPEP 9 MET B 157 PRO B 158 0 -0.70 CISPEP 10 ASN B 193 PRO B 194 0 -1.20 SITE 1 AC1 7 LEU A 151 HOH A 624 HOH A 625 LEU B 151 SITE 2 AC1 7 HOH B 525 HOH B 526 HOH B 527 CRYST1 113.758 88.132 90.512 90.00 90.02 90.00 C 1 2 1 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 0.008791 0.000000 0.000002 0.00000 SCALE2 0.000000 0.011347 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011048 0.00000