HEADER OXIDOREDUCTASE 14-AUG-01 1J49 TITLE INSIGHTS INTO DOMAIN CLOSURE, SUBSTRATE SPECIFICITY AND CATALYSIS OF TITLE 2 D-LACTATE DEHYDROGENASE FROM LACTOBACILLUS BULGARICUS COMPND MOL_ID: 1; COMPND 2 MOLECULE: D-LACTATE DEHYDROGENASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: D-LDH; COMPND 5 EC: 1.1.1.28; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: LACTOBACILLUS DELBRUECKII SUBSP. BULGARICUS; SOURCE 3 ORGANISM_TAXID: 1585; SOURCE 4 STRAIN: N42; SOURCE 5 CELLULAR_LOCATION: CYTOPLASM; SOURCE 6 GENE: LDHA; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: SURE; SOURCE 10 EXPRESSION_SYSTEM_CELLULAR_LOCATION: CYTOPLASM; SOURCE 11 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 12 EXPRESSION_SYSTEM_PLASMID: PKBULDH; SOURCE 13 EXPRESSION_SYSTEM_GENE: LDHA; SOURCE 14 OTHER_DETAILS: NESTLE CULTURE COLLECTION. PCR AMPLIFIED LDHA GENE KEYWDS NAD-DEPENDENT DEHYDROGENASE, LAST STEP OF GLYCOLYSIS UNDER ANAEROBIC KEYWDS 2 CONDITIONS, REVERSIBLE INTERCONVERSION OF PYRUVATE INTO D-LACTATE, KEYWDS 3 OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR A.RAZETO,S.KOCHHAR,H.HOTTINGER,M.DAUTER,K.S.WILSON,V.S.LAMZIN REVDAT 4 16-AUG-23 1J49 1 REMARK REVDAT 3 24-FEB-09 1J49 1 VERSN REVDAT 2 09-OCT-02 1J49 1 REMARK CRYST1 SCALE1 SCALE2 REVDAT 2 2 1 SCALE3 MASTER REVDAT 1 29-MAY-02 1J49 0 JRNL AUTH A.RAZETO,S.KOCHHAR,H.HOTTINGER,M.DAUTER,K.S.WILSON, JRNL AUTH 2 V.S.LAMZIN JRNL TITL DOMAIN CLOSURE, SUBSTRATE SPECIFICITY AND CATALYSIS OF JRNL TITL 2 D-LACTATE DEHYDROGENASE FROM LACTOBACILLUS BULGARICUS. JRNL REF J.MOL.BIOL. V. 318 109 2002 JRNL REFN ISSN 0022-2836 JRNL PMID 12054772 JRNL DOI 10.1016/S0022-2836(02)00086-4 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 15.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 3 NUMBER OF REFLECTIONS : 37544 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT (EXCEPT FOR THE REMARK 3 LAST 2 REFINEMENT CYCLES) REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.209 REMARK 3 R VALUE (WORKING SET) : 0.207 REMARK 3 FREE R VALUE : 0.271 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1884 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5205 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 93 REMARK 3 SOLVENT ATOMS : 279 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 36.10 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 44.40 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): 0.270 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.240 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.110 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.350 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : 0.015 ; 0.015 REMARK 3 ANGLE DISTANCE (A) : 0.025 ; 0.020 REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : 0.033 ; 0.030 REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : 0.026 ; 0.030 REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : 0.030 ; 0.050 REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : 0.200 ; 0.200 REMARK 3 MULTIPLE TORSION (A) : 0.300 ; 0.300 REMARK 3 H-BOND (X...Y) (A) : 0.230 ; 1.000 REMARK 3 H-BOND (X-H...Y) (A) : 0.230 ; 1.000 REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : 0.000 ; 15.000 REMARK 3 PLANAR (DEGREES) : 4.300 ; 7.000 REMARK 3 STAGGERED (DEGREES) : 18.800; 15.000 REMARK 3 TRANSVERSE (DEGREES) : 35.600; 20.000 REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 0.800 ; 1.000 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.500 ; 1.500 REMARK 3 SIDE-CHAIN BOND (A**2) : 0.800 ; 1.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 1.400 ; 1.500 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1J49 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-SEP-01. REMARK 100 THE DEPOSITION ID IS D_1000001593. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-DEC-94 REMARK 200 TEMPERATURE (KELVIN) : 298 REMARK 200 PH : 5.0 REMARK 200 NUMBER OF CRYSTALS USED : 2 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : EMBL/DESY, HAMBURG REMARK 200 BEAMLINE : X11 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.916 REMARK 200 MONOCHROMATOR : SILICON CRYSTAL REMARK 200 OPTICS : MIRRORS 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 : 38147 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 15.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 200 DATA REDUNDANCY : 5.800 REMARK 200 R MERGE (I) : 0.07100 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 19.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.24 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.3 REMARK 200 DATA REDUNDANCY IN SHELL : 6.82 REMARK 200 R MERGE FOR SHELL (I) : 0.21000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.730 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 2DLD REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.45 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 5.0 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 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+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 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 114.25000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 39.70000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 39.70000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 171.37500 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 39.70000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 39.70000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 57.12500 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 39.70000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 39.70000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 171.37500 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 39.70000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 39.70000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 57.12500 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 114.25000 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 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 REMARK 350 TOTAL BURIED SURFACE AREA: 8250 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 25340 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -59.0 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 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 GLY A 333 REMARK 465 GLY B 333 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ASN A 69 CG OD1 ND2 REMARK 470 LYS A 331 CG CD CE NZ REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 GLU A 39 CD OE1 OE2 REMARK 480 GLN A 55 CD OE1 NE2 REMARK 480 ASP A 122 CG OD1 OD2 REMARK 480 GLN A 163 CD OE1 NE2 REMARK 480 THR A 174 OG1 CG2 REMARK 480 GLU A 220 CG CD OE1 OE2 REMARK 480 ARG A 236 NE CZ NH1 NH2 REMARK 480 GLU A 277 CD OE1 OE2 REMARK 480 LYS A 312 CE NZ REMARK 480 LYS A 324 CE NZ REMARK 480 GLU A 325 CD OE1 OE2 REMARK 480 LYS B 14 NZ REMARK 480 GLU B 61 CD OE1 OE2 REMARK 480 ASP B 122 CG OD1 OD2 REMARK 480 GLN B 163 CD OE1 NE2 REMARK 480 THR B 174 OG1 CG2 REMARK 480 LYS B 198 CD CE NZ REMARK 480 GLU B 220 CD OE1 OE2 REMARK 480 LYS B 224 NZ REMARK 480 ILE B 254 CD1 REMARK 480 GLU B 277 CD OE1 OE2 REMARK 480 GLU B 325 CD OE1 OE2 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 B 122 O HOH B 370 1.23 REMARK 500 OD1 ASP B 122 O HOH B 385 1.37 REMARK 500 CE LYS B 3 O HOH B 481 1.54 REMARK 500 CG ASP B 122 O HOH B 370 1.83 REMARK 500 OD1 ASP A 122 O HOH A 353 1.83 REMARK 500 OE1 GLU B 28 O HOH B 481 2.07 REMARK 500 CE MET A 309 O HOH A 395 2.12 REMARK 500 OG1 THR B 139 O HOH B 449 2.16 REMARK 500 OD1 ASP A 48 O HOH A 460 2.17 REMARK 500 OE2 GLU A 19 NH2 ARG A 307 2.17 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 CB MET A 1 O GLY A 169 7546 2.11 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 THR A 174 CB THR A 174 OG1 0.135 REMARK 500 ARG A 236 CD ARG A 236 NE -0.112 REMARK 500 GLU A 277 CG GLU A 277 CD -0.135 REMARK 500 LYS B 14 CE LYS B 14 NZ -0.167 REMARK 500 GLU B 61 CG GLU B 61 CD -0.170 REMARK 500 ASP B 122 CB ASP B 122 CG 0.230 REMARK 500 THR B 174 CB THR B 174 OG1 -0.130 REMARK 500 GLU B 220 CG GLU B 220 CD -0.181 REMARK 500 GLU B 277 CG GLU B 277 CD -0.159 REMARK 500 GLU B 325 CG GLU B 325 CD -0.113 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 77 NE - CZ - NH1 ANGL. DEV. = -3.1 DEGREES REMARK 500 ARG A 135 NE - CZ - NH1 ANGL. DEV. = -4.1 DEGREES REMARK 500 ARG A 135 NE - CZ - NH2 ANGL. DEV. = 3.8 DEGREES REMARK 500 ARG A 142 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 ASP A 209 CB - CG - OD1 ANGL. DEV. = -5.7 DEGREES REMARK 500 ARG A 236 CG - CD - NE ANGL. DEV. = 13.2 DEGREES REMARK 500 ARG A 236 CD - NE - CZ ANGL. DEV. = 12.6 DEGREES REMARK 500 ASP A 280 CB - CG - OD2 ANGL. DEV. = 7.0 DEGREES REMARK 500 ARG A 289 NE - CZ - NH2 ANGL. DEV. = -3.5 DEGREES REMARK 500 ARG B 77 NE - CZ - NH1 ANGL. DEV. = -4.0 DEGREES REMARK 500 ARG B 120 NE - CZ - NH2 ANGL. DEV. = -5.4 DEGREES REMARK 500 ASP B 133 CB - CG - OD1 ANGL. DEV. = 5.5 DEGREES REMARK 500 ARG B 135 NE - CZ - NH1 ANGL. DEV. = -8.1 DEGREES REMARK 500 ARG B 135 NE - CZ - NH2 ANGL. DEV. = 6.4 DEGREES REMARK 500 ARG B 145 NE - CZ - NH2 ANGL. DEV. = -3.5 DEGREES REMARK 500 GLU B 263 OE1 - CD - OE2 ANGL. DEV. = 9.8 DEGREES REMARK 500 GLU B 274 CA - CB - CG ANGL. DEV. = 16.9 DEGREES REMARK 500 ARG B 307 CD - NE - CZ ANGL. DEV. = -11.4 DEGREES REMARK 500 ARG B 307 NE - CZ - NH1 ANGL. DEV. = -3.4 DEGREES REMARK 500 GLU B 325 CG - CD - OE1 ANGL. DEV. = 12.9 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 THR A 2 70.73 70.15 REMARK 500 HIS A 24 54.99 -147.71 REMARK 500 PRO A 38 -19.77 -49.08 REMARK 500 TYR A 53 107.82 -165.86 REMARK 500 GLN A 54 148.77 -175.59 REMARK 500 ASP A 57 154.26 -37.69 REMARK 500 ASN A 78 -164.58 -123.17 REMARK 500 ASP A 85 92.34 -54.18 REMARK 500 SER A 103 97.02 -169.26 REMARK 500 HIS A 132 33.15 74.36 REMARK 500 THR A 139 61.97 -68.70 REMARK 500 ASP A 209 37.98 -71.64 REMARK 500 SER A 235 -80.66 -88.66 REMARK 500 ASN A 270 31.64 71.07 REMARK 500 LYS A 331 108.98 -57.77 REMARK 500 THR B 2 98.16 -50.07 REMARK 500 HIS B 24 57.63 -146.44 REMARK 500 LYS B 45 122.18 -29.39 REMARK 500 TYR B 53 112.08 -164.80 REMARK 500 ASP B 68 27.45 -58.72 REMARK 500 ASN B 69 7.01 -154.84 REMARK 500 SER B 103 83.27 179.21 REMARK 500 HIS B 132 20.65 84.02 REMARK 500 THR B 154 46.03 -106.77 REMARK 500 SER B 235 -73.58 -90.38 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 THR B 2 11.11 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 341 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NAD A 350 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NAD B 360 REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE AUTHORS MAINTAIN THAT THEIR SEQUENCE IS REMARK 999 CORRECT. THE DENSITY FOR THESE RESIDUES SUGGESTS REMARK 999 ILE59, ARG117, AND VAL152 INSTEAD OF THOSE IN REMARK 999 THE DATABASE REFERENCE MATCH. DBREF 1J49 A 1 333 UNP P26297 LDHD_LACDE 1 333 DBREF 1J49 B 1 333 UNP P26297 LDHD_LACDE 1 333 SEQADV 1J49 ILE A 59 UNP P26297 THR 59 SEE REMARK 999 SEQADV 1J49 ARG A 117 UNP P26297 ALA 117 SEE REMARK 999 SEQADV 1J49 VAL A 152 UNP P26297 ILE 152 SEE REMARK 999 SEQADV 1J49 ILE B 59 UNP P26297 THR 59 SEE REMARK 999 SEQADV 1J49 ARG B 117 UNP P26297 ALA 117 SEE REMARK 999 SEQADV 1J49 VAL B 152 UNP P26297 ILE 152 SEE REMARK 999 SEQRES 1 A 333 MET THR LYS ILE PHE ALA TYR ALA ILE ARG GLU ASP GLU SEQRES 2 A 333 LYS PRO PHE LEU LYS GLU TRP GLU ASP ALA HIS LYS ASP SEQRES 3 A 333 VAL GLU VAL GLU TYR THR ASP LYS LEU LEU THR PRO GLU SEQRES 4 A 333 THR VAL ALA LEU ALA LYS GLY ALA ASP GLY VAL VAL VAL SEQRES 5 A 333 TYR GLN GLN LEU ASP TYR ILE ALA GLU THR LEU GLN ALA SEQRES 6 A 333 LEU ALA ASP ASN GLY ILE THR LYS MET SER LEU ARG ASN SEQRES 7 A 333 VAL GLY VAL ASP ASN ILE ASP MET ALA LYS ALA LYS GLU SEQRES 8 A 333 LEU GLY PHE GLN ILE THR ASN VAL PRO VAL TYR SER PRO SEQRES 9 A 333 ASN ALA ILE ALA GLU HIS ALA ALA ILE GLN ALA ALA ARG SEQRES 10 A 333 ILE LEU ARG GLN ASP LYS ALA MET ASP GLU LYS VAL ALA SEQRES 11 A 333 ARG HIS ASP LEU ARG TRP ALA PRO THR ILE GLY ARG GLU SEQRES 12 A 333 VAL ARG ASP GLN VAL VAL GLY VAL VAL GLY THR GLY HIS SEQRES 13 A 333 ILE GLY GLN VAL PHE MET GLN ILE MET GLU GLY PHE GLY SEQRES 14 A 333 ALA LYS VAL ILE THR TYR ASP ILE PHE ARG ASN PRO GLU SEQRES 15 A 333 LEU GLU LYS LYS GLY TYR TYR VAL ASP SER LEU ASP ASP SEQRES 16 A 333 LEU TYR LYS GLN ALA ASP VAL ILE SER LEU HIS VAL PRO SEQRES 17 A 333 ASP VAL PRO ALA ASN VAL HIS MET ILE ASN ASP GLU SER SEQRES 18 A 333 ILE ALA LYS MET LYS GLN ASP VAL VAL ILE VAL ASN VAL SEQRES 19 A 333 SER ARG GLY PRO LEU VAL ASP THR ASP ALA VAL ILE ARG SEQRES 20 A 333 GLY LEU ASP SER GLY LYS ILE PHE GLY TYR ALA MET ASP SEQRES 21 A 333 VAL TYR GLU GLY GLU VAL GLY ILE PHE ASN GLU ASP TRP SEQRES 22 A 333 GLU GLY LYS GLU PHE PRO ASP ALA ARG LEU ALA ASP LEU SEQRES 23 A 333 ILE ALA ARG PRO ASN VAL LEU VAL THR PRO HIS THR ALA SEQRES 24 A 333 PHE TYR THR THR HIS ALA VAL ARG ASN MET VAL VAL LYS SEQRES 25 A 333 ALA PHE ASP ASN ASN LEU GLU LEU VAL GLU GLY LYS GLU SEQRES 26 A 333 ALA GLU THR PRO VAL LYS VAL GLY SEQRES 1 B 333 MET THR LYS ILE PHE ALA TYR ALA ILE ARG GLU ASP GLU SEQRES 2 B 333 LYS PRO PHE LEU LYS GLU TRP GLU ASP ALA HIS LYS ASP SEQRES 3 B 333 VAL GLU VAL GLU TYR THR ASP LYS LEU LEU THR PRO GLU SEQRES 4 B 333 THR VAL ALA LEU ALA LYS GLY ALA ASP GLY VAL VAL VAL SEQRES 5 B 333 TYR GLN GLN LEU ASP TYR ILE ALA GLU THR LEU GLN ALA SEQRES 6 B 333 LEU ALA ASP ASN GLY ILE THR LYS MET SER LEU ARG ASN SEQRES 7 B 333 VAL GLY VAL ASP ASN ILE ASP MET ALA LYS ALA LYS GLU SEQRES 8 B 333 LEU GLY PHE GLN ILE THR ASN VAL PRO VAL TYR SER PRO SEQRES 9 B 333 ASN ALA ILE ALA GLU HIS ALA ALA ILE GLN ALA ALA ARG SEQRES 10 B 333 ILE LEU ARG GLN ASP LYS ALA MET ASP GLU LYS VAL ALA SEQRES 11 B 333 ARG HIS ASP LEU ARG TRP ALA PRO THR ILE GLY ARG GLU SEQRES 12 B 333 VAL ARG ASP GLN VAL VAL GLY VAL VAL GLY THR GLY HIS SEQRES 13 B 333 ILE GLY GLN VAL PHE MET GLN ILE MET GLU GLY PHE GLY SEQRES 14 B 333 ALA LYS VAL ILE THR TYR ASP ILE PHE ARG ASN PRO GLU SEQRES 15 B 333 LEU GLU LYS LYS GLY TYR TYR VAL ASP SER LEU ASP ASP SEQRES 16 B 333 LEU TYR LYS GLN ALA ASP VAL ILE SER LEU HIS VAL PRO SEQRES 17 B 333 ASP VAL PRO ALA ASN VAL HIS MET ILE ASN ASP GLU SER SEQRES 18 B 333 ILE ALA LYS MET LYS GLN ASP VAL VAL ILE VAL ASN VAL SEQRES 19 B 333 SER ARG GLY PRO LEU VAL ASP THR ASP ALA VAL ILE ARG SEQRES 20 B 333 GLY LEU ASP SER GLY LYS ILE PHE GLY TYR ALA MET ASP SEQRES 21 B 333 VAL TYR GLU GLY GLU VAL GLY ILE PHE ASN GLU ASP TRP SEQRES 22 B 333 GLU GLY LYS GLU PHE PRO ASP ALA ARG LEU ALA ASP LEU SEQRES 23 B 333 ILE ALA ARG PRO ASN VAL LEU VAL THR PRO HIS THR ALA SEQRES 24 B 333 PHE TYR THR THR HIS ALA VAL ARG ASN MET VAL VAL LYS SEQRES 25 B 333 ALA PHE ASP ASN ASN LEU GLU LEU VAL GLU GLY LYS GLU SEQRES 26 B 333 ALA GLU THR PRO VAL LYS VAL GLY HET NAD A 350 44 HET SO4 B 341 5 HET NAD B 360 44 HETNAM NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE HETNAM SO4 SULFATE ION FORMUL 3 NAD 2(C21 H27 N7 O14 P2) FORMUL 4 SO4 O4 S 2- FORMUL 6 HOH *279(H2 O) HELIX 1 1 ARG A 10 ASP A 12 5 3 HELIX 2 2 GLU A 13 ALA A 23 1 11 HELIX 3 3 THR A 40 LYS A 45 5 6 HELIX 4 4 ILE A 59 ASP A 68 1 10 HELIX 5 5 ASP A 85 GLY A 93 1 9 HELIX 6 6 SER A 103 ARG A 120 1 18 HELIX 7 7 GLN A 121 ARG A 131 1 11 HELIX 8 8 GLU A 143 ASP A 146 5 4 HELIX 9 9 GLY A 155 PHE A 168 1 14 HELIX 10 10 ASN A 180 GLY A 187 1 8 HELIX 11 11 SER A 192 ALA A 200 1 9 HELIX 12 12 ASN A 218 MET A 225 1 8 HELIX 13 13 ARG A 236 VAL A 240 5 5 HELIX 14 14 ASP A 241 SER A 251 1 11 HELIX 15 15 ASP A 280 ARG A 289 1 10 HELIX 16 16 THR A 302 GLU A 322 1 21 HELIX 17 17 ARG B 10 ASP B 12 5 3 HELIX 18 18 GLU B 13 ASP B 22 1 10 HELIX 19 19 THR B 37 ALA B 42 1 6 HELIX 20 20 LEU B 43 LYS B 45 5 3 HELIX 21 21 ILE B 59 ASP B 68 1 10 HELIX 22 22 ASP B 85 LEU B 92 1 8 HELIX 23 23 SER B 103 GLN B 121 1 19 HELIX 24 24 GLN B 121 ARG B 131 1 11 HELIX 25 25 GLU B 143 ASP B 146 5 4 HELIX 26 26 GLY B 155 PHE B 168 1 14 HELIX 27 27 ASN B 180 GLY B 187 1 8 HELIX 28 28 SER B 192 ALA B 200 1 9 HELIX 29 29 VAL B 210 VAL B 214 5 5 HELIX 30 30 ASN B 218 LYS B 224 1 7 HELIX 31 31 ARG B 236 VAL B 240 5 5 HELIX 32 32 ASP B 241 SER B 251 1 11 HELIX 33 33 ASP B 280 ARG B 289 1 10 HELIX 34 34 THR B 302 GLU B 322 1 21 SHEET 1 A 5 GLU A 28 TYR A 31 0 SHEET 2 A 5 LYS A 3 ALA A 6 1 N ILE A 4 O GLU A 30 SHEET 3 A 5 GLY A 49 VAL A 52 1 O GLY A 49 N PHE A 5 SHEET 4 A 5 LYS A 73 LEU A 76 1 O SER A 75 N VAL A 52 SHEET 5 A 5 GLN A 95 THR A 97 1 O THR A 97 N MET A 74 SHEET 1 B 6 LYS A 171 TYR A 175 0 SHEET 2 B 6 VAL A 148 VAL A 152 1 N VAL A 149 O LYS A 171 SHEET 3 B 6 VAL A 202 LEU A 205 1 O VAL A 202 N GLY A 150 SHEET 4 B 6 VAL A 229 ASN A 233 1 O VAL A 232 N ILE A 203 SHEET 5 B 6 ILE A 254 MET A 259 1 O PHE A 255 N VAL A 229 SHEET 6 B 6 VAL A 292 VAL A 294 1 O LEU A 293 N MET A 259 SHEET 1 C 5 GLU B 28 TYR B 31 0 SHEET 2 C 5 LYS B 3 ALA B 6 1 N ALA B 6 O GLU B 30 SHEET 3 C 5 GLY B 49 VAL B 52 1 O VAL B 51 N PHE B 5 SHEET 4 C 5 LYS B 73 LEU B 76 1 O SER B 75 N VAL B 52 SHEET 5 C 5 GLN B 95 THR B 97 1 O GLN B 95 N MET B 74 SHEET 1 D 6 LYS B 171 TYR B 175 0 SHEET 2 D 6 VAL B 148 VAL B 152 1 N VAL B 149 O LYS B 171 SHEET 3 D 6 VAL B 202 LEU B 205 1 O VAL B 202 N GLY B 150 SHEET 4 D 6 VAL B 229 ASN B 233 1 O VAL B 232 N ILE B 203 SHEET 5 D 6 ILE B 254 MET B 259 1 O ALA B 258 N ASN B 233 SHEET 6 D 6 VAL B 292 VAL B 294 1 O LEU B 293 N MET B 259 CISPEP 1 ALA A 137 PRO A 138 0 -0.66 CISPEP 2 ALA B 137 PRO B 138 0 -0.45 SITE 1 AC1 8 ASN B 78 VAL B 79 GLY B 80 TYR B 102 SITE 2 AC1 8 ARG B 236 HIS B 297 NAD B 360 HOH B 422 SITE 1 AC2 26 TYR A 102 ILE A 107 GLY A 153 GLY A 155 SITE 2 AC2 26 HIS A 156 ILE A 157 TYR A 175 ASP A 176 SITE 3 AC2 26 ILE A 177 HIS A 206 VAL A 207 PRO A 208 SITE 4 AC2 26 ASN A 213 VAL A 234 SER A 235 ARG A 236 SITE 5 AC2 26 ASP A 260 HIS A 297 ALA A 299 PHE A 300 SITE 6 AC2 26 HOH A 390 HOH A 428 HOH A 463 HOH A 470 SITE 7 AC2 26 HOH A 485 HOH A 487 SITE 1 AC3 26 TYR B 102 ILE B 107 GLY B 155 HIS B 156 SITE 2 AC3 26 ILE B 157 TYR B 175 ASP B 176 ILE B 177 SITE 3 AC3 26 HIS B 206 VAL B 207 PRO B 208 ASN B 213 SITE 4 AC3 26 VAL B 234 SER B 235 ARG B 236 ASP B 260 SITE 5 AC3 26 HIS B 297 ALA B 299 PHE B 300 SO4 B 341 SITE 6 AC3 26 HOH B 376 HOH B 379 HOH B 382 HOH B 386 SITE 7 AC3 26 HOH B 395 HOH B 453 CRYST1 79.400 79.400 228.500 90.00 90.00 90.00 P 43 21 2 16 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.012594 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012594 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004376 0.00000 MTRIX1 1 -0.310730 -0.062030 0.948470 -1.19188 1 MTRIX2 1 0.096710 -0.994750 -0.033370 54.58400 1 MTRIX3 1 0.945570 0.081360 0.315100 -0.08465 1