HEADER OXIDOREDUCTASE 02-FEB-99 1B8U TITLE MALATE DEHYDROGENASE FROM AQUASPIRILLUM ARCTICUM COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN (MALATE DEHYDROGENASE); COMPND 3 CHAIN: A SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: AQUASPIRILLUM ARCTICUM; SOURCE 3 ORGANISM_TAXID: 87645 KEYWDS DEHYDROGENASE, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR S.Y.KIM,K.Y.HWANG,S.-H.KIM,Y.S.HAN,Y.CHO REVDAT 6 03-APR-24 1B8U 1 REMARK REVDAT 5 27-DEC-23 1B8U 1 REMARK REVDAT 4 13-JUL-11 1B8U 1 VERSN REVDAT 3 24-FEB-09 1B8U 1 VERSN REVDAT 2 01-APR-03 1B8U 1 JRNL REVDAT 1 09-JUL-99 1B8U 0 JRNL AUTH S.Y.KIM,K.Y.HWANG,S.H.KIM,H.C.SUNG,Y.S.HAN,Y.CHO JRNL TITL STRUCTURAL BASIS FOR COLD ADAPTATION. SEQUENCE, BIOCHEMICAL JRNL TITL 2 PROPERTIES, AND CRYSTAL STRUCTURE OF MALATE DEHYDROGENASE JRNL TITL 3 FROM A PSYCHROPHILE AQUASPIRILLIUM ARCTICUM. JRNL REF J.BIOL.CHEM. V. 274 11761 1999 JRNL REFN ISSN 0021-9258 JRNL PMID 10206992 JRNL DOI 10.1074/JBC.274.17.11761 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 81.2 REMARK 3 NUMBER OF REFLECTIONS : 8908 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.198 REMARK 3 FREE R VALUE : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2461 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 53 REMARK 3 SOLVENT ATOMS : 62 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.650 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL 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 : PARHCSDX.PRO REMARK 3 PARAMETER FILE 2 : NULL REMARK 3 TOPOLOGY FILE 1 : TOPHCSDX.PRO REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1B8U COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-FEB-99. REMARK 100 THE DEPOSITION ID IS D_1000000433. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 83 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RU200 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NI FILTER 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 : 9952 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 87.4 REMARK 200 DATA REDUNDANCY : 6.800 REMARK 200 R MERGE (I) : 0.09000 REMARK 200 R SYM (I) : 0.07500 REMARK 200 FOR THE DATA SET : 23.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: X-PLOR 3.1 REMARK 200 STARTING MODEL: APO MDH FROM A. ARCTICUM REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.30 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 7.0 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 29.15000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 50.85000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 29.15000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 50.85000 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA,PQS REMARK 350 TOTAL BURIED SURFACE AREA: 5940 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 23750 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -29.0 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 58.30000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 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 ALA A 2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 MET A 71 119.75 -166.75 REMARK 500 ASN A 126 40.59 -144.95 REMARK 500 LYS A 183 17.78 55.80 REMARK 500 THR A 221 -56.38 -124.88 REMARK 500 SER A 240 -178.88 -53.45 REMARK 500 GLU A 290 143.11 -178.61 REMARK 500 LEU A 328 40.43 -100.27 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 OAA A 350 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NAD A 334 DBREF 1B8U A 1 329 UNP Q9ZF99 MDH_AQUAR 1 329 SEQRES 1 A 329 MET ALA LYS THR PRO MET ARG VAL ALA VAL THR GLY ALA SEQRES 2 A 329 ALA GLY GLN ILE CYS TYR SER LEU LEU PHE ARG ILE ALA SEQRES 3 A 329 ASN GLY ASP MET LEU GLY LYS ASP GLN PRO VAL ILE LEU SEQRES 4 A 329 GLN LEU LEU GLU ILE PRO ASN GLU LYS ALA GLN LYS ALA SEQRES 5 A 329 LEU GLN GLY VAL MET MET GLU ILE ASP ASP CYS ALA PHE SEQRES 6 A 329 PRO LEU LEU ALA GLY MET THR ALA HIS ALA ASP PRO MET SEQRES 7 A 329 THR ALA PHE LYS ASP ALA ASP VAL ALA LEU LEU VAL GLY SEQRES 8 A 329 ALA ARG PRO ARG GLY PRO GLY MET GLU ARG LYS ASP LEU SEQRES 9 A 329 LEU GLU ALA ASN ALA GLN ILE PHE THR VAL GLN GLY LYS SEQRES 10 A 329 ALA ILE ASP ALA VAL ALA SER ARG ASN ILE LYS VAL LEU SEQRES 11 A 329 VAL VAL GLY ASN PRO ALA ASN THR ASN ALA TYR ILE ALA SEQRES 12 A 329 MET LYS SER ALA PRO SER LEU PRO ALA LYS ASN PHE THR SEQRES 13 A 329 ALA MET LEU ARG LEU ASP HIS ASN ARG ALA LEU SER GLN SEQRES 14 A 329 ILE ALA ALA LYS THR GLY LYS PRO VAL SER SER ILE GLU SEQRES 15 A 329 LYS LEU PHE VAL TRP GLY ASN HIS SER PRO THR MET TYR SEQRES 16 A 329 ALA ASP TYR ARG TYR ALA GLN ILE ASP GLY ALA SER VAL SEQRES 17 A 329 LYS ASP MET ILE ASN ASP ASP ALA TRP ASN ARG ASP THR SEQRES 18 A 329 PHE LEU PRO THR VAL GLY LYS ARG GLY ALA ALA ILE ILE SEQRES 19 A 329 ASP ALA ARG GLY VAL SER SER ALA ALA SER ALA ALA ASN SEQRES 20 A 329 ALA ALA ILE ASP HIS ILE HIS ASP TRP VAL LEU GLY THR SEQRES 21 A 329 ALA GLY LYS TRP THR THR MET GLY ILE PRO SER ASP GLY SEQRES 22 A 329 SER TYR GLY ILE PRO GLU GLY VAL ILE PHE GLY PHE PRO SEQRES 23 A 329 VAL THR THR GLU ASN GLY GLU TYR LYS ILE VAL GLN GLY SEQRES 24 A 329 LEU SER ILE ASP ALA PHE SER GLN GLU ARG ILE ASN VAL SEQRES 25 A 329 THR LEU ASN GLU LEU LEU GLU GLU GLN ASN GLY VAL GLN SEQRES 26 A 329 HIS LEU LEU GLY HET OAA A 350 9 HET NAD A 334 44 HETNAM OAA OXALOACETATE ION HETNAM NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE FORMUL 2 OAA C4 H3 O5 1- FORMUL 3 NAD C21 H27 N7 O14 P2 FORMUL 4 HOH *62(H2 O) HELIX 1 1 GLN A 16 ALA A 26 1 11 HELIX 2 2 GLU A 47 CYS A 63 1 17 HELIX 3 3 PRO A 77 ALA A 80 1 4 HELIX 4 4 ARG A 101 VAL A 122 1 22 HELIX 5 5 ALA A 136 LYS A 145 1 10 HELIX 6 6 ALA A 152 ASN A 154 5 3 HELIX 7 7 ARG A 160 THR A 174 1 15 HELIX 8 8 VAL A 178 SER A 180 5 3 HELIX 9 9 VAL A 208 ILE A 212 1 5 HELIX 10 10 ASP A 215 ASP A 220 1 6 HELIX 11 11 PHE A 222 GLY A 227 1 6 HELIX 12 12 ARG A 229 ARG A 237 1 9 HELIX 13 13 ALA A 242 LEU A 258 1 17 HELIX 14 14 SER A 274 GLY A 276 5 3 HELIX 15 15 ALA A 304 LEU A 327 1 24 SHEET 1 A 6 PHE A 155 ALA A 157 0 SHEET 2 A 6 LYS A 128 VAL A 131 1 N VAL A 129 O THR A 156 SHEET 3 A 6 VAL A 86 LEU A 89 1 N ALA A 87 O LYS A 128 SHEET 4 A 6 MET A 6 THR A 11 1 N ALA A 9 O VAL A 86 SHEET 5 A 6 VAL A 37 LEU A 42 1 N ILE A 38 O MET A 6 SHEET 6 A 6 LEU A 68 HIS A 74 1 N ALA A 69 O VAL A 37 SHEET 1 B 2 PHE A 185 TRP A 187 0 SHEET 2 B 2 TYR A 195 ASP A 197 -1 N ASP A 197 O PHE A 185 SHEET 1 C 3 THR A 265 PRO A 270 0 SHEET 2 C 3 ILE A 282 GLU A 290 -1 N VAL A 287 O THR A 265 SHEET 3 C 3 GLU A 293 ILE A 296 -1 N LYS A 295 O THR A 288 CISPEP 1 ASN A 134 PRO A 135 0 -0.67 SITE 1 AC1 12 LEU A 161 ARG A 165 HIS A 190 SER A 191 SITE 2 AC1 12 GLY A 227 LYS A 228 ARG A 229 GLY A 230 SITE 3 AC1 12 SER A 241 NAD A 334 HOH A 356 HOH A 359 SITE 1 AC2 19 THR A 11 GLY A 12 GLY A 15 GLN A 16 SITE 2 AC2 19 ILE A 17 GLU A 43 ILE A 44 VAL A 90 SITE 3 AC2 19 GLY A 91 ALA A 92 GLN A 115 VAL A 132 SITE 4 AC2 19 GLY A 133 ASN A 134 MET A 158 HIS A 190 SITE 5 AC2 19 OAA A 350 HOH A 367 HOH A 381 CRYST1 58.300 101.700 52.760 90.00 90.00 90.00 P 21 21 2 4 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 0.017153 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009833 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018954 0.00000