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Yorodumi- PDB-2v6b: Crystal structure of lactate dehydrogenase from Deinococcus Radio... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2v6b | ||||||
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Title | Crystal structure of lactate dehydrogenase from Deinococcus Radiodurans (apo form) | ||||||
Components | L-LACTATE DEHYDROGENASE | ||||||
Keywords | OXIDOREDUCTASE / RADIORESISTANCE / LACTATE DEHYDROGENASE / LDH / NAD / CYTOPLASM / MESOPHILIC / GLYCOLYSIS | ||||||
Function / homology | Function and homology information L-lactate dehydrogenase / L-lactate dehydrogenase activity / glycolytic process / cytoplasm Similarity search - Function | ||||||
Biological species | DEINOCOCCUS RADIODURANS (radioresistant) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Coquelle, N. / Fioravanti, E. / Weik, M. / Vellieux, F. | ||||||
Citation | Journal: J. Mol. Biol. / Year: 2007 Title: Activity, stability and structural studies of lactate dehydrogenases adapted to extreme thermal environments. Authors: Coquelle, N. / Fioravanti, E. / Weik, M. / Vellieux, F. / Madern, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2v6b.cif.gz | 211.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2v6b.ent.gz | 171 KB | Display | PDB format |
PDBx/mmJSON format | 2v6b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2v6b_validation.pdf.gz | 459.6 KB | Display | wwPDB validaton report |
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Full document | 2v6b_full_validation.pdf.gz | 490.1 KB | Display | |
Data in XML | 2v6b_validation.xml.gz | 43.1 KB | Display | |
Data in CIF | 2v6b_validation.cif.gz | 59.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v6/2v6b ftp://data.pdbj.org/pub/pdb/validation_reports/v6/2v6b | HTTPS FTP |
-Related structure data
Related structure data | 2v65C 2v6mC 2v7pC 1ldnS S: Starting model for refinement C: citing same article (ref.) |
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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: 32201.383 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) DEINOCOCCUS RADIODURANS (radioresistant) Plasmid: PKDL302 / Production host: Escherichia coli DH5[alpha] (bacteria) / References: UniProt: P50933, L-lactate dehydrogenase #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 45.02 % / Description: NONE |
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Crystal grow | pH: 9 / Details: 0.1M BICINE PH 9, 20% PEG 5K MME |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.979 |
Detector | Type: MARRESEARCH / Detector: CCD / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→20 Å / Num. obs: 40233 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 4.35 % / Biso Wilson estimate: 41.6 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 17.06 |
Reflection shell | Resolution: 2.5→2.55 Å / Redundancy: 4.28 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 3.12 / % possible all: 94.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1LDN Resolution: 2.5→19.83 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 2727105.55 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 32.9803 Å2 / ksol: 0.284268 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 51 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→19.83 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.66 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
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Xplor file |
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