10 20 30 40 50 60 70 80 2ZTM - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER OXIDOREDUCTASE 07-OCT-08 2ZTM
TITLE T190S MUTANT OF D-3-HYDROXYBUTYRATE DEHYDROGENASE
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 REDACTASE, 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 2ZTM 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. 2.30 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) : 2.30 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) (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 57882 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) : 0.227 REMARK 3 FREE R VALUE : 0.266 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 2931 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) : 2.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.38 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.50 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2730 REMARK 3 BIN FREE R VALUE : 0.3200 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 296 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 : 7002 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 141 REMARK 3 SOLVENT ATOMS : 408 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 43.10 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 42.50 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) : 0.31 REMARK 3 ESD FROM SIGMAA (A) : 0.25 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) : 0.30 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.21 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 22.00 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.74 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 2ZTM COMPLIES WITH FORMAT V. 3.20, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 09-OCT-08. REMARK 100 THE RCSB ID CODE IS RCSB028409.
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 : 58373 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 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 (%) : 99.9 REMARK 200 DATA REDUNDANCY : 5.200 REMARK 200 R MERGE (I) : 0.08600 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 21.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.38 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.5 REMARK 200 DATA REDUNDANCY IN SHELL : 4.20 REMARK 200 R MERGE FOR SHELL (I) : 0.35900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.900 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 (%): 59.14 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.01 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 16%(W/V) PEG 8000, 10 MM 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 36.89650 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 82.24750 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 52.96300 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 82.24750 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 36.89650 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 52.96300 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: 15580 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 30520 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -121.0 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 MET A 1 REMARK 465 LEU A 2 REMARK 465 LYS A 3 REMARK 465 GLY A 4 REMARK 465 LYS A 5 REMARK 465 MET B 1 REMARK 465 LEU B 2 REMARK 465 LYS B 3 REMARK 465 GLY B 4 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 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 ASN C 204 REMARK 465 GLY C 205 REMARK 465 VAL C 206 REMARK 465 ASP C 207 REMARK 465 GLN C 208 REMARK 465 GLU C 209 REMARK 465 THR C 210 REMARK 465 ALA C 211 REMARK 465 ALA C 212 REMARK 465 ARG C 213 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 465 GLU D 209 REMARK 465 THR D 210 REMARK 465 ALA D 211 REMARK 465 ALA D 212
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 B 49 CG CD1 CD2 REMARK 470 LYS B 66 CG CD CE NZ REMARK 470 GLU B 68 CG CD OE1 OE2 REMARK 470 LYS B 131 CG CD CE NZ REMARK 470 LYS C 195 CG CD CE NZ REMARK 470 GLU C 202 CG CD OE1 OE2 REMARK 470 LYS C 203 CG CD CE NZ REMARK 470 LYS D 195 CG CD CE NZ REMARK 470 ARG D 213 CG CD NE CZ NH1 NH2 REMARK 470 GLU D 214 CG CD OE1 OE2
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 26 -2.28 -57.60 REMARK 500 PHE A 36 -168.69 -116.42 REMARK 500 LEU A 64 3.76 -65.10 REMARK 500 LEU A 115 -51.53 -123.09 REMARK 500 ALA A 141 -116.78 -87.35 REMARK 500 SER A 142 165.04 171.84 REMARK 500 ARG A 189 54.22 -67.16 REMARK 500 SER A 240 174.06 -54.54 REMARK 500 ALA B 97 143.85 177.60 REMARK 500 LEU B 113 -73.60 -78.66 REMARK 500 ALA B 141 -117.30 -81.62 REMARK 500 SER B 142 167.54 174.98 REMARK 500 VAL B 188 -142.40 -111.65 REMARK 500 SER B 240 162.20 -48.59 REMARK 500 VAL B 253 75.05 -114.55 REMARK 500 ALA C 97 161.68 177.14 REMARK 500 ALA C 141 -112.40 -97.66 REMARK 500 SER C 142 164.45 168.76 REMARK 500 ALA D 97 149.34 168.68 REMARK 500 LEU D 115 -50.24 -122.38 REMARK 500 ALA D 141 -114.96 -90.08 REMARK 500 SER D 142 167.26 175.32 REMARK 500 ARG D 189 83.42 -68.67 REMARK 500 REMARK 500 REMARK: NULL
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 123.7 REMARK 620 3 HOH D1018 O 77.6 70.4 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 401 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ARG B 260 OXT REMARK 620 2 ARG C 260 OXT 140.3 REMARK 620 3 HOH B1013 O 87.6 85.8 REMARK 620 4 HOH C1102 O 85.8 83.2 153.6 REMARK 620 N 1 2 3
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 3HL A 301 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 406 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 401 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NAD C 300 REMARK 800 SITE_IDENTIFIER: AC6 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 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 TERNARY COMPLEX OF THE WILD-TYPE ENZYME WITH CLOSED REMARK 900 CONFORMATION
DBREF 2ZTM A 1 260 UNP Q5KST5 Q5KST5_PSEFR 1 260 DBREF 2ZTM B 1 260 UNP Q5KST5 Q5KST5_PSEFR 1 260 DBREF 2ZTM C 1 260 UNP Q5KST5 Q5KST5_PSEFR 1 260 DBREF 2ZTM D 1 260 UNP Q5KST5 Q5KST5_PSEFR 1 260
SEQADV 2ZTM SER A 190 UNP Q5KST5 THR 190 ENGINEERED SEQADV 2ZTM SER B 190 UNP Q5KST5 THR 190 ENGINEERED SEQADV 2ZTM SER C 190 UNP Q5KST5 THR 190 ENGINEERED SEQADV 2ZTM SER 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 SER 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 SER 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 SER 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 SER 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 3HL A 301 7 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 3HL (3S)-3-HYDROXYBUTANOIC ACID HETNAM MG MAGNESIUM ION
FORMUL 5 NAD 3(C21 H27 N7 O14 P2) FORMUL 6 3HL C4 H8 O3 FORMUL 7 MG 2(MG 2+) FORMUL 11 HOH *408(H2 O)
HELIX 1 1 SER A 14 ALA A 26 1 13 HELIX 2 2 ASP A 38 HIS A 53 1 16 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 GLN A 132 1 18 HELIX 7 7 SER A 142 LEU A 146 5 5 HELIX 8 8 LYS A 152 THR A 173 1 22 HELIX 9 9 SER A 190 ASN A 204 1 15 HELIX 10 10 ASP A 207 GLN A 220 1 14 HELIX 11 11 THR A 227 SER A 240 1 14 HELIX 12 12 GLY A 256 ARG A 260 5 5 HELIX 13 13 SER B 14 GLN B 27 1 14 HELIX 14 14 GLY B 48 HIS B 53 1 6 HELIX 15 15 LYS B 66 MET B 81 1 16 HELIX 16 16 PRO B 103 LEU B 115 1 13 HELIX 17 17 LEU B 115 GLY B 133 1 19 HELIX 18 18 SER B 142 LEU B 146 5 5 HELIX 19 19 LYS B 152 THR B 173 1 22 HELIX 20 20 ALA B 212 GLN B 220 1 9 HELIX 21 21 THR B 227 SER B 240 1 14 HELIX 22 22 ASP B 241 ALA B 244 5 4 HELIX 23 23 SER C 14 ALA C 26 1 13 HELIX 24 24 ASP C 38 GLY C 54 1 17 HELIX 25 25 LYS C 66 GLY C 82 1 17 HELIX 26 26 PRO C 103 LEU C 115 1 13 HELIX 27 27 LEU C 115 GLY C 133 1 19 HELIX 28 28 SER C 142 LEU C 146 5 5 HELIX 29 29 LYS C 152 ALA C 174 1 23 HELIX 30 30 SER C 190 GLU C 202 1 13 HELIX 31 31 LEU C 215 GLN C 220 1 6 HELIX 32 32 THR C 227 SER C 240 1 14 HELIX 33 33 ASP C 241 ALA C 244 5 4 HELIX 34 34 SER D 14 GLN D 27 1 14 HELIX 35 35 ASP D 38 GLY D 54 1 17 HELIX 36 36 LYS D 66 GLY D 82 1 17 HELIX 37 37 PRO D 103 LEU D 115 1 13 HELIX 38 38 LEU D 115 GLY D 133 1 19 HELIX 39 39 SER D 142 LEU D 146 5 5 HELIX 40 40 LYS D 152 ALA D 174 1 23 HELIX 41 41 SER D 190 SER D 198 1 9 HELIX 42 42 LEU D 215 GLN D 220 1 6 HELIX 43 43 THR D 227 SER D 240 1 14 HELIX 44 44 ASP D 241 ALA D 244 5 4 HELIX 45 45 GLY D 256 ARG D 260 5 5
SHEET 1 A 7 VAL A 57 TYR A 59 0 SHEET 2 A 7 ILE A 31 LEU A 33 1 N LEU A 33 O LEU A 58 SHEET 3 A 7 ALA A 7 VAL A 9 1 N ALA A 7 O VAL A 32 SHEET 4 A 7 ILE A 86 ASN A 89 1 O ILE A 86 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 ASN A 181 N ASN A 139 SHEET 7 A 7 THR A 250 VAL A 253 1 O VAL A 251 N CYS A 184 SHEET 1 B 7 LEU B 58 ASP B 60 0 SHEET 2 B 7 ASP B 30 ASN B 34 1 N ILE B 31 O LEU B 58 SHEET 3 B 7 VAL B 6 VAL B 9 1 N ALA B 7 O VAL B 32 SHEET 4 B 7 ILE B 86 ASN B 89 1 O ILE B 86 N VAL B 8 SHEET 5 B 7 GLY B 135 ILE B 140 1 O ILE B 138 N LEU B 87 SHEET 6 B 7 ILE B 178 PRO B 185 1 O THR B 179 N ILE B 137 SHEET 7 B 7 THR B 249 VAL B 253 1 O VAL B 251 N ALA B 182 SHEET 1 C 7 VAL C 57 TYR C 59 0 SHEET 2 C 7 ASP C 30 LEU C 33 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 ILE D 183 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 2.42 LINK OXT ARG B 260 MG MG B 401 1555 1555 2.34 LINK OXT ARG C 260 MG MG B 401 1555 1555 2.36 LINK OXT ARG D 260 MG MG A 406 1555 1555 2.38 LINK MG MG A 406 O HOH D1018 1555 1555 2.40 LINK MG MG B 401 O HOH B1013 1555 1555 2.28 LINK MG MG B 401 O HOH C1102 1555 1555 2.34
SITE 1 AC1 31 GLY A 11 THR A 13 SER A 14 GLY A 15 SITE 2 AC1 31 ILE A 16 ASN A 34 GLY A 35 PHE A 36 SITE 3 AC1 31 ALA A 62 ASP A 63 LEU A 64 ASN A 90 SITE 4 AC1 31 GLY A 92 LEU A 113 ILE A 140 ALA A 141 SITE 5 AC1 31 SER A 142 TYR A 155 LYS A 159 PRO A 185 SITE 6 AC1 31 GLY A 186 VAL A 188 SER A 190 PRO A 191 SITE 7 AC1 31 LEU A 192 VAL A 193 3HL A 301 HOH A1087 SITE 8 AC1 31 HOH A1097 HOH A1229 HOH A1255 SITE 1 AC2 8 GLN A 94 SER A 142 HIS A 144 LYS A 152 SITE 2 AC2 8 TYR A 155 LEU A 192 GLN A 196 NAD A 300 SITE 1 AC3 5 ARG A 260 HOH A1167 ARG D 260 HOH D1018 SITE 2 AC3 5 HOH D1318 SITE 1 AC4 6 ARG B 260 HOH B1013 HOH B1135 ARG C 260 SITE 2 AC4 6 HOH C1102 HOH C1367 SITE 1 AC5 28 GLY C 11 THR C 13 SER C 14 GLY C 15 SITE 2 AC5 28 ILE C 16 ASN C 34 GLY C 35 PHE C 36 SITE 3 AC5 28 ALA C 62 ASP C 63 LEU C 64 ASN C 90 SITE 4 AC5 28 GLY C 92 LEU C 113 ILE C 140 ALA C 141 SITE 5 AC5 28 SER C 142 TYR C 155 LYS C 159 PRO C 185 SITE 6 AC5 28 GLY C 186 TRP C 187 VAL C 188 SER C 190 SITE 7 AC5 28 PRO C 191 LEU C 192 VAL C 193 HOH C1011 SITE 1 AC6 29 GLY D 11 THR D 13 SER D 14 GLY D 15 SITE 2 AC6 29 ILE D 16 ASN D 34 GLY D 35 PHE D 36 SITE 3 AC6 29 ALA D 62 ASP D 63 LEU D 64 ASN D 90 SITE 4 AC6 29 ALA D 91 GLY D 92 LEU D 113 ILE D 140 SITE 5 AC6 29 ALA D 141 SER D 142 TYR D 155 LYS D 159 SITE 6 AC6 29 PRO D 185 GLY D 186 TRP D 187 VAL D 188 SITE 7 AC6 29 SER D 190 LEU D 192 VAL D 193 HOH D1083 SITE 8 AC6 29 HOH D1176
CRYST1 73.793 105.926 164.495 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 0.013551 0.000000 0.000000 0.00000
SCALE2 0.000000 0.009441 0.000000 0.00000
SCALE3 0.000000 0.000000 0.006079 0.00000