10 20 30 40 50 60 70 80 2ZTU - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER OXIDOREDUCTASE 09-OCT-08 2ZTU
TITLE T190A MUTANT OF D-3-HYDROXYBUTYRATE DEHYDROGENASE COMPLEXED TITLE 2 WITH NAD+
COMPND MOL_ID: 1; COMPND 2 MOLECULE: D(-)-3-HYDROXYBUTYRATE DEHYDROGENASE; COMPND 3 CHAIN: A, B, C, D; COMPND 4 EC: 1.1.1.30; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PSEUDOMONAS FRAGI; SOURCE 3 ORGANISM_TAXID: 296; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: XL1BLUE; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PKK233-3
KEYWDS SHORT CHAIN DEHYDROGENASE/REDUCTASE, SDR FAMILY, NAD, NADH, KEYWDS 2 HBDH, OXIDOREDUCTASE
EXPDTA X-RAY DIFFRACTION
AUTHOR K.NAKASHIMA,Y.NAKAJIMA,K.ITO,T.YOSHIMOTO
REVDAT 1 25-AUG-09 2ZTU 0
JRNL AUTH K.NAKASHIMA,K.ITO,Y.NAKAJIMA,R.YAMAZAWA,S.MIYAKAWA, JRNL AUTH 2 T.YOSHIMOTO JRNL TITL CLOSED COMPLEX OF THE D-3-HYDROXYBUTYRATE JRNL TITL 2 DEHYDROGENASE INDUCED BY AN ENANTIOMERIC JRNL TITL 3 COMPETITIVE INHIBITOR. JRNL REF J.BIOCHEM. V. 145 467 2009 JRNL REFN ISSN 0021-924X JRNL PMID 19122202 JRNL DOI 10.1093/JB/MVN186
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 98.3 REMARK 3 NUMBER OF REFLECTIONS : 86158 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) : 0.238 REMARK 3 FREE R VALUE : 0.268 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 4321 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) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.07 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 84.80 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2860 REMARK 3 BIN FREE R VALUE : 0.3050 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 371 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 : 6601 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 134 REMARK 3 SOLVENT ATOMS : 633 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 28.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 34.00 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) : 0.28 REMARK 3 ESD FROM SIGMAA (A) : 0.19 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) : 0.32 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.21 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.17 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 21.90 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.69 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : ISOTROPIC 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 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : 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 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4 REMARK 4 2ZTU COMPLIES WITH FORMAT V. 3.20, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 10-OCT-08. REMARK 100 THE RCSB ID CODE IS RCSB028417.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-FEB-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : BL-17A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000 REMARK 200 MONOCHROMATOR : SI(111) DOUBLE CRYSTAL REMARK 200 MONOCHROMATOR REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 270 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 86335 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 200 DATA REDUNDANCY : 5.400 REMARK 200 R MERGE (I) : 0.06500 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 27.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 88.1 REMARK 200 DATA REDUNDANCY IN SHELL : 4.30 REMARK 200 R MERGE FOR SHELL (I) : 0.28000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: 2ZTL REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.13 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.01 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 16%(W/V) PEG8000, 100MM MAGNESIUM REMARK 280 CHLORIDE, 100MM HEPES-NA BUFFER, PH 7.5, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 293K
REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 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 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 36.55750 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 82.42450 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 53.30450 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 82.42450 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 36.55750 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 53.30450 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: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 14900 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 28730 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -113.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C, B, 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 ALA A 190 REMARK 465 PRO A 191 REMARK 465 LEU A 192 REMARK 465 VAL A 193 REMARK 465 GLU A 194 REMARK 465 LYS A 195 REMARK 465 GLN A 196 REMARK 465 ILE A 197 REMARK 465 SER A 198 REMARK 465 ALA A 199 REMARK 465 LEU A 200 REMARK 465 ALA A 201 REMARK 465 GLU A 202 REMARK 465 LYS A 203 REMARK 465 ASN A 204 REMARK 465 GLY A 205 REMARK 465 VAL A 206 REMARK 465 ASP A 207 REMARK 465 GLN A 208 REMARK 465 GLU A 209 REMARK 465 THR A 210 REMARK 465 ALA A 211 REMARK 465 ALA A 212 REMARK 465 ARG A 213 REMARK 465 GLU A 214 REMARK 465 MET B 1 REMARK 465 LEU B 2 REMARK 465 LYS B 3 REMARK 465 GLY B 4 REMARK 465 LYS B 5 REMARK 465 VAL B 6 REMARK 465 ALA B 7 REMARK 465 GLY B 37 REMARK 465 ASP B 38 REMARK 465 ALA B 39 REMARK 465 ALA B 40 REMARK 465 GLU B 41 REMARK 465 ILE B 42 REMARK 465 GLU B 43 REMARK 465 LYS B 44 REMARK 465 VAL B 45 REMARK 465 ARG B 46 REMARK 465 ALA B 47 REMARK 465 GLY B 48 REMARK 465 LEU B 49 REMARK 465 ALA B 50 REMARK 465 ALA B 51 REMARK 465 GLN B 52 REMARK 465 HIS B 53 REMARK 465 GLY B 54 REMARK 465 VAL B 55 REMARK 465 LYS B 56 REMARK 465 VAL B 57 REMARK 465 ARG B 189 REMARK 465 ALA B 190 REMARK 465 PRO B 191 REMARK 465 LEU B 192 REMARK 465 VAL B 193 REMARK 465 GLU B 194 REMARK 465 LYS B 195 REMARK 465 GLN B 196 REMARK 465 ILE B 197 REMARK 465 SER B 198 REMARK 465 ALA B 199 REMARK 465 LEU B 200 REMARK 465 ALA B 201 REMARK 465 GLU B 202 REMARK 465 LYS B 203 REMARK 465 ASN B 204 REMARK 465 GLY B 205 REMARK 465 VAL B 206 REMARK 465 ASP B 207 REMARK 465 GLN B 208 REMARK 465 GLU B 209 REMARK 465 THR B 210 REMARK 465 ALA B 211 REMARK 465 ALA B 212 REMARK 465 ARG B 213 REMARK 465 ALA C 190 REMARK 465 PRO C 191 REMARK 465 LEU C 192 REMARK 465 VAL C 193 REMARK 465 GLU C 194 REMARK 465 LYS C 195 REMARK 465 GLN C 196 REMARK 465 ILE C 197 REMARK 465 SER C 198 REMARK 465 ALA C 199 REMARK 465 LEU C 200 REMARK 465 ALA C 201 REMARK 465 GLU C 202 REMARK 465 LYS C 203 REMARK 465 ASN C 204 REMARK 465 GLY C 205 REMARK 465 VAL C 206 REMARK 465 ASP C 207 REMARK 465 ALA D 190 REMARK 465 PRO D 191 REMARK 465 LEU D 192 REMARK 465 VAL D 193 REMARK 465 GLU D 194 REMARK 465 LYS D 195 REMARK 465 GLN D 196 REMARK 465 ILE D 197 REMARK 465 SER D 198 REMARK 465 ALA D 199 REMARK 465 LEU D 200 REMARK 465 ALA D 201 REMARK 465 GLU D 202 REMARK 465 LYS D 203 REMARK 465 ASN D 204 REMARK 465 GLY D 205 REMARK 465 VAL D 206 REMARK 465 ASP D 207 REMARK 465 GLN D 208
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 LEU A 215 CG CD1 CD2 REMARK 470 PHE B 36 CG CD1 CD2 CE1 CE2 CZ REMARK 470 ARG B 79 CG CD NE CZ NH1 NH2 REMARK 470 GLU B 214 CG CD OE1 OE2 REMARK 470 LEU B 215 CG CD1 CD2 REMARK 470 GLN C 208 CG CD OE1 NE2 REMARK 470 GLU C 209 CG CD OE1 OE2 REMARK 470 THR C 210 OG1 CG2 REMARK 470 ARG C 213 CG CD NE CZ NH1 NH2 REMARK 470 GLU C 214 CG CD OE1 OE2 REMARK 470 LEU C 215 CG CD1 CD2 REMARK 470 GLU D 209 CG CD OE1 OE2 REMARK 470 THR D 210 OG1 CG2 REMARK 470 ARG D 213 CG CD NE CZ NH1 NH2 REMARK 470 GLU D 214 CG CD OE1 OE2 REMARK 470 LEU D 215 CG CD1 CD2
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 97 159.02 178.73 REMARK 500 LEU A 115 -58.30 -123.87 REMARK 500 ALA A 141 -113.80 -90.56 REMARK 500 SER A 142 164.98 173.32 REMARK 500 SER B 14 -171.96 -171.01 REMARK 500 ALA B 26 -0.40 -56.87 REMARK 500 ALA B 62 133.75 -35.99 REMARK 500 ARG B 83 175.12 177.68 REMARK 500 ALA B 97 144.09 168.16 REMARK 500 LEU B 115 -57.48 -127.87 REMARK 500 ALA B 141 -117.55 -78.83 REMARK 500 SER B 142 169.61 176.51 REMARK 500 ASP B 254 22.96 -141.45 REMARK 500 ALA C 97 155.67 174.28 REMARK 500 LEU C 115 -59.37 -125.24 REMARK 500 ALA C 141 -113.45 -92.92 REMARK 500 SER C 142 165.64 175.26 REMARK 500 ALA D 97 149.11 168.25 REMARK 500 LEU D 115 -57.86 -126.72 REMARK 500 ALA D 141 -109.28 -96.69 REMARK 500 SER D 142 166.99 172.18 REMARK 500 LYS D 152 45.17 -147.65 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 525 REMARK 525 M RES CSSEQI REMARK 525 HOH B1610 DISTANCE = 6.28 ANGSTROMS REMARK 525 HOH D1608 DISTANCE = 5.40 ANGSTROMS
REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 406 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ARG A 260 OXT REMARK 620 2 ARG D 260 OXT 163.3 REMARK 620 3 HOH A1003 O 98.7 93.5 REMARK 620 4 HOH D1006 O 91.8 75.2 98.0 REMARK 620 5 HOH D1005 O 107.9 82.0 95.5 154.1 REMARK 620 6 HOH D1004 O 88.6 79.5 172.6 82.8 81.0 REMARK 620 N 1 2 3 4 5
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 300 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 406 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 401 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NAD C 300 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NAD D 300
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1WMB RELATED DB: PDB REMARK 900 THE WILD-TYPE ENZYME WITH THE OPEN CONFORMATION REMARK 900 RELATED ID: 1X1T RELATED DB: PDB REMARK 900 THE WILD-TYPE ENZYME COMPLEXED WITH NAD+ REMARK 900 RELATED ID: 2ZTL RELATED DB: PDB REMARK 900 THE TERNAY COMPLEX OF THE WILD-TYPE ENZYME WITH THE CLOSED REMARK 900 CONFORMATION REMARK 900 RELATED ID: 2ZTM RELATED DB: PDB REMARK 900 T190S MUTANT ENZYME REMARK 900 RELATED ID: 2ZTV RELATED DB: PDB
DBREF 2ZTU A 1 260 UNP Q5KST5 Q5KST5_PSEFR 1 260 DBREF 2ZTU B 1 260 UNP Q5KST5 Q5KST5_PSEFR 1 260 DBREF 2ZTU C 1 260 UNP Q5KST5 Q5KST5_PSEFR 1 260 DBREF 2ZTU D 1 260 UNP Q5KST5 Q5KST5_PSEFR 1 260
SEQADV 2ZTU ALA A 190 UNP Q5KST5 THR 190 ENGINEERED SEQADV 2ZTU ALA B 190 UNP Q5KST5 THR 190 ENGINEERED SEQADV 2ZTU ALA C 190 UNP Q5KST5 THR 190 ENGINEERED SEQADV 2ZTU ALA D 190 UNP Q5KST5 THR 190 ENGINEERED
SEQRES 1 A 260 MET LEU LYS GLY LYS VAL ALA VAL VAL THR GLY SER THR SEQRES 2 A 260 SER GLY ILE GLY LEU GLY ILE ALA THR ALA LEU ALA ALA SEQRES 3 A 260 GLN GLY ALA ASP ILE VAL LEU ASN GLY PHE GLY ASP ALA SEQRES 4 A 260 ALA GLU ILE GLU LYS VAL ARG ALA GLY LEU ALA ALA GLN SEQRES 5 A 260 HIS GLY VAL LYS VAL LEU TYR ASP GLY ALA ASP LEU SER SEQRES 6 A 260 LYS GLY GLU ALA VAL ARG GLY LEU VAL ASP ASN ALA VAL SEQRES 7 A 260 ARG GLN MET GLY ARG ILE ASP ILE LEU VAL ASN ASN ALA SEQRES 8 A 260 GLY ILE GLN HIS THR ALA LEU ILE GLU ASP PHE PRO THR SEQRES 9 A 260 GLU LYS TRP ASP ALA ILE LEU ALA LEU ASN LEU SER ALA SEQRES 10 A 260 VAL PHE HIS GLY THR ALA ALA ALA LEU PRO HIS MET LYS SEQRES 11 A 260 LYS GLN GLY PHE GLY ARG ILE ILE ASN ILE ALA SER ALA SEQRES 12 A 260 HIS GLY LEU VAL ALA SER ALA ASN LYS SER ALA TYR VAL SEQRES 13 A 260 ALA ALA LYS HIS GLY VAL VAL GLY PHE THR LYS VAL THR SEQRES 14 A 260 ALA LEU GLU THR ALA GLY GLN GLY ILE THR ALA ASN ALA SEQRES 15 A 260 ILE CYS PRO GLY TRP VAL ARG ALA PRO LEU VAL GLU LYS SEQRES 16 A 260 GLN ILE SER ALA LEU ALA GLU LYS ASN GLY VAL ASP GLN SEQRES 17 A 260 GLU THR ALA ALA ARG GLU LEU LEU SER GLU LYS GLN PRO SEQRES 18 A 260 SER LEU GLN PHE VAL THR PRO GLU GLN LEU GLY GLY THR SEQRES 19 A 260 ALA VAL PHE LEU ALA SER ASP ALA ALA ALA GLN ILE THR SEQRES 20 A 260 GLY THR THR VAL SER VAL ASP GLY GLY TRP THR ALA ARG SEQRES 1 B 260 MET LEU LYS GLY LYS VAL ALA VAL VAL THR GLY SER THR SEQRES 2 B 260 SER GLY ILE GLY LEU GLY ILE ALA THR ALA LEU ALA ALA SEQRES 3 B 260 GLN GLY ALA ASP ILE VAL LEU ASN GLY PHE GLY ASP ALA SEQRES 4 B 260 ALA GLU ILE GLU LYS VAL ARG ALA GLY LEU ALA ALA GLN SEQRES 5 B 260 HIS GLY VAL LYS VAL LEU TYR ASP GLY ALA ASP LEU SER SEQRES 6 B 260 LYS GLY GLU ALA VAL ARG GLY LEU VAL ASP ASN ALA VAL SEQRES 7 B 260 ARG GLN MET GLY ARG ILE ASP ILE LEU VAL ASN ASN ALA SEQRES 8 B 260 GLY ILE GLN HIS THR ALA LEU ILE GLU ASP PHE PRO THR SEQRES 9 B 260 GLU LYS TRP ASP ALA ILE LEU ALA LEU ASN LEU SER ALA SEQRES 10 B 260 VAL PHE HIS GLY THR ALA ALA ALA LEU PRO HIS MET LYS SEQRES 11 B 260 LYS GLN GLY PHE GLY ARG ILE ILE ASN ILE ALA SER ALA SEQRES 12 B 260 HIS GLY LEU VAL ALA SER ALA ASN LYS SER ALA TYR VAL SEQRES 13 B 260 ALA ALA LYS HIS GLY VAL VAL GLY PHE THR LYS VAL THR SEQRES 14 B 260 ALA LEU GLU THR ALA GLY GLN GLY ILE THR ALA ASN ALA SEQRES 15 B 260 ILE CYS PRO GLY TRP VAL ARG ALA PRO LEU VAL GLU LYS SEQRES 16 B 260 GLN ILE SER ALA LEU ALA GLU LYS ASN GLY VAL ASP GLN SEQRES 17 B 260 GLU THR ALA ALA ARG GLU LEU LEU SER GLU LYS GLN PRO SEQRES 18 B 260 SER LEU GLN PHE VAL THR PRO GLU GLN LEU GLY GLY THR SEQRES 19 B 260 ALA VAL PHE LEU ALA SER ASP ALA ALA ALA GLN ILE THR SEQRES 20 B 260 GLY THR THR VAL SER VAL ASP GLY GLY TRP THR ALA ARG SEQRES 1 C 260 MET LEU LYS GLY LYS VAL ALA VAL VAL THR GLY SER THR SEQRES 2 C 260 SER GLY ILE GLY LEU GLY ILE ALA THR ALA LEU ALA ALA SEQRES 3 C 260 GLN GLY ALA ASP ILE VAL LEU ASN GLY PHE GLY ASP ALA SEQRES 4 C 260 ALA GLU ILE GLU LYS VAL ARG ALA GLY LEU ALA ALA GLN SEQRES 5 C 260 HIS GLY VAL LYS VAL LEU TYR ASP GLY ALA ASP LEU SER SEQRES 6 C 260 LYS GLY GLU ALA VAL ARG GLY LEU VAL ASP ASN ALA VAL SEQRES 7 C 260 ARG GLN MET GLY ARG ILE ASP ILE LEU VAL ASN ASN ALA SEQRES 8 C 260 GLY ILE GLN HIS THR ALA LEU ILE GLU ASP PHE PRO THR SEQRES 9 C 260 GLU LYS TRP ASP ALA ILE LEU ALA LEU ASN LEU SER ALA SEQRES 10 C 260 VAL PHE HIS GLY THR ALA ALA ALA LEU PRO HIS MET LYS SEQRES 11 C 260 LYS GLN GLY PHE GLY ARG ILE ILE ASN ILE ALA SER ALA SEQRES 12 C 260 HIS GLY LEU VAL ALA SER ALA ASN LYS SER ALA TYR VAL SEQRES 13 C 260 ALA ALA LYS HIS GLY VAL VAL GLY PHE THR LYS VAL THR SEQRES 14 C 260 ALA LEU GLU THR ALA GLY GLN GLY ILE THR ALA ASN ALA SEQRES 15 C 260 ILE CYS PRO GLY TRP VAL ARG ALA PRO LEU VAL GLU LYS SEQRES 16 C 260 GLN ILE SER ALA LEU ALA GLU LYS ASN GLY VAL ASP GLN SEQRES 17 C 260 GLU THR ALA ALA ARG GLU LEU LEU SER GLU LYS GLN PRO SEQRES 18 C 260 SER LEU GLN PHE VAL THR PRO GLU GLN LEU GLY GLY THR SEQRES 19 C 260 ALA VAL PHE LEU ALA SER ASP ALA ALA ALA GLN ILE THR SEQRES 20 C 260 GLY THR THR VAL SER VAL ASP GLY GLY TRP THR ALA ARG SEQRES 1 D 260 MET LEU LYS GLY LYS VAL ALA VAL VAL THR GLY SER THR SEQRES 2 D 260 SER GLY ILE GLY LEU GLY ILE ALA THR ALA LEU ALA ALA SEQRES 3 D 260 GLN GLY ALA ASP ILE VAL LEU ASN GLY PHE GLY ASP ALA SEQRES 4 D 260 ALA GLU ILE GLU LYS VAL ARG ALA GLY LEU ALA ALA GLN SEQRES 5 D 260 HIS GLY VAL LYS VAL LEU TYR ASP GLY ALA ASP LEU SER SEQRES 6 D 260 LYS GLY GLU ALA VAL ARG GLY LEU VAL ASP ASN ALA VAL SEQRES 7 D 260 ARG GLN MET GLY ARG ILE ASP ILE LEU VAL ASN ASN ALA SEQRES 8 D 260 GLY ILE GLN HIS THR ALA LEU ILE GLU ASP PHE PRO THR SEQRES 9 D 260 GLU LYS TRP ASP ALA ILE LEU ALA LEU ASN LEU SER ALA SEQRES 10 D 260 VAL PHE HIS GLY THR ALA ALA ALA LEU PRO HIS MET LYS SEQRES 11 D 260 LYS GLN GLY PHE GLY ARG ILE ILE ASN ILE ALA SER ALA SEQRES 12 D 260 HIS GLY LEU VAL ALA SER ALA ASN LYS SER ALA TYR VAL SEQRES 13 D 260 ALA ALA LYS HIS GLY VAL VAL GLY PHE THR LYS VAL THR SEQRES 14 D 260 ALA LEU GLU THR ALA GLY GLN GLY ILE THR ALA ASN ALA SEQRES 15 D 260 ILE CYS PRO GLY TRP VAL ARG ALA PRO LEU VAL GLU LYS SEQRES 16 D 260 GLN ILE SER ALA LEU ALA GLU LYS ASN GLY VAL ASP GLN SEQRES 17 D 260 GLU THR ALA ALA ARG GLU LEU LEU SER GLU LYS GLN PRO SEQRES 18 D 260 SER LEU GLN PHE VAL THR PRO GLU GLN LEU GLY GLY THR SEQRES 19 D 260 ALA VAL PHE LEU ALA SER ASP ALA ALA ALA GLN ILE THR SEQRES 20 D 260 GLY THR THR VAL SER VAL ASP GLY GLY TRP THR ALA ARG
HET NAD A 300 44 HET MG A 406 1 HET MG B 401 1 HET NAD C 300 44 HET NAD D 300 44
HETNAM NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE HETNAM MG MAGNESIUM ION
FORMUL 5 NAD 3(C21 H27 N7 O14 P2) FORMUL 6 MG 2(MG 2+) FORMUL 10 HOH *633(H2 O)
HELIX 1 1 SER A 14 ALA A 26 1 13 HELIX 2 2 ASP A 38 GLY A 54 1 17 HELIX 3 3 LYS A 66 GLY A 82 1 17 HELIX 4 4 LEU A 98 PHE A 102 5 5 HELIX 5 5 PRO A 103 LEU A 115 1 13 HELIX 6 6 LEU A 115 GLY A 133 1 19 HELIX 7 7 SER A 142 LEU A 146 5 5 HELIX 8 8 LYS A 152 ALA A 174 1 23 HELIX 9 9 THR A 227 SER A 240 1 14 HELIX 10 10 ASP A 241 ALA A 244 5 4 HELIX 11 11 SER B 14 ALA B 26 1 13 HELIX 12 12 LYS B 66 GLY B 82 1 17 HELIX 13 13 LEU B 98 PHE B 102 5 5 HELIX 14 14 PRO B 103 LEU B 115 1 13 HELIX 15 15 LEU B 115 GLY B 133 1 19 HELIX 16 16 SER B 142 LEU B 146 5 5 HELIX 17 17 LYS B 152 ALA B 174 1 23 HELIX 18 18 THR B 227 SER B 240 1 14 HELIX 19 19 ASP B 241 ALA B 244 5 4 HELIX 20 20 SER C 14 ALA C 26 1 13 HELIX 21 21 ASP C 38 GLY C 54 1 17 HELIX 22 22 LYS C 66 GLY C 82 1 17 HELIX 23 23 LEU C 98 PHE C 102 5 5 HELIX 24 24 PRO C 103 LEU C 115 1 13 HELIX 25 25 LEU C 115 GLY C 133 1 19 HELIX 26 26 SER C 142 LEU C 146 5 5 HELIX 27 27 LYS C 152 ALA C 174 1 23 HELIX 28 28 GLN C 208 GLU C 218 1 11 HELIX 29 29 THR C 227 SER C 240 1 14 HELIX 30 30 ASP C 241 ALA C 244 5 4 HELIX 31 31 GLY C 256 ARG C 260 5 5 HELIX 32 32 SER D 14 GLN D 27 1 14 HELIX 33 33 ASP D 38 GLY D 54 1 17 HELIX 34 34 LYS D 66 GLY D 82 1 17 HELIX 35 35 LEU D 98 PHE D 102 5 5 HELIX 36 36 PRO D 103 LEU D 115 1 13 HELIX 37 37 LEU D 115 GLY D 133 1 19 HELIX 38 38 SER D 142 LEU D 146 5 5 HELIX 39 39 LYS D 152 ALA D 174 1 23 HELIX 40 40 GLU D 209 SER D 217 1 9 HELIX 41 41 THR D 227 SER D 240 1 14 HELIX 42 42 ASP D 241 ALA D 244 5 4 HELIX 43 43 GLY D 256 ARG D 260 5 5
SHEET 1 A 7 VAL A 57 TYR A 59 0 SHEET 2 A 7 ASP A 30 LEU A 33 1 N LEU A 33 O LEU A 58 SHEET 3 A 7 VAL A 6 VAL A 9 1 N ALA A 7 O ASP A 30 SHEET 4 A 7 ILE A 86 ASN A 89 1 O VAL A 88 N VAL A 8 SHEET 5 A 7 GLY A 135 ILE A 140 1 O ILE A 138 N LEU A 87 SHEET 6 A 7 ILE A 178 PRO A 185 1 O THR A 179 N ILE A 137 SHEET 7 A 7 THR A 250 VAL A 253 1 O VAL A 251 N ALA A 182 SHEET 1 B 4 ILE B 86 ASN B 89 0 SHEET 2 B 4 GLY B 135 ILE B 140 1 O ILE B 138 N LEU B 87 SHEET 3 B 4 ILE B 178 PRO B 185 1 O THR B 179 N ILE B 137 SHEET 4 B 4 THR B 250 VAL B 253 1 O VAL B 251 N CYS B 184 SHEET 1 C 7 VAL C 57 ASP C 60 0 SHEET 2 C 7 ASP C 30 ASN C 34 1 N LEU C 33 O LEU C 58 SHEET 3 C 7 VAL C 6 VAL C 9 1 N ALA C 7 O ASP C 30 SHEET 4 C 7 ILE C 86 ASN C 89 1 O VAL C 88 N VAL C 8 SHEET 5 C 7 GLY C 135 ILE C 140 1 O ILE C 138 N LEU C 87 SHEET 6 C 7 ILE C 178 PRO C 185 1 O ASN C 181 N ASN C 139 SHEET 7 C 7 THR C 249 VAL C 253 1 O THR C 249 N ALA C 182 SHEET 1 D 7 VAL D 57 ASP D 60 0 SHEET 2 D 7 ASP D 30 ASN D 34 1 N LEU D 33 O LEU D 58 SHEET 3 D 7 VAL D 6 VAL D 9 1 N ALA D 7 O ASP D 30 SHEET 4 D 7 ILE D 86 ASN D 89 1 O ILE D 86 N VAL D 8 SHEET 5 D 7 GLY D 135 ILE D 140 1 O ILE D 138 N LEU D 87 SHEET 6 D 7 ILE D 178 PRO D 185 1 O ASN D 181 N ASN D 139 SHEET 7 D 7 THR D 250 VAL D 253 1 O VAL D 251 N CYS D 184
LINK OXT ARG A 260 MG MG A 406 1555 1555 2.34 LINK OXT ARG D 260 MG MG A 406 1555 1555 2.36 LINK MG MG A 406 O HOH A1003 1555 1555 2.27 LINK MG MG A 406 O HOH D1006 1555 1555 2.36 LINK MG MG A 406 O HOH D1005 1555 1555 2.44 LINK MG MG A 406 O HOH D1004 1555 1555 2.38
SITE 1 AC1 24 GLY A 11 THR A 13 SER A 14 GLY A 15 SITE 2 AC1 24 ILE A 16 ASN A 34 GLY A 35 PHE A 36 SITE 3 AC1 24 ALA A 62 ASP A 63 LEU A 64 ASN A 90 SITE 4 AC1 24 GLY A 92 LEU A 113 ALA A 141 SER A 142 SITE 5 AC1 24 TYR A 155 LYS A 159 PRO A 185 GLY A 186 SITE 6 AC1 24 TRP A 187 VAL A 188 HOH A1160 HOH A1544 SITE 1 AC2 6 ARG A 260 HOH A1003 ARG D 260 HOH D1004 SITE 2 AC2 6 HOH D1005 HOH D1006 SITE 1 AC3 5 VAL B 147 ARG B 260 HOH B1001 ARG C 260 SITE 2 AC3 5 HOH C1002 SITE 1 AC4 27 GLY C 11 THR C 13 SER C 14 GLY C 15 SITE 2 AC4 27 ILE C 16 GLY C 35 PHE C 36 ALA C 62 SITE 3 AC4 27 ASP C 63 LEU C 64 ASN C 90 ALA C 91 SITE 4 AC4 27 LEU C 113 ILE C 140 ALA C 141 SER C 142 SITE 5 AC4 27 TYR C 155 LYS C 159 PRO C 185 GLY C 186 SITE 6 AC4 27 TRP C 187 VAL C 188 HOH C1087 HOH C1180 SITE 7 AC4 27 HOH C1242 HOH C1368 HOH C1420 SITE 1 AC5 23 GLY D 11 THR D 13 SER D 14 GLY D 15 SITE 2 AC5 23 ILE D 16 ASN D 34 GLY D 35 PHE D 36 SITE 3 AC5 23 ALA D 62 ASP D 63 LEU D 64 SER D 65 SITE 4 AC5 23 ASN D 90 ALA D 141 SER D 142 TYR D 155 SITE 5 AC5 23 LYS D 159 PRO D 185 GLY D 186 TRP D 187 SITE 6 AC5 23 VAL D 188 HOH D1124 HOH D1466
CRYST1 73.115 106.609 164.849 90.00 90.00 90.00 P 21 21 21 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 0.013677 0.000000 0.000000 0.00000
SCALE2 0.000000 0.009380 0.000000 0.00000
SCALE3 0.000000 0.000000 0.006066 0.00000