HEADER OXIDOREDUCTASE 26-NOV-07 2VHZ TITLE CRYSTAL STRUCTURE OF HOLO L-ALANINE DEHYDROGENASE FROM TITLE 2 MYCOBACTERIUM TUBERCULOSIS IN THE CLOSED CONFORMATION COMPND MOL_ID: 1; COMPND 2 MOLECULE: ALANINE DEHYDROGENASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: 40 KDA ANTIGEN, TB43; COMPND 5 EC: 1.4.1.1; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTERIUM TUBERCULOSIS; SOURCE 3 ORGANISM_TAXID: 1773; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PET26 KEYWDS NAD, SECRETED, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR D.AGREN,G.SCHNEIDER REVDAT 3 24-FEB-09 2VHZ 1 VERSN REVDAT 2 11-NOV-08 2VHZ 1 COMPND SOURCE JRNL REMARK REVDAT 2 2 HET HETNAM FORMUL HETATM REVDAT 2 3 MASTER REVDAT 1 11-MAR-08 2VHZ 0 JRNL AUTH D.AGREN,M.STEHR,C.L.BERTHOLD,S.KAPOOR,W.OEHLMANN, JRNL AUTH 2 M.SINGH,G.SCHNEIDER JRNL TITL THREE-DIMENSIONAL STRUCTURES OF APO- AND HOLO-L- JRNL TITL 2 ALANINE DEHYDROGENASE FROM MYCOBACTERIUM JRNL TITL 3 TUBERCULOSIS REVEAL CONFORMATIONAL CHANGES UPON JRNL TITL 4 COENZYME BINDING. JRNL REF J.MOL.BIOL. V. 377 1161 2008 JRNL REFN ISSN 0022-2836 JRNL PMID 18304579 JRNL DOI 10.1016/J.JMB.2008.01.091 REMARK 2 REMARK 2 RESOLUTION. 2.04 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.04 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 56464 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) : 0.166 REMARK 3 R VALUE (WORKING SET) : 0.164 REMARK 3 FREE R VALUE : 0.204 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2984 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) : 2.04 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.09 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4138 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.00 REMARK 3 BIN R VALUE (WORKING SET) : 0.2100 REMARK 3 BIN FREE R VALUE SET COUNT : 219 REMARK 3 BIN FREE R VALUE : 0.2460 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5452 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 88 REMARK 3 SOLVENT ATOMS : 497 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 40.07 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.147 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.138 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.096 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.565 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.964 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.949 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5656 ; 0.013 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7726 ; 1.464 ; 1.987 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 744 ; 5.716 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 212 ;33.610 ;23.396 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 853 ;14.615 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 39 ;16.152 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 912 ; 0.099 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4251 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 2783 ; 0.200 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 3842 ; 0.302 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 412 ; 0.144 ; 0.200 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): 51 ; 0.118 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 26 ; 0.162 ; 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): 3786 ; 0.747 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 5872 ; 1.166 ; 2.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2117 ; 2.139 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1852 ; 3.263 ; 4.500 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 : NULL 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 REMARK 3 RIDING POSITIONS REMARK 4 REMARK 4 2VHZ COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 26-NOV-07. REMARK 100 THE PDBE ID CODE IS EBI-34543. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-MAR-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID23-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9792 REMARK 200 MONOCHROMATOR : SINGLE CRYSTAL REMARK 200 OPTICS : SINGLE SILICON REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 359770 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.04 REMARK 200 RESOLUTION RANGE LOW (A) : 47.70 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.8 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 6.0 REMARK 200 R MERGE (I) : 0.10 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.10 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.04 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.15 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.2 REMARK 200 R MERGE FOR SHELL (I) : 0.58 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.80 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.11 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.76 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 3 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 5555 Z,X,Y REMARK 290 6555 Z+1/2,-X+1/2,-Y REMARK 290 7555 -Z+1/2,-X,Y+1/2 REMARK 290 8555 -Z,X+1/2,-Y+1/2 REMARK 290 9555 Y,Z,X REMARK 290 10555 -Y,Z+1/2,-X+1/2 REMARK 290 11555 Y+1/2,-Z+1/2,-X REMARK 290 12555 -Y+1/2,-Z,X+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 70.49550 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 70.49550 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 70.49550 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 70.49550 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 70.49550 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 70.49550 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY2 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY1 6 0.000000 0.000000 1.000000 70.49550 REMARK 290 SMTRY2 6 -1.000000 0.000000 0.000000 70.49550 REMARK 290 SMTRY3 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 0.000000 -1.000000 70.49550 REMARK 290 SMTRY2 7 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 1.000000 0.000000 70.49550 REMARK 290 SMTRY1 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY2 8 1.000000 0.000000 0.000000 70.49550 REMARK 290 SMTRY3 8 0.000000 -1.000000 0.000000 70.49550 REMARK 290 SMTRY1 9 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 9 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY3 9 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 10 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 10 0.000000 0.000000 1.000000 70.49550 REMARK 290 SMTRY3 10 -1.000000 0.000000 0.000000 70.49550 REMARK 290 SMTRY1 11 0.000000 1.000000 0.000000 70.49550 REMARK 290 SMTRY2 11 0.000000 0.000000 -1.000000 70.49550 REMARK 290 SMTRY3 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 12 0.000000 -1.000000 0.000000 70.49550 REMARK 290 SMTRY2 12 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY3 12 1.000000 0.000000 0.000000 70.49550 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 GENERATING THE BIOMOLECULE 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: HEXAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: HEXAMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 TOTAL BURIED SURFACE AREA: 20680 ANGSTROM**2 REMARK 350 TOTAL SURFACE AREA FOR THE COMPLEX: 85420 ANGSTROM**2 REMARK 350 GAIN IN SOLVENT FREE ENERGY: -104 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 350 BIOMT1 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT2 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT1 3 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT3 3 1.000000 0.000000 0.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 HOH B2151 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 HIS A 372 REMARK 465 HIS A 373 REMARK 465 HIS A 374 REMARK 465 HIS A 375 REMARK 465 HIS A 376 REMARK 465 HIS A 377 REMARK 465 HIS B 372 REMARK 465 HIS B 373 REMARK 465 HIS B 374 REMARK 465 HIS B 375 REMARK 465 HIS B 376 REMARK 465 HIS B 377 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 B 205 CG - CD - NE ANGL. DEV. = -13.2 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 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 HIS A 291 -125.51 48.99 REMARK 500 SER A 344 -51.17 -120.85 REMARK 500 HIS A 346 117.36 -163.31 REMARK 500 ALA B 238 36.68 -140.13 REMARK 500 HIS B 291 -124.39 47.20 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CHIRAL CENTERS REMARK 500 REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY REMARK 500 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,A1,6X,F5.1,6X,A1,10X,A1,3X,A16) REMARK 500 REMARK 500 M RES CSSEQI IMPROPER EXPECTED FOUND DETAILS REMARK 500 VAL B 290 24.9 L L OUTSIDE RANGE 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 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NAI A1372 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NAI B1372 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2VHV RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE D270A MUTANT OF REMARK 900 L-ALANINE DEHYDROGENASE FROM MYCOBACTERIUM REMARK 900 TUBERCULOSIS IN COMPLEX WITH NADH. REMARK 900 RELATED ID: 2VHW RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HOLO L-ALANINE DEHYDROGENASE REMARK 900 FROM MYCOBACTERIUM TUBERCULOSIS IN THE OPEN AND REMARK 900 CLOSED CONFORMATION REMARK 900 RELATED ID: 2VHX RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE TERNARY COMPLEX OF REMARK 900 L-ALANINE DEHYDROGENASE FROM MYCOBACTERIUM REMARK 900 TUBERCULOSIS WITH NAD+ AND PYRUVATE REMARK 900 RELATED ID: 2VHY RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF APO L-ALANINE DEHYDROGENASE REMARK 900 FROM MYCOBACTERIUM TUBERCULOSIS REMARK 999 REMARK 999 SEQUENCE REMARK 999 EXPRESSED WITH A C-TERMINAL 6XHIS TAG. DBREF 2VHZ A 1 371 UNP P30234 DHA_MYCTU 1 371 DBREF 2VHZ A 372 377 PDB 2VHZ 2VHZ 372 377 DBREF 2VHZ B 1 371 UNP P30234 DHA_MYCTU 1 371 DBREF 2VHZ B 372 377 PDB 2VHZ 2VHZ 372 377 SEQRES 1 A 377 MET ARG VAL GLY ILE PRO THR GLU THR LYS ASN ASN GLU SEQRES 2 A 377 PHE ARG VAL ALA ILE THR PRO ALA GLY VAL ALA GLU LEU SEQRES 3 A 377 THR ARG ARG GLY HIS GLU VAL LEU ILE GLN ALA GLY ALA SEQRES 4 A 377 GLY GLU GLY SER ALA ILE THR ASP ALA ASP PHE LYS ALA SEQRES 5 A 377 ALA GLY ALA GLN LEU VAL GLY THR ALA ASP GLN VAL TRP SEQRES 6 A 377 ALA ASP ALA ASP LEU LEU LEU LYS VAL LYS GLU PRO ILE SEQRES 7 A 377 ALA ALA GLU TYR GLY ARG LEU ARG HIS GLY GLN ILE LEU SEQRES 8 A 377 PHE THR PHE LEU HIS LEU ALA ALA SER ARG ALA CYS THR SEQRES 9 A 377 ASP ALA LEU LEU ASP SER GLY THR THR SER ILE ALA TYR SEQRES 10 A 377 GLU THR VAL GLN THR ALA ASP GLY ALA LEU PRO LEU LEU SEQRES 11 A 377 ALA PRO MET SER GLU VAL ALA GLY ARG LEU ALA ALA GLN SEQRES 12 A 377 VAL GLY ALA TYR HIS LEU MET ARG THR GLN GLY GLY ARG SEQRES 13 A 377 GLY VAL LEU MET GLY GLY VAL PRO GLY VAL GLU PRO ALA SEQRES 14 A 377 ASP VAL VAL VAL ILE GLY ALA GLY THR ALA GLY TYR ASN SEQRES 15 A 377 ALA ALA ARG ILE ALA ASN GLY MET GLY ALA THR VAL THR SEQRES 16 A 377 VAL LEU ASP ILE ASN ILE ASP LYS LEU ARG GLN LEU ASP SEQRES 17 A 377 ALA GLU PHE CYS GLY ARG ILE HIS THR ARG TYR SER SER SEQRES 18 A 377 ALA TYR GLU LEU GLU GLY ALA VAL LYS ARG ALA ASP LEU SEQRES 19 A 377 VAL ILE GLY ALA VAL LEU VAL PRO GLY ALA LYS ALA PRO SEQRES 20 A 377 LYS LEU VAL SER ASN SER LEU VAL ALA HIS MET LYS PRO SEQRES 21 A 377 GLY ALA VAL LEU VAL ASP ILE ALA ILE ASP GLN GLY GLY SEQRES 22 A 377 CYS PHE GLU GLY SER ARG PRO THR THR TYR ASP HIS PRO SEQRES 23 A 377 THR PHE ALA VAL HIS ASP THR LEU PHE TYR CYS VAL ALA SEQRES 24 A 377 ASN MET PRO ALA SER VAL PRO LYS THR SER THR TYR ALA SEQRES 25 A 377 LEU THR ASN ALA THR MET PRO TYR VAL LEU GLU LEU ALA SEQRES 26 A 377 ASP HIS GLY TRP ARG ALA ALA CYS ARG SER ASN PRO ALA SEQRES 27 A 377 LEU ALA LYS GLY LEU SER THR HIS GLU GLY ALA LEU LEU SEQRES 28 A 377 SER GLU ARG VAL ALA THR ASP LEU GLY VAL PRO PHE THR SEQRES 29 A 377 GLU PRO ALA SER VAL LEU ALA HIS HIS HIS HIS HIS HIS SEQRES 1 B 377 MET ARG VAL GLY ILE PRO THR GLU THR LYS ASN ASN GLU SEQRES 2 B 377 PHE ARG VAL ALA ILE THR PRO ALA GLY VAL ALA GLU LEU SEQRES 3 B 377 THR ARG ARG GLY HIS GLU VAL LEU ILE GLN ALA GLY ALA SEQRES 4 B 377 GLY GLU GLY SER ALA ILE THR ASP ALA ASP PHE LYS ALA SEQRES 5 B 377 ALA GLY ALA GLN LEU VAL GLY THR ALA ASP GLN VAL TRP SEQRES 6 B 377 ALA ASP ALA ASP LEU LEU LEU LYS VAL LYS GLU PRO ILE SEQRES 7 B 377 ALA ALA GLU TYR GLY ARG LEU ARG HIS GLY GLN ILE LEU SEQRES 8 B 377 PHE THR PHE LEU HIS LEU ALA ALA SER ARG ALA CYS THR SEQRES 9 B 377 ASP ALA LEU LEU ASP SER GLY THR THR SER ILE ALA TYR SEQRES 10 B 377 GLU THR VAL GLN THR ALA ASP GLY ALA LEU PRO LEU LEU SEQRES 11 B 377 ALA PRO MET SER GLU VAL ALA GLY ARG LEU ALA ALA GLN SEQRES 12 B 377 VAL GLY ALA TYR HIS LEU MET ARG THR GLN GLY GLY ARG SEQRES 13 B 377 GLY VAL LEU MET GLY GLY VAL PRO GLY VAL GLU PRO ALA SEQRES 14 B 377 ASP VAL VAL VAL ILE GLY ALA GLY THR ALA GLY TYR ASN SEQRES 15 B 377 ALA ALA ARG ILE ALA ASN GLY MET GLY ALA THR VAL THR SEQRES 16 B 377 VAL LEU ASP ILE ASN ILE ASP LYS LEU ARG GLN LEU ASP SEQRES 17 B 377 ALA GLU PHE CYS GLY ARG ILE HIS THR ARG TYR SER SER SEQRES 18 B 377 ALA TYR GLU LEU GLU GLY ALA VAL LYS ARG ALA ASP LEU SEQRES 19 B 377 VAL ILE GLY ALA VAL LEU VAL PRO GLY ALA LYS ALA PRO SEQRES 20 B 377 LYS LEU VAL SER ASN SER LEU VAL ALA HIS MET LYS PRO SEQRES 21 B 377 GLY ALA VAL LEU VAL ASP ILE ALA ILE ASP GLN GLY GLY SEQRES 22 B 377 CYS PHE GLU GLY SER ARG PRO THR THR TYR ASP HIS PRO SEQRES 23 B 377 THR PHE ALA VAL HIS ASP THR LEU PHE TYR CYS VAL ALA SEQRES 24 B 377 ASN MET PRO ALA SER VAL PRO LYS THR SER THR TYR ALA SEQRES 25 B 377 LEU THR ASN ALA THR MET PRO TYR VAL LEU GLU LEU ALA SEQRES 26 B 377 ASP HIS GLY TRP ARG ALA ALA CYS ARG SER ASN PRO ALA SEQRES 27 B 377 LEU ALA LYS GLY LEU SER THR HIS GLU GLY ALA LEU LEU SEQRES 28 B 377 SER GLU ARG VAL ALA THR ASP LEU GLY VAL PRO PHE THR SEQRES 29 B 377 GLU PRO ALA SER VAL LEU ALA HIS HIS HIS HIS HIS HIS HET NAI A1372 44 HET NAI B1372 44 HETNAM NAI 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE FORMUL 3 NAI 2(C21 H29 N7 O14 P2) FORMUL 4 HOH *497(H2 O1) HELIX 1 1 THR A 19 ARG A 29 1 11 HELIX 2 2 GLY A 40 ALA A 44 5 5 HELIX 3 3 THR A 46 GLY A 54 1 9 HELIX 4 4 THR A 60 ALA A 68 1 9 HELIX 5 5 ILE A 78 LEU A 85 5 8 HELIX 6 6 HIS A 96 ALA A 99 5 4 HELIX 7 7 SER A 100 GLY A 111 1 12 HELIX 8 8 GLU A 118 VAL A 120 5 3 HELIX 9 9 LEU A 130 LEU A 149 1 20 HELIX 10 10 MET A 150 GLY A 154 5 5 HELIX 11 11 GLY A 177 MET A 190 1 14 HELIX 12 12 ASN A 200 PHE A 211 1 12 HELIX 13 13 SER A 221 ALA A 232 1 12 HELIX 14 14 SER A 251 HIS A 257 1 7 HELIX 15 15 ALA A 268 GLY A 272 5 5 HELIX 16 16 ASN A 300 SER A 304 5 5 HELIX 17 17 VAL A 305 LYS A 341 1 37 HELIX 18 18 SER A 352 GLY A 360 1 9 HELIX 19 19 GLU A 365 ALA A 371 1 7 HELIX 20 20 THR B 19 ARG B 29 1 11 HELIX 21 21 GLY B 40 ALA B 44 5 5 HELIX 22 22 THR B 46 GLY B 54 1 9 HELIX 23 23 THR B 60 ALA B 68 1 9 HELIX 24 24 ILE B 78 TYR B 82 5 5 HELIX 25 25 HIS B 96 ALA B 99 5 4 HELIX 26 26 SER B 100 GLY B 111 1 12 HELIX 27 27 GLU B 118 VAL B 120 5 3 HELIX 28 28 LEU B 130 LEU B 149 1 20 HELIX 29 29 MET B 150 GLY B 154 5 5 HELIX 30 30 GLY B 177 MET B 190 1 14 HELIX 31 31 ASN B 200 PHE B 211 1 12 HELIX 32 32 SER B 221 ALA B 232 1 12 HELIX 33 33 SER B 251 HIS B 257 1 7 HELIX 34 34 ALA B 268 GLY B 272 5 5 HELIX 35 35 ASN B 300 SER B 304 5 5 HELIX 36 36 VAL B 305 LYS B 341 1 37 HELIX 37 37 SER B 352 GLY B 360 1 9 HELIX 38 38 GLU B 365 ALA B 371 1 7 SHEET 1 AA 8 GLN A 56 VAL A 58 0 SHEET 2 AA 8 GLU A 32 GLN A 36 1 O VAL A 33 N GLN A 56 SHEET 3 AA 8 ARG A 2 ILE A 5 1 O VAL A 3 N LEU A 34 SHEET 4 AA 8 LEU A 70 LEU A 72 1 O LEU A 70 N GLY A 4 SHEET 5 AA 8 ILE A 90 THR A 93 1 O ILE A 90 N LEU A 71 SHEET 6 AA 8 THR A 113 ALA A 116 1 O THR A 113 N LEU A 91 SHEET 7 AA 8 LEU A 343 HIS A 346 -1 N SER A 344 O SER A 114 SHEET 8 AA 8 ALA A 349 LEU A 350 -1 O ALA A 349 N HIS A 346 SHEET 1 AB 7 HIS A 216 TYR A 219 0 SHEET 2 AB 7 THR A 193 ASP A 198 1 O VAL A 194 N HIS A 216 SHEET 3 AB 7 ASP A 170 ILE A 174 1 O VAL A 171 N THR A 195 SHEET 4 AB 7 LEU A 234 GLY A 237 1 O LEU A 234 N VAL A 172 SHEET 5 AB 7 VAL A 263 ASP A 266 1 O VAL A 263 N VAL A 235 SHEET 6 AB 7 THR A 293 TYR A 296 1 O LEU A 294 N LEU A 264 SHEET 7 AB 7 THR A 287 VAL A 290 -1 O PHE A 288 N PHE A 295 SHEET 1 BA 8 GLN B 56 VAL B 58 0 SHEET 2 BA 8 GLU B 32 GLN B 36 1 O VAL B 33 N GLN B 56 SHEET 3 BA 8 ARG B 2 ILE B 5 1 O VAL B 3 N LEU B 34 SHEET 4 BA 8 LEU B 70 LEU B 72 1 O LEU B 70 N GLY B 4 SHEET 5 BA 8 ILE B 90 THR B 93 1 O ILE B 90 N LEU B 71 SHEET 6 BA 8 THR B 113 ALA B 116 1 O THR B 113 N LEU B 91 SHEET 7 BA 8 LEU B 343 HIS B 346 -1 N SER B 344 O SER B 114 SHEET 8 BA 8 ALA B 349 LEU B 350 -1 O ALA B 349 N HIS B 346 SHEET 1 BB 7 HIS B 216 TYR B 219 0 SHEET 2 BB 7 THR B 193 ASP B 198 1 O VAL B 194 N HIS B 216 SHEET 3 BB 7 ASP B 170 ILE B 174 1 O VAL B 171 N THR B 195 SHEET 4 BB 7 LEU B 234 GLY B 237 1 O LEU B 234 N VAL B 172 SHEET 5 BB 7 VAL B 263 ASP B 266 1 O VAL B 263 N VAL B 235 SHEET 6 BB 7 THR B 293 TYR B 296 1 O LEU B 294 N LEU B 264 SHEET 7 BB 7 THR B 287 VAL B 290 -1 O PHE B 288 N PHE B 295 SITE 1 AC1 32 MET A 133 SER A 134 ALA A 137 GLY A 177 SITE 2 AC1 32 THR A 178 ALA A 179 ASP A 198 LYS A 203 SITE 3 AC1 32 ALA A 238 VAL A 239 LEU A 240 LEU A 249 SITE 4 AC1 32 ILE A 267 ASP A 270 GLN A 271 VAL A 298 SITE 5 AC1 32 ALA A 299 ASN A 300 MET A 301 PRO A 302 SITE 6 AC1 32 HOH A2166 HOH A2232 HOH A2233 HOH A2234 SITE 7 AC1 32 HOH A2235 HOH A2236 HOH A2237 HOH A2238 SITE 8 AC1 32 HOH A2239 HOH A2240 HOH A2241 HOH A2242 SITE 1 AC2 33 MET B 133 SER B 134 ALA B 137 GLY B 177 SITE 2 AC2 33 THR B 178 ALA B 179 ASP B 198 ILE B 199 SITE 3 AC2 33 LYS B 203 ALA B 238 VAL B 239 LEU B 240 SITE 4 AC2 33 LEU B 249 ILE B 267 ASP B 270 GLN B 271 SITE 5 AC2 33 VAL B 298 ALA B 299 ASN B 300 MET B 301 SITE 6 AC2 33 PRO B 302 HOH B2178 HOH B2190 HOH B2246 SITE 7 AC2 33 HOH B2247 HOH B2248 HOH B2249 HOH B2250 SITE 8 AC2 33 HOH B2251 HOH B2252 HOH B2253 HOH B2254 SITE 9 AC2 33 HOH B2255 CRYST1 140.991 140.991 140.991 90.00 90.00 90.00 P 21 3 24 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 0.007093 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007093 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007093 0.00000 MTRIX1 1 0.000300 -1.000000 0.000200 35.22580 1 MTRIX2 1 -1.000000 -0.000300 0.000100 35.24880 1 MTRIX3 1 -0.000100 -0.000200 -1.000000 35.24830 1