HEADER HYDROLASE/HYDROLASE INHIBITOR 07-JUL-14 4QTF TITLE STRUCTURE AND SPECIFICITY OF L-D-TRANSPEPTIDASE FROM MYCOBACTERIUM TITLE 2 TUBERCULOSIS AND ANTIBIOTIC RESISTANCE: CALCIUM BINDING PROMOTES TITLE 3 DIMER FORMATION CAVEAT 4QTF C-N BOND BETWEEN A CYS 354 AND A LEU 355 IS OUTSIDE ACCEPTED CAVEAT 2 4QTF RANGE COMPND MOL_ID: 1; COMPND 2 MOLECULE: L,D-TRANSPEPTIDASE LDTB; COMPND 3 CHAIN: A; 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, IMIPENEM, MEROPENEM, KEYWDS 4 PEPTIDOGLYCAN, BETA-LACTAMASE, CROSS-LINKAGE, HYDROLASE-HYDROLASE KEYWDS 5 INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR K.GOKULAN,K.I.VARUGHESE REVDAT 3 20-SEP-23 4QTF 1 REMARK LINK REVDAT 2 24-AUG-16 4QTF 1 AUTHOR REVDAT 1 29-JUL-15 4QTF 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. 2.00 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.35 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 25603 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) : 0.215 REMARK 3 R VALUE (WORKING SET) : 0.213 REMARK 3 FREE R VALUE : 0.258 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1356 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) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.05 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1863 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.49 REMARK 3 BIN R VALUE (WORKING SET) : 0.2450 REMARK 3 BIN FREE R VALUE SET COUNT : 94 REMARK 3 BIN FREE R VALUE : 0.3040 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2635 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 65 REMARK 3 SOLVENT ATOMS : 76 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 37.45 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.98000 REMARK 3 B22 (A**2) : 0.38000 REMARK 3 B33 (A**2) : -1.36000 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): 0.191 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.173 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.123 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 8.918 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.942 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.921 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2786 ; 0.019 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2568 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3812 ; 2.162 ; 1.955 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5891 ; 0.955 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 349 ; 7.239 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 118 ;31.385 ;24.153 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 391 ;15.215 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 16 ;17.005 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 433 ; 0.129 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3216 ; 0.010 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 644 ; 0.002 ; 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 : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 59 A 407 REMARK 3 RESIDUE RANGE : A 501 A 501 REMARK 3 ORIGIN FOR THE GROUP (A): 12.5731 15.7551 19.5679 REMARK 3 T TENSOR REMARK 3 T11: 0.0580 T22: 0.0284 REMARK 3 T33: 0.0923 T12: 0.0325 REMARK 3 T13: -0.0430 T23: -0.0429 REMARK 3 L TENSOR REMARK 3 L11: 0.0795 L22: 0.5535 REMARK 3 L33: 1.4056 L12: 0.0181 REMARK 3 L13: -0.0253 L23: 0.3102 REMARK 3 S TENSOR REMARK 3 S11: -0.0185 S12: -0.0243 S13: 0.0257 REMARK 3 S21: 0.1523 S22: 0.0895 S23: -0.1039 REMARK 3 S31: 0.0034 S32: 0.0836 S33: -0.0710 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 4QTF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-JUL-14. REMARK 100 THE DEPOSITION ID IS D_1000086490. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 120 REMARK 200 PH : 7,6 REMARK 200 NUMBER OF CRYSTALS USED : NULL 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) : 1 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR-325 CCD DETECTOR REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25603 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 43.300 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL 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: PHENIX REMARK 200 STARTING MODEL: 4QR7 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.01 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.62 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.03 M CITRIC ACID, 0.07 M BIS-TRIS REMARK 280 PROPANE PH 7.6 AND 20% PEG 3350, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 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 -X,Y,-Z+1/2 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+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 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 103.72800 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 103.72800 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 28.63600 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 32.94050 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 28.63600 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 32.94050 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 103.72800 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 28.63600 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 32.94050 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 103.72800 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 28.63600 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 32.94050 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 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3150 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 31670 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -14.0 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 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 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 A 626 LIES ON A SPECIAL POSITION. 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 OD2 ASP A 108 NH1 ARG A 111 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 TRP A 216 CB TRP A 216 CG -0.117 REMARK 500 CYS A 354 C LEU A 355 N -0.336 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 ARG A 123 NE - CZ - NH1 ANGL. DEV. = -3.2 DEGREES REMARK 500 GLY A 353 O - C - N ANGL. DEV. = -12.4 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 MET A 280 -159.28 -101.56 REMARK 500 TYR A 308 -70.85 -73.86 REMARK 500 HIS A 347 -54.90 -142.09 REMARK 500 ASN A 405 34.95 -147.33 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 GLY A 353 -17.83 REMARK 500 CYS A 354 13.09 REMARK 500 REMARK 500 REMARK: NULL 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 MLD A 501 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MLD A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 3V5 A 502 DBREF 4QTF A 59 407 UNP I6Y9J2 I6Y9J2_MYCTU 59 407 SEQRES 1 A 349 VAL PRO LYS LEU THR ALA SER VAL THR ASP GLY ALA VAL SEQRES 2 A 349 GLY VAL THR VAL ASP ALA PRO VAL SER VAL THR ALA ALA SEQRES 3 A 349 ASP GLY VAL LEU ALA ALA VAL THR MET VAL ASN ASP ASN SEQRES 4 A 349 GLY ARG PRO VAL ALA GLY ARG LEU SER PRO ASP GLY LEU SEQRES 5 A 349 ARG TRP SER THR THR GLU GLN LEU GLY TYR ASN ARG ARG SEQRES 6 A 349 TYR THR LEU ASN ALA THR ALA LEU GLY LEU GLY GLY ALA SEQRES 7 A 349 ALA THR ARG GLN LEU THR PHE GLN THR SER SER PRO ALA SEQRES 8 A 349 HIS LEU THR MET PRO TYR VAL MET PRO GLY ASP GLY GLU SEQRES 9 A 349 VAL VAL GLY VAL GLY GLU PRO VAL ALA ILE ARG PHE ASP SEQRES 10 A 349 GLU ASN ILE ALA ASP ARG GLY ALA ALA GLU LYS ALA ILE SEQRES 11 A 349 LYS ILE THR THR ASN PRO PRO VAL GLU GLY ALA PHE TYR SEQRES 12 A 349 TRP LEU ASN ASN ARG GLU VAL ARG TRP ARG PRO GLU HIS SEQRES 13 A 349 PHE TRP LYS PRO GLY THR ALA VAL ASP VAL ALA VAL ASN SEQRES 14 A 349 THR TYR GLY VAL ASP LEU GLY GLU GLY MET PHE GLY GLU SEQRES 15 A 349 ASP ASN VAL GLN THR HIS PHE THR ILE GLY ASP GLU VAL SEQRES 16 A 349 ILE ALA THR ALA ASP ASP ASN THR LYS ILE LEU THR VAL SEQRES 17 A 349 ARG VAL ASN GLY GLU VAL VAL LYS SER MET PRO THR SER SEQRES 18 A 349 MET GLY LYS ASP SER THR PRO THR ALA ASN GLY ILE TYR SEQRES 19 A 349 ILE VAL GLY SER ARG TYR LYS HIS ILE ILE MET ASP SER SEQRES 20 A 349 SER THR TYR GLY VAL PRO VAL ASN SER PRO ASN GLY TYR SEQRES 21 A 349 ARG THR ASP VAL ASP TRP ALA THR GLN ILE SER TYR SER SEQRES 22 A 349 GLY VAL PHE VAL HIS SER ALA PRO TRP SER VAL GLY ALA SEQRES 23 A 349 GLN GLY HIS THR ASN THR SER HIS GLY CYS LEU ASN VAL SEQRES 24 A 349 SER PRO SER ASN ALA GLN TRP PHE TYR ASP HIS VAL LYS SEQRES 25 A 349 ARG GLY ASP ILE VAL GLU VAL VAL ASN THR VAL GLY GLY SEQRES 26 A 349 THR LEU PRO GLY ILE ASP GLY LEU GLY ASP TRP ASN ILE SEQRES 27 A 349 PRO TRP ASP GLN TRP ARG ALA GLY ASN ALA LYS HET MLD A 501 46 HET 3V5 A 502 19 HETNAM MLD GLCNAC(BETA1-4)-MURNAC(1,6-ANHYDRO)-L-ALA-GAMMA-D-GLU- HETNAM 2 MLD MESO-A2PM-D-ALA HETNAM 3V5 (3S,5S)-3-({[(AMINOMETHYL)AMINO]METHYL}SULFANYL)-5- HETNAM 2 3V5 [(2S)-1,3-DIOXOBUTAN-2-YL]-L-PROLINE HETSYN MLD 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE(BETA1-4)-2- HETSYN 2 MLD ACETAMIDO-1,6-ANHYDRO-3-O-[(R)-1-CARBOXYETHYL]-2- HETSYN 3 MLD DEOXY-BETA-D-GLUCOPYRANOSE-L-ALANYL-GAMMA-D-GLUTAMYL- HETSYN 4 MLD MESO-DIAMINOPIMELYL-D-ALANINE HETSYN 3V5 OLIVANIC ACID ANALOG, OPEN FROM FORMUL 2 MLD C37 H59 N7 O20 FORMUL 3 3V5 C11 H19 N3 O4 S FORMUL 4 HOH *76(H2 O) HELIX 1 1 ASP A 180 ALA A 187 1 8 HELIX 2 2 SER A 306 TYR A 308 5 3 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 SHEET 1 A 4 LYS A 61 ALA A 64 0 SHEET 2 A 4 SER A 80 ALA A 84 -1 O ALA A 84 N LYS A 61 SHEET 3 A 4 ARG A 111 THR A 114 -1 O TRP A 112 N VAL A 81 SHEET 4 A 4 GLY A 103 LEU A 105 -1 N ARG A 104 O SER A 113 SHEET 1 B 3 VAL A 87 ASN A 95 0 SHEET 2 B 3 ARG A 123 GLY A 132 -1 O THR A 129 N ALA A 89 SHEET 3 B 3 GLY A 135 GLN A 144 -1 O ALA A 137 N ALA A 130 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 TRP A 210 N VAL A 170 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 224 O THR A 245 SHEET 4 E 4 ILE A 188 ASN A 193 -1 N LYS A 189 O ALA A 225 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 257 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 ALA A 325 N TYR A 298 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 VAL A 357 N HIS A 336 LINK SG CYS A 354 CAT 3V5 A 502 1555 1555 1.66 CISPEP 1 MET A 157 PRO A 158 0 1.17 CISPEP 2 ASN A 193 PRO A 194 0 2.25 SITE 1 AC1 7 LEU A 62 THR A 63 ALA A 64 SER A 65 SITE 2 AC1 7 THR A 67 SER A 80 ARG A 139 SITE 1 AC2 8 MET A 303 SER A 331 GLY A 332 PHE A 334 SITE 2 AC2 8 HIS A 336 HIS A 352 GLY A 353 CYS A 354 CRYST1 57.272 65.881 207.456 90.00 90.00 90.00 C 2 2 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 0.017461 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015179 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004820 0.00000