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Yorodumi- PDB-1bdm: THE STRUCTURE AT 1.8 ANGSTROMS RESOLUTION OF A SINGLE SITE MUTANT... -
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-Basic information
Entry | Database: PDB / ID: 1bdm | ||||||
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Title | THE STRUCTURE AT 1.8 ANGSTROMS RESOLUTION OF A SINGLE SITE MUTANT (T189I) OF MALATE DEHYDROGENASE FROM THERMUS FLAVUS WITH INCREASED ENZYMATIC ACTIVITY | ||||||
Components | MALATE DEHYDROGENASE | ||||||
Keywords | OXIDOREDUCTASE(NAD(A)-CHOH(D)) | ||||||
Function / homology | Function and homology information malate dehydrogenase / L-malate dehydrogenase activity / malate metabolic process / tricarboxylic acid cycle Similarity search - Function | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 1.8 Å | ||||||
Authors | Kelly, C.A. / Birktoft, J.J. | ||||||
Citation | Journal: Biochemistry / Year: 1993 Title: Determinants of protein thermostability observed in the 1.9-A crystal structure of malate dehydrogenase from the thermophilic bacterium Thermus flavus. Authors: Kelly, C.A. / Nishiyama, M. / Ohnishi, Y. / Beppu, T. / Birktoft, J.J. #1: Journal: J.Mol.Biol. / Year: 1991 Title: Preliminary X-Ray Diffraction Analysis of a Crystallizable Mutant of Malate Dehydrogenase from the Thermophile Thermus Flavus Authors: Kelly, C.A. / Sarfaty, S. / Nishiyama, M. / Beppu, T. / Birktoft, J.J. #2: Journal: J.Biol.Chem. / Year: 1991 Title: Role of Threonine 190 in Modulating the Catalytic Function of Malate Dehydrogenase from a Thermophile Thermus Flavus Authors: Nishiyama, M. / Shimada, K. / Horinouchi, S. / Beppu, T. #3: Journal: Biochemistry / Year: 1989 Title: Refined Crystal Structure of Cytoplasmic Malate Dehydrogenase at 2.5-Angstroms Resolution Authors: Birktoft, J.J. / Rhodes, G. / Banaszak, L.J. #4: Journal: J.Biol.Chem. / Year: 1986 Title: Nucleotide Sequence of the Malate Dehydrogenase Gene of Thermus Flavus and its Mutation Directing an Increase in Enzyme Activity Authors: Nishiyama, M. / Matsubara, N. / Yamamoto, K. / Iijima, S. / Uozumi, T. / Beppu, T. #5: Journal: The Pyridine Nucleotide Coenzymes / Year: 1982 Title: Chemistry and Solution Conformation of the Pyridine Coenzymes Authors: Oppenheimer, N.J. #6: Journal: The Enzymes,Third Edition / Year: 1975 Title: Malate Dehydrogenase Authors: Banaszak, L.J. / Bradshaw, R.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1bdm.cif.gz | 139.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1bdm.ent.gz | 109.8 KB | Display | PDB format |
PDBx/mmJSON format | 1bdm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bd/1bdm ftp://data.pdbj.org/pub/pdb/validation_reports/bd/1bdm | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Atom site foot note | 1: CIS PROLINE - PRO A 131 / 2: CIS PROLINE - PRO B 131 | ||||||||
Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.6098, 0.0011, -0.7926), Vector: Details | THE ASYMMETRIC UNIT CONTAINS TWO SUBUNITS WHICH HAVE BEEN ASSIGNED CHAIN IDENTIFIERS *A* AND *B*. THEY ARE RELATED BY A NON-CRYSTALLOGRAPHIC SYMMETRY AXIS WITH A ROTATION ANGLE OF 180.0 DEGREES. THE TRANSFORMATION PROVIDED ON THE *MTRIX* RECORDS BELOW YIELDS OPTIMAL SUPERPOSITION OF SUBUNIT A UPON SUBUNIT B BASED UPON ALL ALPHA CARBON ATOMS. | |
-Components
#1: Protein | Mass: 35464.746 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / References: UniProt: P10584, malate dehydrogenase #2: Chemical | #3: Water | ChemComp-HOH / | Nonpolymer details | WHILE THE ENZYME WAS CRYSTALLIZED AT PH 7.5 IN THE PRESENCE OF THE REDUCED COENZYME NADH, THE ...WHILE THE ENZYME WAS CRYSTALLIZ | Sequence details | THE NUMBERING SYSTEM IS THE SAME AS THAT USED FOR THE CYTOPLASMIC MALATE DEHYDROGENASE STRUCTURE. ...THE NUMBERING SYSTEM IS THE SAME AS THAT USED FOR THE CYTOPLASMI | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.67 Å3/Da / Density % sol: 53.86 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 8.5 / Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Num. obs: 63904 / Num. measured all: 376446 / Rmerge(I) obs: 0.071 |
-Processing
Software | Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Rfactor Rwork: 0.169 / Rfactor obs: 0.169 / Highest resolution: 1.8 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 1.8 Å
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