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Yorodumi- PDB-1bmd: DETERMINANTS OF PROTEIN THERMOSTABILITY OBSERVED IN THE 1.9 ANGST... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1bmd | ||||||
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Title | DETERMINANTS OF PROTEIN THERMOSTABILITY OBSERVED IN THE 1.9 ANGSTROMS CRYSTAL STRUCTURE OF MALATE DEHYDROGENASE FROM THE THERMOPHILIC BACTERIUM THERMUS FLAVUS | ||||||
Components | MALATE DEHYDROGENASE | ||||||
Keywords | OXIDOREDUCTASE(CHOH(D)-NAD+(A)) | ||||||
Function / homology | Function and homology information malate dehydrogenase / L-malate dehydrogenase (NAD+) activity / malate metabolic process / oxaloacetate metabolic process / NADH metabolic process / tricarboxylic acid cycle Similarity search - Function | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 1.9 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: 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. #3: 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. #4: Journal: J.Biol.Chem. / Year: 1983 Title: The Presence of a Histidine-Aspartic Acid Pair in the Active Site of 2-Hydroxyacid Dehydrogenases Authors: Birktoft, J.J. / Banaszak, L.J. #5: Journal: Enzyme / Year: 1975 Title: Malate Dehydrogenases 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 | 1bmd.cif.gz | 142 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1bmd.ent.gz | 112 KB | Display | PDB format |
PDBx/mmJSON format | 1bmd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1bmd_validation.pdf.gz | 538.6 KB | Display | wwPDB validaton report |
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Full document | 1bmd_full_validation.pdf.gz | 564.8 KB | Display | |
Data in XML | 1bmd_validation.xml.gz | 17.6 KB | Display | |
Data in CIF | 1bmd_validation.cif.gz | 27.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bm/1bmd ftp://data.pdbj.org/pub/pdb/validation_reports/bm/1bmd | HTTPS FTP |
-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: SIDE CHAINS HAVE BEEN MODELED IN TWO ALTERNATE CONFORMATIONS AND ASSIGNED ALTERNATE LOCATION INDICATORS *1* AND *2*. 2: RESIDUES PRO A 131 AND PRO B 131 ARE CIS PROLINES. | ||||||||
Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.6068, 0.0021, -0.7948), 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 PRESENTED ON *MTRIX* RECORDS BELOW YIELDS OPTIMAL SUPERPOSITION OF SUBUNIT A UPON SUBUNIT B BASED UPON ALL ALPHA CARBON ATOMS. | |
-Components
#1: Protein | Mass: 35452.691 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 / | 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: 2.63 Å3/Da / Density % sol: 53.17 % | ||||||||||||||||||||||||||||||||||||||||||
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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 Highest resolution: 1.9 Å / Num. obs: 63904 / Num. measured all: 376446 / Rmerge(I) obs: 0.071 |
-Processing
Software |
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Refinement | Rfactor Rwork: 0.154 / Rfactor obs: 0.154 / Highest resolution: 1.9 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 1.9 Å
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Refine LS restraints |
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Refinement | *PLUS Rfactor obs: 0.154 / Rfactor Rwork: 0.154 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_angle_d / Dev ideal: 2.85 |