HEADER OXIDOREDUCTASE 14-MAY-08 3D4P TITLE CRYSTAL STRUCTURE OF LACTATE DEHYDROGENASE FROM STAPHYLOCOCCUS AUREUS TITLE 2 COMPLEXED WITH NAD AND PYRUVATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: L-LACTATE DEHYDROGENASE 1; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: L-LDH 1; COMPND 5 EC: 1.1.1.27; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STAPHYLOCOCCUS AUREUS SUBSP. AUREUS COL; SOURCE 3 ORGANISM_TAXID: 93062; SOURCE 4 GENE: LDH1, SACOL0222; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS LACTATE DEHYDROGENASE, STAPHYLOCOCCUS AUREUS, NAD, PYRUVATE, KEYWDS 2 CYTOPLASM, GLYCOLYSIS, OXIDOREDUCTASE, PHOSPHOPROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR V.L.SCHRAMM,S.C.ALMO,J.A.GUTIERREZ,M.HO REVDAT 3 15-NOV-23 3D4P 1 REMARK ATOM REVDAT 2 25-OCT-17 3D4P 1 REMARK REVDAT 1 02-JUN-09 3D4P 0 JRNL AUTH V.L.SCHRAMM,S.C.ALMO,J.A.GUTIERREZ,M.HO JRNL TITL CRYSTAL STRUCTURE OF LACTATE DEHYDROGENASE FROM JRNL TITL 2 STAPHYLOCOCCUS AUREUS COMPLEXED WITH NAD AND PYRUVATE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.4.0069 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 3 NUMBER OF REFLECTIONS : 66322 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) : 0.164 REMARK 3 R VALUE (WORKING SET) : 0.163 REMARK 3 FREE R VALUE : 0.188 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 3361 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.84 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4138 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 87.14 REMARK 3 BIN R VALUE (WORKING SET) : 0.1930 REMARK 3 BIN FREE R VALUE SET COUNT : 200 REMARK 3 BIN FREE R VALUE : 0.2260 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4730 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 100 REMARK 3 SOLVENT ATOMS : 305 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 14.77 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.17000 REMARK 3 B22 (A**2) : 0.21000 REMARK 3 B33 (A**2) : -1.10000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.84000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.105 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.099 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.058 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.796 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.955 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.943 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5001 ; 0.016 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6816 ; 1.480 ; 1.989 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 640 ; 5.115 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 216 ;39.657 ;24.769 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 851 ;13.541 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 29 ;16.404 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 796 ; 0.115 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3735 ; 0.006 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL 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): 3101 ; 0.838 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 5019 ; 1.547 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1900 ; 2.674 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1785 ; 4.477 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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: NULL REMARK 4 REMARK 4 3D4P COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-MAY-08. REMARK 100 THE DEPOSITION ID IS D_1000047588. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-MAY-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X29A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0809 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 66324 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 200 DATA REDUNDANCY : 4.000 REMARK 200 R MERGE (I) : 0.09700 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 7.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.86 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.7 REMARK 200 DATA REDUNDANCY IN SHELL : 2.90 REMARK 200 R MERGE FOR SHELL (I) : 0.24900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.43 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.64 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 35% 2-METHYL-2,4-PENTANEDIOL, 0.1M REMARK 280 ACETATE PH 4.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291K 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 65.43400 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 37.45800 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 65.43400 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 37.45800 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, 3 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 21640 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 40650 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -77.0 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 70.66267 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 74.61328 REMARK 350 REMARK 350 BIOMOLECULE: 2 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: 7490 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 23650 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -30.0 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 70.66267 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 74.61328 REMARK 350 REMARK 350 BIOMOLECULE: 3 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: 7540 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 23610 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -31.0 KCAL/MOL 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 70.66267 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 74.61328 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A 1 REMARK 465 ASN A 2 REMARK 465 LYS A 3 REMARK 465 GLY A 89 REMARK 465 GLU A 90 REMARK 465 ALA A 313 REMARK 465 GLU A 314 REMARK 465 GLU A 315 REMARK 465 LEU A 316 REMARK 465 LYS A 317 REMARK 465 MET B 1 REMARK 465 ASN B 2 REMARK 465 LYS B 3 REMARK 465 GLU B 314 REMARK 465 GLU B 315 REMARK 465 LEU B 316 REMARK 465 LYS B 317 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 HIS A 189 CA CB CG ND1 CD2 CE1 NE2 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 143 NE - CZ - NH1 ANGL. DEV. = -3.4 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 LYS A 114 9.28 89.76 REMARK 500 ASP A 116 49.20 -144.65 REMARK 500 TYR A 233 -31.82 -155.79 REMARK 500 ASP B 116 50.99 -146.15 REMARK 500 TYR B 233 -31.40 -155.28 REMARK 500 ASN B 250 55.87 39.16 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 NAD A 318 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PYR A 319 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NAD B 318 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PYR B 319 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3D0O RELATED DB: PDB REMARK 900 THE SAME PROTEIN COMPLEXED WITH NAD AND PYRUVATE DBREF 3D4P A 1 317 UNP Q5HJD7 LDH1_STAAC 1 317 DBREF 3D4P B 1 317 UNP Q5HJD7 LDH1_STAAC 1 317 SEQRES 1 A 317 MET ASN LYS PHE LYS GLY ASN LYS VAL VAL LEU ILE GLY SEQRES 2 A 317 ASN GLY ALA VAL GLY SER SER TYR ALA PHE SER LEU VAL SEQRES 3 A 317 ASN GLN SER ILE VAL ASP GLU LEU VAL ILE ILE ASP LEU SEQRES 4 A 317 ASP THR GLU LYS VAL ARG GLY ASP VAL MET ASP LEU LYS SEQRES 5 A 317 HIS ALA THR PRO TYR SER PRO THR THR VAL ARG VAL LYS SEQRES 6 A 317 ALA GLY GLU TYR SER ASP CYS HIS ASP ALA ASP LEU VAL SEQRES 7 A 317 VAL ILE CYS ALA GLY ALA ALA GLN LYS PRO GLY GLU THR SEQRES 8 A 317 ARG LEU ASP LEU VAL SER LYS ASN LEU LYS ILE PHE LYS SEQRES 9 A 317 SER ILE VAL GLY GLU VAL MET ALA SER LYS PHE ASP GLY SEQRES 10 A 317 ILE PHE LEU VAL ALA THR ASN PRO VAL ASP ILE LEU ALA SEQRES 11 A 317 TYR ALA THR TRP LYS PHE SER GLY LEU PRO LYS GLU ARG SEQRES 12 A 317 VAL ILE GLY SER GLY THR ILE LEU ASP SER ALA ARG PHE SEQRES 13 A 317 ARG LEU LEU LEU SER GLU ALA PHE ASP VAL ALA PRO ARG SEQRES 14 A 317 SER VAL ASP ALA GLN ILE ILE GLY GLU HIS GLY ASP THR SEQRES 15 A 317 GLU LEU PRO VAL TRP SER HIS ALA ASN ILE ALA GLY GLN SEQRES 16 A 317 PRO LEU LYS THR LEU LEU GLU GLN ARG PRO GLU GLY LYS SEQRES 17 A 317 ALA GLN ILE GLU GLN ILE PHE VAL GLN THR ARG ASP ALA SEQRES 18 A 317 ALA TYR ASP ILE ILE GLN ALA LYS GLY ALA THR TYR TYR SEQRES 19 A 317 GLY VAL ALA MET GLY LEU ALA ARG ILE THR GLU ALA ILE SEQRES 20 A 317 PHE ARG ASN GLU ASP ALA VAL LEU THR VAL SER ALA LEU SEQRES 21 A 317 LEU GLU GLY GLU TYR GLU GLU GLU ASP VAL TYR ILE GLY SEQRES 22 A 317 VAL PRO ALA VAL ILE ASN ARG ASN GLY ILE ARG ASN VAL SEQRES 23 A 317 VAL GLU ILE PRO LEU ASN ASP GLU GLU GLN SER LYS PHE SEQRES 24 A 317 ALA HIS SER ALA LYS THR LEU LYS ASP ILE MET ALA GLU SEQRES 25 A 317 ALA GLU GLU LEU LYS SEQRES 1 B 317 MET ASN LYS PHE LYS GLY ASN LYS VAL VAL LEU ILE GLY SEQRES 2 B 317 ASN GLY ALA VAL GLY SER SER TYR ALA PHE SER LEU VAL SEQRES 3 B 317 ASN GLN SER ILE VAL ASP GLU LEU VAL ILE ILE ASP LEU SEQRES 4 B 317 ASP THR GLU LYS VAL ARG GLY ASP VAL MET ASP LEU LYS SEQRES 5 B 317 HIS ALA THR PRO TYR SER PRO THR THR VAL ARG VAL LYS SEQRES 6 B 317 ALA GLY GLU TYR SER ASP CYS HIS ASP ALA ASP LEU VAL SEQRES 7 B 317 VAL ILE CYS ALA GLY ALA ALA GLN LYS PRO GLY GLU THR SEQRES 8 B 317 ARG LEU ASP LEU VAL SER LYS ASN LEU LYS ILE PHE LYS SEQRES 9 B 317 SER ILE VAL GLY GLU VAL MET ALA SER LYS PHE ASP GLY SEQRES 10 B 317 ILE PHE LEU VAL ALA THR ASN PRO VAL ASP ILE LEU ALA SEQRES 11 B 317 TYR ALA THR TRP LYS PHE SER GLY LEU PRO LYS GLU ARG SEQRES 12 B 317 VAL ILE GLY SER GLY THR ILE LEU ASP SER ALA ARG PHE SEQRES 13 B 317 ARG LEU LEU LEU SER GLU ALA PHE ASP VAL ALA PRO ARG SEQRES 14 B 317 SER VAL ASP ALA GLN ILE ILE GLY GLU HIS GLY ASP THR SEQRES 15 B 317 GLU LEU PRO VAL TRP SER HIS ALA ASN ILE ALA GLY GLN SEQRES 16 B 317 PRO LEU LYS THR LEU LEU GLU GLN ARG PRO GLU GLY LYS SEQRES 17 B 317 ALA GLN ILE GLU GLN ILE PHE VAL GLN THR ARG ASP ALA SEQRES 18 B 317 ALA TYR ASP ILE ILE GLN ALA LYS GLY ALA THR TYR TYR SEQRES 19 B 317 GLY VAL ALA MET GLY LEU ALA ARG ILE THR GLU ALA ILE SEQRES 20 B 317 PHE ARG ASN GLU ASP ALA VAL LEU THR VAL SER ALA LEU SEQRES 21 B 317 LEU GLU GLY GLU TYR GLU GLU GLU ASP VAL TYR ILE GLY SEQRES 22 B 317 VAL PRO ALA VAL ILE ASN ARG ASN GLY ILE ARG ASN VAL SEQRES 23 B 317 VAL GLU ILE PRO LEU ASN ASP GLU GLU GLN SER LYS PHE SEQRES 24 B 317 ALA HIS SER ALA LYS THR LEU LYS ASP ILE MET ALA GLU SEQRES 25 B 317 ALA GLU GLU LEU LYS HET NAD A 318 44 HET PYR A 319 6 HET NAD B 318 44 HET PYR B 319 6 HETNAM NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE HETNAM PYR PYRUVIC ACID FORMUL 3 NAD 2(C21 H27 N7 O14 P2) FORMUL 4 PYR 2(C3 H4 O3) FORMUL 7 HOH *305(H2 O) HELIX 1 1 GLY A 15 SER A 29 1 15 HELIX 2 2 ASP A 40 THR A 55 1 16 HELIX 3 3 PRO A 56 SER A 58 5 3 HELIX 4 4 GLU A 68 HIS A 73 5 6 HELIX 5 5 THR A 91 SER A 113 1 23 HELIX 6 6 PRO A 125 GLY A 138 1 14 HELIX 7 7 PRO A 140 GLU A 142 5 3 HELIX 8 8 THR A 149 ASP A 165 1 17 HELIX 9 9 ALA A 167 VAL A 171 5 5 HELIX 10 10 LEU A 197 GLN A 203 1 7 HELIX 11 11 GLU A 206 ASP A 220 1 15 HELIX 12 12 ASP A 220 GLY A 230 1 11 HELIX 13 13 TYR A 233 ARG A 249 1 17 HELIX 14 14 GLU A 264 GLU A 266 5 3 HELIX 15 15 ASN A 292 GLU A 312 1 21 HELIX 16 16 GLY B 15 SER B 29 1 15 HELIX 17 17 ASP B 40 THR B 55 1 16 HELIX 18 18 PRO B 56 SER B 58 5 3 HELIX 19 19 GLU B 68 HIS B 73 5 6 HELIX 20 20 THR B 91 SER B 113 1 23 HELIX 21 21 PRO B 125 GLY B 138 1 14 HELIX 22 22 PRO B 140 GLU B 142 5 3 HELIX 23 23 THR B 149 ASP B 165 1 17 HELIX 24 24 ALA B 167 VAL B 171 5 5 HELIX 25 25 LEU B 197 ARG B 204 1 8 HELIX 26 26 GLU B 206 ASP B 220 1 15 HELIX 27 27 ASP B 220 GLY B 230 1 11 HELIX 28 28 TYR B 233 ARG B 249 1 17 HELIX 29 29 GLU B 264 GLU B 266 5 3 HELIX 30 30 ASN B 292 ALA B 313 1 22 SHEET 1 A 6 ARG A 63 ALA A 66 0 SHEET 2 A 6 GLU A 33 ILE A 37 1 N LEU A 34 O ARG A 63 SHEET 3 A 6 LYS A 8 ILE A 12 1 N LEU A 11 O VAL A 35 SHEET 4 A 6 LEU A 77 ILE A 80 1 O VAL A 79 N ILE A 12 SHEET 5 A 6 ILE A 118 VAL A 121 1 O LEU A 120 N VAL A 78 SHEET 6 A 6 VAL A 144 GLY A 146 1 O ILE A 145 N VAL A 121 SHEET 1 B 2 ILE A 175 ILE A 176 0 SHEET 2 B 2 LEU A 184 PRO A 185 -1 O LEU A 184 N ILE A 176 SHEET 1 C 2 ASN A 191 ILE A 192 0 SHEET 2 C 2 GLN A 195 PRO A 196 -1 O GLN A 195 N ILE A 192 SHEET 1 D 3 ALA A 253 GLU A 262 0 SHEET 2 D 3 GLU A 268 ASN A 279 -1 O ILE A 278 N ALA A 253 SHEET 3 D 3 GLY A 282 VAL A 286 -1 O ARG A 284 N VAL A 277 SHEET 1 E 6 ARG B 63 ALA B 66 0 SHEET 2 E 6 GLU B 33 ILE B 37 1 N LEU B 34 O ARG B 63 SHEET 3 E 6 LYS B 8 ILE B 12 1 N LEU B 11 O VAL B 35 SHEET 4 E 6 LEU B 77 ILE B 80 1 O VAL B 79 N ILE B 12 SHEET 5 E 6 ILE B 118 VAL B 121 1 O LEU B 120 N VAL B 78 SHEET 6 E 6 VAL B 144 GLY B 146 1 O ILE B 145 N VAL B 121 SHEET 1 F 2 ILE B 175 ILE B 176 0 SHEET 2 F 2 LEU B 184 PRO B 185 -1 O LEU B 184 N ILE B 176 SHEET 1 G 2 ASN B 191 ILE B 192 0 SHEET 2 G 2 GLN B 195 PRO B 196 -1 O GLN B 195 N ILE B 192 SHEET 1 H 3 ALA B 253 GLU B 262 0 SHEET 2 H 3 GLU B 268 ASN B 279 -1 O ILE B 278 N ALA B 253 SHEET 3 H 3 GLY B 282 VAL B 286 -1 O ARG B 284 N VAL B 277 CISPEP 1 ASN A 124 PRO A 125 0 -4.52 CISPEP 2 ASN B 124 PRO B 125 0 -2.45 SITE 1 AC1 15 GLY A 15 ALA A 16 ASP A 38 LEU A 39 SITE 2 AC1 15 CYS A 81 ALA A 82 GLY A 83 ALA A 84 SITE 3 AC1 15 ALA A 122 THR A 123 ASN A 124 SER A 147 SITE 4 AC1 15 LEU A 151 HIS A 179 THR A 232 SITE 1 AC2 6 ASN A 124 LEU A 151 ARG A 155 HIS A 179 SITE 2 AC2 6 ALA A 222 THR A 232 SITE 1 AC3 15 GLY B 15 ALA B 16 ASP B 38 LEU B 39 SITE 2 AC3 15 CYS B 81 ALA B 82 GLY B 83 ALA B 84 SITE 3 AC3 15 ALA B 122 THR B 123 ASN B 124 SER B 147 SITE 4 AC3 15 LEU B 151 HIS B 179 THR B 232 SITE 1 AC4 6 ASN B 124 LEU B 151 ARG B 155 HIS B 179 SITE 2 AC4 6 ALA B 222 THR B 232 CRYST1 130.868 74.916 95.874 90.00 128.90 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 0.007641 0.000000 0.006166 0.00000 SCALE2 0.000000 0.013348 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013402 0.00000