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Yorodumi- PDB-2x0i: 2.9 A RESOLUTION STRUCTURE OF MALATE DEHYDROGENASE FROM ARCHAEOGL... -
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-Basic information
Entry | Database: PDB / ID: 2x0i | |||||||||
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Title | 2.9 A RESOLUTION STRUCTURE OF MALATE DEHYDROGENASE FROM ARCHAEOGLOBUS FULGIDUS IN COMPLEX WITH NADH | |||||||||
Components | MALATE DEHYDROGENASE | |||||||||
Keywords | OXIDOREDUCTASE / HYPERTHERMOPHILIC / TRICARBOXYLIC ACID CYCLE | |||||||||
Function / homology | Function and homology information malate dehydrogenase / L-malate dehydrogenase (NAD+) activity / lactate metabolic process / L-lactate dehydrogenase activity / pyruvate metabolic process / tricarboxylic acid cycle / cytoplasm Similarity search - Function | |||||||||
Biological species | ARCHAEOGLOBUS FULGIDUS DSM 4304 (archaea) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.91 Å | |||||||||
Authors | Irimia, A. / Madern, D. / Zaccai, G. / Vellieux, F.M.D. / Karshikoff, A. / Tibbelin, G. / Ladenstein, R. / Lien, T. / Birkeland, N.-K. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 2004 Title: The 2.9A Resolution Crystal Structure of Malate Dehydrogenase from Archaeoglobus Fulgidus: Mechanisms of Oligomerisation and Thermal Stabilisation. Authors: Irimia, A. / Vellieux, F.M.D. / Madern, D. / Zaccai, G. / Karshikoff, A. / Tibbelin, G. / Ladenstein, R. / Lien, T. / Birkeland, N.-K. #1: Journal: Biochemistry / Year: 2001 Title: Differences in the Oligomeric States of the Ldh- Like L-Maldh from the Hyperthermophilic Archaea Methanococcus Jannaschii and Archaeoglobus Fulgidus. Authors: Madern, D. / Ebel, C. / Dale, H.A. / Lien, T. / Steen, I.H. / Birkeland, N.K. / Zaccai, G. #2: Journal: Arch.Microbiol. / Year: 1997 Title: Properties and Primary Structure of a Thermostable L-Malate Dehydrogenase from Archaeoglobus Fulgidus Authors: Langelandsvik, A.S. / Steen, I.H. / Birkeland, N.K. / Lien, T. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2x0i.cif.gz | 130.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2x0i.ent.gz | 101.4 KB | Display | PDB format |
PDBx/mmJSON format | 2x0i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2x0i_validation.pdf.gz | 718.2 KB | Display | wwPDB validaton report |
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Full document | 2x0i_full_validation.pdf.gz | 724.4 KB | Display | |
Data in XML | 2x0i_validation.xml.gz | 14.3 KB | Display | |
Data in CIF | 2x0i_validation.cif.gz | 18.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x0/2x0i ftp://data.pdbj.org/pub/pdb/validation_reports/x0/2x0i | HTTPS FTP |
-Related structure data
Related structure data | 2x0jC 2hlpS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 31913.785 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ARCHAEOGLOBUS FULGIDUS DSM 4304 (archaea) Plasmid: PSJS1240 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ONE SHOT / References: UniProt: O08349, malate dehydrogenase |
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#2: Chemical | ChemComp-NAI / |
#3: Chemical | ChemComp-SO4 / |
#4: Chemical | ChemComp-NA / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.6 Å3/Da / Density % sol: 62.93 % / Description: NONE |
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Crystal grow | pH: 4 Details: INITIAL PROTEIN DROPLET: 16 MG/ML PROTEIN, 10 MM NADH, 20 M RESERVOIR: 1.6 M AMMONIUM SULPHATE, 20% (V/V) GLYCEROL, 80 M DROPLET: EQUAL VOLUMES OF INITIAL PROTEIN DROPLET AND RESERVOIR WERE MIXED., pH 4.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.933 |
Detector | Type: ADSC CCD / Detector: CCD / Details: TOROIDAL MIRROR |
Radiation | Monochromator: DIAMOND CRYSTALS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 2.91→59.76 Å / Num. obs: 8949 / % possible obs: 83.6 % / Observed criterion σ(I): 0.5 / Redundancy: 8.7 % / Biso Wilson estimate: 62.26 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 26.9 |
Reflection shell | Resolution: 2.91→3.01 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.1 / Mean I/σ(I) obs: 9.7 / % possible all: 45.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2HLP Resolution: 2.91→56.48 Å / SU ML: 0.32 / σ(F): 2.17 / Phase error: 20.12 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 62.248 Å2 / ksol: 0.364 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 62.89 Å2
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Refinement step | Cycle: LAST / Resolution: 2.91→56.48 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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