PDB Short entry for 2V6B HEADER OXIDOREDUCTASE 16-JUL-07 2V6B TITLE CRYSTAL STRUCTURE OF LACTATE DEHYDROGENASE FROM DEINOCOCCUS TITLE 2 RADIODURANS (APO FORM) COMPND MOL_ID: 1; COMPND 2 MOLECULE: L-LACTATE DEHYDROGENASE; COMPND 3 CHAIN: A, B, C, D; COMPND 4 SYNONYM: L-LDH; COMPND 5 EC: 1.1.1.27; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DEINOCOCCUS RADIODURANS; SOURCE 3 ORGANISM_TAXID: 1299; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI DH5[ALPHA]; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 668369; SOURCE 6 EXPRESSION_SYSTEM_PLASMID: PKDL302 KEYWDS OXIDOREDUCTASE, RADIORESISTANCE, LACTATE DEHYDROGENASE, LDH, NAD, KEYWDS 2 CYTOPLASM, MESOPHILIC, GLYCOLYSIS EXPDTA X-RAY DIFFRACTION AUTHOR N.COQUELLE,E.FIORAVANTI,M.WEIK,F.VELLIEUX REVDAT 5 13-DEC-23 2V6B 1 REMARK REVDAT 4 28-FEB-18 2V6B 1 SOURCE JRNL REVDAT 3 24-FEB-09 2V6B 1 VERSN REVDAT 2 13-NOV-07 2V6B 1 JRNL REVDAT 1 25-SEP-07 2V6B 0 JRNL AUTH N.COQUELLE,E.FIORAVANTI,M.WEIK,F.VELLIEUX,D.MADERN JRNL TITL ACTIVITY, STABILITY AND STRUCTURAL STUDIES OF LACTATE JRNL TITL 2 DEHYDROGENASES ADAPTED TO EXTREME THERMAL ENVIRONMENTS. JRNL REF J. MOL. BIOL. V. 374 547 2007 JRNL REFN ESSN 1089-8638 JRNL PMID 17936781 JRNL DOI 10.1016/J.JMB.2007.09.049 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.83 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 2727105.550 REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 40233 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 SET) : 0.230 REMARK 3 FREE R VALUE : 0.250 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2012 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.006 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.66 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.80 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 6186 REMARK 3 BIN R VALUE (WORKING SET) : 0.3020 REMARK 3 BIN FREE R VALUE : 0.3630 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.00 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 325 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.020 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 8218 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 121 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 41.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 51.00 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.35000 REMARK 3 B22 (A**2) : -5.45000 REMARK 3 B33 (A**2) : 3.10000 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 COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.33 REMARK 3 ESD FROM SIGMAA (A) : 0.35 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.38 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.43 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 1.100 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 22.10 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.890 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 2.030 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 3.320 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.970 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 4.340 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.28 REMARK 3 BSOL : 32.98 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_JPP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN_JPP.TOP REMARK 3 TOPOLOGY FILE 2 : WATER_REP.TOP REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2V6B COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 16-JUL-07. REMARK 100 THE DEPOSITION ID IS D_1290033201. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 9 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : BM14 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9790 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 40233 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 200 DATA REDUNDANCY : 4.350 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 17.0600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.55 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.6 REMARK 200 DATA REDUNDANCY IN SHELL : 4.28 REMARK 200 R MERGE FOR SHELL (I) : 0.46000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.120 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 1LDN REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.02 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.24 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M BICINE PH 9, 20% PEG 5K MME REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 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 61.67500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 63.96500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 61.67500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 63.96500 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 TOTAL BURIED SURFACE AREA: 9090 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 50210 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -65.3 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D 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 99 REMARK 465 ALA A 100 REMARK 465 ASN A 101 REMARK 465 GLN A 102 REMARK 465 LYS A 103 REMARK 465 PRO A 104 REMARK 465 GLY A 105 REMARK 465 GLU A 106 REMARK 465 SER A 107 REMARK 465 ARG A 108 REMARK 465 LEU A 109 REMARK 465 ASP A 110 REMARK 465 ALA A 235 REMARK 465 ALA A 236 REMARK 465 ALA A 237 REMARK 465 SER A 238 REMARK 465 ILE A 239 REMARK 465 ILE A 240 REMARK 465 GLU A 241 REMARK 465 GLY A 242 REMARK 465 LYS A 243 REMARK 465 ARG A 244 REMARK 465 ALA A 245 REMARK 465 PHE A 325 REMARK 465 LYS A 326 REMARK 465 GLN A 327 REMARK 465 GLN A 328 REMARK 465 LEU A 329 REMARK 465 GLY A 330 REMARK 465 LEU A 331 REMARK 465 ASN B 101 REMARK 465 GLN B 102 REMARK 465 LYS B 103 REMARK 465 PRO B 104 REMARK 465 GLY B 105 REMARK 465 ASN B 234 REMARK 465 ALA B 235 REMARK 465 ALA B 236 REMARK 465 ALA B 237 REMARK 465 SER B 238 REMARK 465 ILE B 239 REMARK 465 ILE B 240 REMARK 465 GLU B 241 REMARK 465 GLY B 242 REMARK 465 LYS B 243 REMARK 465 ARG B 244 REMARK 465 ALA B 245 REMARK 465 GLN B 327 REMARK 465 GLN B 328 REMARK 465 LEU B 329 REMARK 465 GLY B 330 REMARK 465 LEU B 331 REMARK 465 ALA C 100 REMARK 465 ASN C 101 REMARK 465 GLN C 102 REMARK 465 LYS C 103 REMARK 465 PRO C 104 REMARK 465 GLY C 105 REMARK 465 GLU C 106 REMARK 465 ALA C 235 REMARK 465 ALA C 236 REMARK 465 ALA C 237 REMARK 465 SER C 238 REMARK 465 ILE C 239 REMARK 465 ILE C 240 REMARK 465 GLU C 241 REMARK 465 GLY C 242 REMARK 465 LYS C 243 REMARK 465 ARG C 244 REMARK 465 ALA C 245 REMARK 465 GLN C 327 REMARK 465 GLN C 328 REMARK 465 LEU C 329 REMARK 465 GLY C 330 REMARK 465 LEU C 331 REMARK 465 ASN D 101 REMARK 465 GLN D 102 REMARK 465 LYS D 103 REMARK 465 PRO D 104 REMARK 465 GLY D 105 REMARK 465 GLU D 106 REMARK 465 SER D 107 REMARK 465 ASN D 234 REMARK 465 ALA D 235 REMARK 465 ALA D 236 REMARK 465 ALA D 237 REMARK 465 SER D 238 REMARK 465 ILE D 239 REMARK 465 ILE D 240 REMARK 465 GLU D 241 REMARK 465 GLY D 242 REMARK 465 LYS D 243 REMARK 465 ARG D 244 REMARK 465 ALA D 245 REMARK 465 LYS D 326 REMARK 465 GLN D 327 REMARK 465 GLN D 328 REMARK 465 LEU D 329 REMARK 465 GLY D 330 REMARK 465 LEU D 331 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 ARG A 54 CB CG CD NE CZ NH1 NH2 REMARK 470 LEU A 112 CB CG CD1 CD2 REMARK 470 GLU A 114 CB CG CD OE1 OE2 REMARK 470 ASP A 118 CB CG OD1 OD2 REMARK 470 ARG A 129 CB CG CD NE CZ NH1 NH2 REMARK 470 ARG A 256 CD NE CZ NH1 NH2 REMARK 470 LYS A 306 CB CG CD CE NZ REMARK 470 PHE B 31 CB CG CD1 CD2 CE1 CE2 CZ REMARK 470 ARG B 54 CB CG CD NE CZ NH1 NH2 REMARK 470 LYS B 306 CB CG CD CE NZ REMARK 470 LYS B 314 CB CG CD CE NZ REMARK 470 PHE C 31 CB CG CD1 CD2 CE1 CE2 CZ REMARK 470 ARG C 54 CB CG CD NE CZ NH1 NH2 REMARK 470 ARG C 58 CB CG CD NE CZ NH1 NH2 REMARK 470 ARG C 109 NE CZ NH1 NH2 REMARK 470 ARG C 256 CD NE CZ NH1 NH2 REMARK 470 LYS C 306 CB CG CD CE NZ REMARK 470 PHE D 31 CB CG CD1 CD2 CE1 CE2 CZ REMARK 470 ARG D 109 CG CD NE CZ NH1 NH2 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 OD1 ASP C 118 NH1 ARG C 121 2.00 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 NZ LYS A 115 OE2 GLU C 316 4455 2.13 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 PHE D 325 CA - C - O ANGL. DEV. = -25.1 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ALA A 67 -17.20 -45.91 REMARK 500 ALA A 69 4.08 -64.18 REMARK 500 HIS A 74 -98.74 -116.79 REMARK 500 GLU A 222 -30.99 -33.04 REMARK 500 TYR A 278 -13.84 -148.33 REMARK 500 VAL A 321 -7.62 -52.02 REMARK 500 ARG A 323 -16.67 -39.43 REMARK 500 HIS B 68 56.01 -67.35 REMARK 500 ALA B 69 -22.96 -150.05 REMARK 500 HIS B 74 80.07 -167.64 REMARK 500 ALA B 89 116.36 -32.88 REMARK 500 ASN B 221 -177.26 -173.01 REMARK 500 ASP B 264 57.20 27.96 REMARK 500 ARG B 266 55.43 39.54 REMARK 500 SER C 73 -3.56 -58.96 REMARK 500 HIS C 74 114.97 -171.51 REMARK 500 SER D 73 -79.17 -50.12 REMARK 500 ALA D 89 118.31 -36.60 REMARK 500 VAL D 321 -71.61 -39.25 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 ALA A 67 HIS A 68 -148.60 REMARK 500 SER A 73 HIS A 74 124.39 REMARK 500 REMARK 500 REMARK: NULL DBREF 2V6B A 22 331 UNP P50933 LDH_DEIRA 1 304 DBREF 2V6B B 22 331 UNP P50933 LDH_DEIRA 1 304 DBREF 2V6B C 22 331 UNP P50933 LDH_DEIRA 1 304 DBREF 2V6B D 22 331 UNP P50933 LDH_DEIRA 1 304 SEQRES 1 A 304 MET LYS VAL GLY VAL VAL GLY THR GLY PHE VAL GLY SER SEQRES 2 A 304 THR ALA ALA PHE ALA LEU VAL LEU ARG GLY SER CYS SER SEQRES 3 A 304 GLU LEU VAL LEU VAL ASP ARG ASP GLU ASP ARG ALA GLN SEQRES 4 A 304 ALA GLU ALA GLU ASP ILE ALA HIS ALA ALA PRO VAL SER SEQRES 5 A 304 HIS GLY THR ARG VAL TRP HIS GLY GLY HIS SER GLU LEU SEQRES 6 A 304 ALA ASP ALA GLN VAL VAL ILE LEU THR ALA GLY ALA ASN SEQRES 7 A 304 GLN LYS PRO GLY GLU SER ARG LEU ASP LEU LEU GLU LYS SEQRES 8 A 304 ASN ALA ASP ILE PHE ARG GLU LEU VAL PRO GLN ILE THR SEQRES 9 A 304 ARG ALA ALA PRO ASP ALA VAL LEU LEU VAL THR SER ASN SEQRES 10 A 304 PRO VAL ASP LEU LEU THR ASP LEU ALA THR GLN LEU ALA SEQRES 11 A 304 PRO GLY GLN PRO VAL ILE GLY SER GLY THR VAL LEU ASP SEQRES 12 A 304 SER ALA ARG PHE ARG HIS LEU MET ALA GLN HIS ALA GLY SEQRES 13 A 304 VAL ASP GLY THR HIS ALA HIS GLY TYR VAL LEU GLY GLU SEQRES 14 A 304 HIS GLY ASP SER GLU VAL LEU ALA TRP SER SER ALA MET SEQRES 15 A 304 VAL ALA GLY MET PRO VAL ALA ASP PHE MET GLN ALA GLN SEQRES 16 A 304 ASN LEU PRO TRP ASN GLU GLN VAL ARG ALA LYS ILE ASP SEQRES 17 A 304 GLU GLY THR ARG ASN ALA ALA ALA SER ILE ILE GLU GLY SEQRES 18 A 304 LYS ARG ALA THR TYR TYR GLY ILE GLY ALA ALA LEU ALA SEQRES 19 A 304 ARG ILE THR GLU ALA VAL LEU ARG ASP ARG ARG ALA VAL SEQRES 20 A 304 LEU THR VAL SER ALA PRO THR PRO GLU TYR GLY VAL SER SEQRES 21 A 304 LEU SER LEU PRO ARG VAL VAL GLY ARG GLN GLY VAL LEU SEQRES 22 A 304 SER THR LEU HIS PRO LYS LEU THR GLY ASP GLU GLN GLN SEQRES 23 A 304 LYS LEU GLU GLN SER ALA GLY VAL LEU ARG GLY PHE LYS SEQRES 24 A 304 GLN GLN LEU GLY LEU SEQRES 1 B 304 MET LYS VAL GLY VAL VAL GLY THR GLY PHE VAL GLY SER SEQRES 2 B 304 THR ALA ALA PHE ALA LEU VAL LEU ARG GLY SER CYS SER SEQRES 3 B 304 GLU LEU VAL LEU VAL ASP ARG ASP GLU ASP ARG ALA GLN SEQRES 4 B 304 ALA GLU ALA GLU ASP ILE ALA HIS ALA ALA PRO VAL SER SEQRES 5 B 304 HIS GLY THR ARG VAL TRP HIS GLY GLY HIS SER GLU LEU SEQRES 6 B 304 ALA ASP ALA GLN VAL VAL ILE LEU THR ALA GLY ALA ASN SEQRES 7 B 304 GLN LYS PRO GLY GLU SER ARG LEU ASP LEU LEU GLU LYS SEQRES 8 B 304 ASN ALA ASP ILE PHE ARG GLU LEU VAL PRO GLN ILE THR SEQRES 9 B 304 ARG ALA ALA PRO ASP ALA VAL LEU LEU VAL THR SER ASN SEQRES 10 B 304 PRO VAL ASP LEU LEU THR ASP LEU ALA THR GLN LEU ALA SEQRES 11 B 304 PRO GLY GLN PRO VAL ILE GLY SER GLY THR VAL LEU ASP SEQRES 12 B 304 SER ALA ARG PHE ARG HIS LEU MET ALA GLN HIS ALA GLY SEQRES 13 B 304 VAL ASP GLY THR HIS ALA HIS GLY TYR VAL LEU GLY GLU SEQRES 14 B 304 HIS GLY ASP SER GLU VAL LEU ALA TRP SER SER ALA MET SEQRES 15 B 304 VAL ALA GLY MET PRO VAL ALA ASP PHE MET GLN ALA GLN SEQRES 16 B 304 ASN LEU PRO TRP ASN GLU GLN VAL ARG ALA LYS ILE ASP SEQRES 17 B 304 GLU GLY THR ARG ASN ALA ALA ALA SER ILE ILE GLU GLY SEQRES 18 B 304 LYS ARG ALA THR TYR TYR GLY ILE GLY ALA ALA LEU ALA SEQRES 19 B 304 ARG ILE THR GLU ALA VAL LEU ARG ASP ARG ARG ALA VAL SEQRES 20 B 304 LEU THR VAL SER ALA PRO THR PRO GLU TYR GLY VAL SER SEQRES 21 B 304 LEU SER LEU PRO ARG VAL VAL GLY ARG GLN GLY VAL LEU SEQRES 22 B 304 SER THR LEU HIS PRO LYS LEU THR GLY ASP GLU GLN GLN SEQRES 23 B 304 LYS LEU GLU GLN SER ALA GLY VAL LEU ARG GLY PHE LYS SEQRES 24 B 304 GLN GLN LEU GLY LEU SEQRES 1 C 304 MET LYS VAL GLY VAL VAL GLY THR GLY PHE VAL GLY SER SEQRES 2 C 304 THR ALA ALA PHE ALA LEU VAL LEU ARG GLY SER CYS SER SEQRES 3 C 304 GLU LEU VAL LEU VAL ASP ARG ASP GLU ASP ARG ALA GLN SEQRES 4 C 304 ALA GLU ALA GLU ASP ILE ALA HIS ALA ALA PRO VAL SER SEQRES 5 C 304 HIS GLY THR ARG VAL TRP HIS GLY GLY HIS SER GLU LEU SEQRES 6 C 304 ALA ASP ALA GLN VAL VAL ILE LEU THR ALA GLY ALA ASN SEQRES 7 C 304 GLN LYS PRO GLY GLU SER ARG LEU ASP LEU LEU GLU LYS SEQRES 8 C 304 ASN ALA ASP ILE PHE ARG GLU LEU VAL PRO GLN ILE THR SEQRES 9 C 304 ARG ALA ALA PRO ASP ALA VAL LEU LEU VAL THR SER ASN SEQRES 10 C 304 PRO VAL ASP LEU LEU THR ASP LEU ALA THR GLN LEU ALA SEQRES 11 C 304 PRO GLY GLN PRO VAL ILE GLY SER GLY THR VAL LEU ASP SEQRES 12 C 304 SER ALA ARG PHE ARG HIS LEU MET ALA GLN HIS ALA GLY SEQRES 13 C 304 VAL ASP GLY THR HIS ALA HIS GLY TYR VAL LEU GLY GLU SEQRES 14 C 304 HIS GLY ASP SER GLU VAL LEU ALA TRP SER SER ALA MET SEQRES 15 C 304 VAL ALA GLY MET PRO VAL ALA ASP PHE MET GLN ALA GLN SEQRES 16 C 304 ASN LEU PRO TRP ASN GLU GLN VAL ARG ALA LYS ILE ASP SEQRES 17 C 304 GLU GLY THR ARG ASN ALA ALA ALA SER ILE ILE GLU GLY SEQRES 18 C 304 LYS ARG ALA THR TYR TYR GLY ILE GLY ALA ALA LEU ALA SEQRES 19 C 304 ARG ILE THR GLU ALA VAL LEU ARG ASP ARG ARG ALA VAL SEQRES 20 C 304 LEU THR VAL SER ALA PRO THR PRO GLU TYR GLY VAL SER SEQRES 21 C 304 LEU SER LEU PRO ARG VAL VAL GLY ARG GLN GLY VAL LEU SEQRES 22 C 304 SER THR LEU HIS PRO LYS LEU THR GLY ASP GLU GLN GLN SEQRES 23 C 304 LYS LEU GLU GLN SER ALA GLY VAL LEU ARG GLY PHE LYS SEQRES 24 C 304 GLN GLN LEU GLY LEU SEQRES 1 D 304 MET LYS VAL GLY VAL VAL GLY THR GLY PHE VAL GLY SER SEQRES 2 D 304 THR ALA ALA PHE ALA LEU VAL LEU ARG GLY SER CYS SER SEQRES 3 D 304 GLU LEU VAL LEU VAL ASP ARG ASP GLU ASP ARG ALA GLN SEQRES 4 D 304 ALA GLU ALA GLU ASP ILE ALA HIS ALA ALA PRO VAL SER SEQRES 5 D 304 HIS GLY THR ARG VAL TRP HIS GLY GLY HIS SER GLU LEU SEQRES 6 D 304 ALA ASP ALA GLN VAL VAL ILE LEU THR ALA GLY ALA ASN SEQRES 7 D 304 GLN LYS PRO GLY GLU SER ARG LEU ASP LEU LEU GLU LYS SEQRES 8 D 304 ASN ALA ASP ILE PHE ARG GLU LEU VAL PRO GLN ILE THR SEQRES 9 D 304 ARG ALA ALA PRO ASP ALA VAL LEU LEU VAL THR SER ASN SEQRES 10 D 304 PRO VAL ASP LEU LEU THR ASP LEU ALA THR GLN LEU ALA SEQRES 11 D 304 PRO GLY GLN PRO VAL ILE GLY SER GLY THR VAL LEU ASP SEQRES 12 D 304 SER ALA ARG PHE ARG HIS LEU MET ALA GLN HIS ALA GLY SEQRES 13 D 304 VAL ASP GLY THR HIS ALA HIS GLY TYR VAL LEU GLY GLU SEQRES 14 D 304 HIS GLY ASP SER GLU VAL LEU ALA TRP SER SER ALA MET SEQRES 15 D 304 VAL ALA GLY MET PRO VAL ALA ASP PHE MET GLN ALA GLN SEQRES 16 D 304 ASN LEU PRO TRP ASN GLU GLN VAL ARG ALA LYS ILE ASP SEQRES 17 D 304 GLU GLY THR ARG ASN ALA ALA ALA SER ILE ILE GLU GLY SEQRES 18 D 304 LYS ARG ALA THR TYR TYR GLY ILE GLY ALA ALA LEU ALA SEQRES 19 D 304 ARG ILE THR GLU ALA VAL LEU ARG ASP ARG ARG ALA VAL SEQRES 20 D 304 LEU THR VAL SER ALA PRO THR PRO GLU TYR GLY VAL SER SEQRES 21 D 304 LEU SER LEU PRO ARG VAL VAL GLY ARG GLN GLY VAL LEU SEQRES 22 D 304 SER THR LEU HIS PRO LYS LEU THR GLY ASP GLU GLN GLN SEQRES 23 D 304 LYS LEU GLU GLN SER ALA GLY VAL LEU ARG GLY PHE LYS SEQRES 24 D 304 GLN GLN LEU GLY LEU FORMUL 5 HOH *121(H2 O) HELIX 1 1 GLY A 30 ARG A 43 1 14 HELIX 2 2 ASP A 55 ALA A 67 1 13 HELIX 3 3 GLY A 84 ALA A 89 5 6 HELIX 4 4 LEU A 112 ALA A 131 1 20 HELIX 5 5 PRO A 141 ALA A 153 1 13 HELIX 6 6 THR A 165 GLY A 181 1 17 HELIX 7 7 ASP A 183 THR A 185 5 3 HELIX 8 8 TRP A 203 SER A 205 5 3 HELIX 9 9 VAL A 210A ASN A 217 1 9 HELIX 10 10 ASN A 221 ARG A 233 1 13 HELIX 11 11 TYR A 247 ARG A 263 1 17 HELIX 12 12 THR A 308 GLY A 324 1 17 HELIX 13 13 GLY B 30 GLY B 44 1 15 HELIX 14 14 ASP B 55 HIS B 68 1 14 HELIX 15 15 PRO B 71 GLY B 75 5 5 HELIX 16 16 GLY B 84 ALA B 89 5 6 HELIX 17 17 SER B 108 ALA B 131 1 24 HELIX 18 18 PRO B 141 ALA B 153 1 13 HELIX 19 19 THR B 165 GLY B 181 1 17 HELIX 20 20 ASP B 183 THR B 185 5 3 HELIX 21 21 TRP B 203 SER B 205 5 3 HELIX 22 22 VAL B 210A GLN B 216 1 8 HELIX 23 23 ASN B 221 ARG B 233 1 13 HELIX 24 24 TYR B 247 ARG B 263 1 17 HELIX 25 25 THR B 308 LYS B 326 1 19 HELIX 26 26 GLY C 30 ARG C 43 1 14 HELIX 27 27 ASP C 55 ALA C 67 1 13 HELIX 28 28 HIS C 68 ALA C 70 5 3 HELIX 29 29 GLY C 84 ALA C 89 5 6 HELIX 30 30 SER C 108 ALA C 131 1 24 HELIX 31 31 PRO C 141 ALA C 153 1 13 HELIX 32 32 THR C 165 GLY C 181 1 17 HELIX 33 33 ASP C 183 THR C 185 5 3 HELIX 34 34 TRP C 203 SER C 205 5 3 HELIX 35 35 VAL C 210A ASN C 217 1 9 HELIX 36 36 ASN C 221 ARG C 233 1 13 HELIX 37 37 TYR C 247 ARG C 263 1 17 HELIX 38 38 THR C 308 LYS C 326 1 19 HELIX 39 39 GLY D 30 ARG D 43 1 14 HELIX 40 40 ASP D 55 HIS D 68 1 14 HELIX 41 41 GLY D 84 ALA D 89 5 6 HELIX 42 42 ARG D 109 ALA D 131 1 23 HELIX 43 43 PRO D 141 ALA D 153 1 13 HELIX 44 44 THR D 165 GLY D 181 1 17 HELIX 45 45 ASP D 183 THR D 185 5 3 HELIX 46 46 TRP D 203 SER D 205 5 3 HELIX 47 47 VAL D 210A GLN D 216 1 8 HELIX 48 48 ASN D 221 ARG D 233 1 13 HELIX 49 49 TYR D 247 ASP D 264 1 18 HELIX 50 50 THR D 308 PHE D 325 1 18 SHEET 1 AA 6 ARG A 77 GLY A 83 0 SHEET 2 AA 6 GLU A 48 VAL A 52 1 O LEU A 49 N TRP A 79 SHEET 3 AA 6 LYS A 23 VAL A 27 1 O VAL A 24 N VAL A 50 SHEET 4 AA 6 VAL A 93 LEU A 96 1 O VAL A 93 N GLY A 25 SHEET 5 AA 6 VAL A 134 VAL A 137 1 O VAL A 134 N VAL A 94 SHEET 6 AA 6 VAL A 160 GLY A 162 1 O ILE A 161 N VAL A 137 SHEET 1 AB 3 ALA A 187 HIS A 188 0 SHEET 2 AB 3 MET A 207 VAL A 208 -1 O MET A 207 N HIS A 188 SHEET 3 AB 3 MET A 209C PRO A 209D-1 O MET A 209C N VAL A 208 SHEET 1 AC 2 VAL A 191 GLY A 193 0 SHEET 2 AC 2 GLU A 199 LEU A 201 -1 O VAL A 200 N LEU A 192 SHEET 1 AD 3 ALA A 267 PRO A 274 0 SHEET 2 AD 3 SER A 286 GLY A 294 -1 O LEU A 287 N ALA A 273 SHEET 3 AD 3 GLY A 297 THR A 302 -1 O GLY A 297 N GLY A 294 SHEET 1 BA 6 ARG B 77 HIS B 80 0 SHEET 2 BA 6 GLU B 48 VAL B 52 1 O LEU B 49 N TRP B 79 SHEET 3 BA 6 LYS B 23 VAL B 27 1 O VAL B 24 N VAL B 50 SHEET 4 BA 6 VAL B 93 LEU B 96 1 O VAL B 93 N GLY B 25 SHEET 5 BA 6 VAL B 134 VAL B 137 1 O VAL B 134 N VAL B 94 SHEET 6 BA 6 VAL B 160 GLY B 162 1 O ILE B 161 N VAL B 137 SHEET 1 BB 3 ALA B 187 HIS B 188 0 SHEET 2 BB 3 MET B 207 VAL B 208 -1 O MET B 207 N HIS B 188 SHEET 3 BB 3 MET B 209C PRO B 209D-1 O MET B 209C N VAL B 208 SHEET 1 BC 2 VAL B 191 LEU B 192 0 SHEET 2 BC 2 VAL B 200 LEU B 201 -1 O VAL B 200 N LEU B 192 SHEET 1 BD 3 ALA B 267 LEU B 269 0 SHEET 2 BD 3 ARG B 291 GLY B 294 -1 O ARG B 291 N LEU B 269 SHEET 3 BD 3 GLY B 297 THR B 302 -1 O GLY B 297 N GLY B 294 SHEET 1 BE 2 SER B 272 PRO B 274 0 SHEET 2 BE 2 SER B 286 SER B 288 -1 O LEU B 287 N ALA B 273 SHEET 1 CA 6 ARG C 77 GLY C 83 0 SHEET 2 CA 6 GLU C 48 VAL C 52 1 O LEU C 49 N TRP C 79 SHEET 3 CA 6 LYS C 23 VAL C 27 1 O VAL C 24 N VAL C 50 SHEET 4 CA 6 VAL C 93 LEU C 96 1 O VAL C 93 N GLY C 25 SHEET 5 CA 6 VAL C 134 VAL C 137 1 O VAL C 134 N VAL C 94 SHEET 6 CA 6 VAL C 160 GLY C 162 1 O ILE C 161 N VAL C 137 SHEET 1 CB 3 ALA C 187 HIS C 188 0 SHEET 2 CB 3 MET C 207 VAL C 208 -1 O MET C 207 N HIS C 188 SHEET 3 CB 3 MET C 209C PRO C 209D-1 O MET C 209C N VAL C 208 SHEET 1 CC 2 VAL C 191 LEU C 192 0 SHEET 2 CC 2 VAL C 200 LEU C 201 -1 O VAL C 200 N LEU C 192 SHEET 1 CD 3 ALA C 267 PRO C 274 0 SHEET 2 CD 3 SER C 286 GLY C 294 -1 O LEU C 287 N ALA C 273 SHEET 3 CD 3 GLY C 297 THR C 302 -1 O GLY C 297 N GLY C 294 SHEET 1 DA 6 ARG D 77 GLY D 83 0 SHEET 2 DA 6 GLU D 48 VAL D 52 1 O LEU D 49 N TRP D 79 SHEET 3 DA 6 LYS D 23 VAL D 27 1 O VAL D 24 N VAL D 50 SHEET 4 DA 6 VAL D 93 LEU D 96 1 O VAL D 93 N GLY D 25 SHEET 5 DA 6 VAL D 134 VAL D 137 1 O VAL D 134 N VAL D 94 SHEET 6 DA 6 VAL D 160 GLY D 162 1 O ILE D 161 N VAL D 137 SHEET 1 DB 3 ALA D 187 HIS D 188 0 SHEET 2 DB 3 MET D 207 VAL D 208 -1 O MET D 207 N HIS D 188 SHEET 3 DB 3 MET D 209C PRO D 209D-1 O MET D 209C N VAL D 208 SHEET 1 DC 2 VAL D 191 LEU D 192 0 SHEET 2 DC 2 VAL D 200 LEU D 201 -1 O VAL D 200 N LEU D 192 SHEET 1 DD 3 ALA D 267 LEU D 269 0 SHEET 2 DD 3 ARG D 291 GLY D 294 -1 O ARG D 291 N LEU D 269 SHEET 3 DD 3 GLY D 297 THR D 302 -1 O GLY D 297 N GLY D 294 SHEET 1 DE 2 SER D 272 PRO D 274 0 SHEET 2 DE 2 SER D 286 SER D 288 -1 O LEU D 287 N ALA D 273 CISPEP 1 ASN A 140 PRO A 141 0 1.16 CISPEP 2 ASN B 140 PRO B 141 0 -11.48 CISPEP 3 ASN C 140 PRO C 141 0 -10.11 CISPEP 4 ASN D 140 PRO D 141 0 -5.59 CRYST1 123.350 127.930 72.920 90.00 90.00 90.00 P 21 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 0.008107 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007817 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013714 0.00000