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Yorodumi- PDB-3gvi: Crystal structure of Lactate/malate dehydrogenase from Brucella m... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3gvi | ||||||
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Title | Crystal structure of Lactate/malate dehydrogenase from Brucella melitensis in complex with ADP | ||||||
Components | Malate dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / LACTATE/MALATE DEHYDROGENASE / BRUCELLA MELITENSIS / NAD / Tricarboxylic acid cycle / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID | ||||||
Function / homology | Function and homology information malate dehydrogenase / L-malate dehydrogenase activity / carboxylic acid metabolic process / tricarboxylic acid cycle Similarity search - Function | ||||||
Biological species | Brucella melitensis biovar Abortus 2308 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / molecular replacement / Resolution: 2.25 Å | ||||||
Authors | Seattle Structural Genomics Center for Infectious Disease (SSGCID) | ||||||
Citation | Journal: To be Published Title: Crystal structure of Lactate/malate dehydrogenase from Brucella melitensis in complex with ADP Authors: Abendroth, J. / Staker, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3gvi.cif.gz | 377.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3gvi.ent.gz | 304.1 KB | Display | PDB format |
PDBx/mmJSON format | 3gvi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gv/3gvi ftp://data.pdbj.org/pub/pdb/validation_reports/gv/3gvi | HTTPS FTP |
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-Related structure data
Related structure data | 3gvhS S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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-Components
#1: Protein | Mass: 34037.238 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Brucella melitensis biovar Abortus 2308 (bacteria) Gene: mdh, BAB1_1927 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q2YLR9, malate dehydrogenase #2: Chemical | ChemComp-ADP / #3: 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: 2.62 Å3/Da / Density % sol: 53.01 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: JCSG+ SCREEN, H3: 25% PEG 3350, 100MM BISTRIS, BRABA.00005.A AT 28.5MG/ML, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 290K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97933 |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 19, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97933 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→193.9 Å / Num. all: 102350 / Num. obs: 99622 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.2 % / Biso Wilson estimate: 28.89 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 18.82 |
Reflection shell | Resolution: 2.25→2.31 Å / Redundancy: 2 % / Rmerge(I) obs: 0.152 / Mean I/σ(I) obs: 5.6 / Num. unique all: 7486 / % possible all: 83.7 |
-Processing
Software |
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Refinement | Method to determine structure: molecular replacement Starting model: pdb entry 3GVH Resolution: 2.25→193 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.922 / SU B: 5.079 / SU ML: 0.128 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.269 / ESU R Free: 0.211 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.95 Å2
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Refinement step | Cycle: LAST / Resolution: 2.25→193 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Ens-ID: 1 / Number: 3760 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.25→2.31 Å / Total num. of bins used: 20
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