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Yorodumi- PDB-3oyz: Haloferax volcanii Malate Synthase Pyruvate/Acetyl-CoA Ternary Complex -
+Open data
-Basic information
Entry | Database: PDB / ID: 3oyz | |||||||||
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Title | Haloferax volcanii Malate Synthase Pyruvate/Acetyl-CoA Ternary Complex | |||||||||
Components | Malate Synthase | |||||||||
Keywords | TRANSFERASE / TIM Barrel | |||||||||
Function / homology | Function and homology information malate synthase / malate synthase activity / glyoxylate cycle / tricarboxylic acid cycle / metal ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Haloferax volcanii (archaea) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | |||||||||
Authors | Howard, B.R. / Bracken, C. / Neighbor, A. / Thomas, G. / Lamlenn, K.K. / Schubert, H.L. / Whitby, F.G. | |||||||||
Citation | Journal: Bmc Struct.Biol. / Year: 2011 Title: Crystal structures of a halophilic archaeal malate synthase from Haloferax volcanii and comparisons with isoforms A and G. Authors: Bracken, C.D. / Neighbor, A.M. / Lamlenn, K.K. / Thomas, G.C. / Schubert, H.L. / Whitby, F.G. / Howard, B.R. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3oyz.cif.gz | 96.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3oyz.ent.gz | 72.3 KB | Display | PDB format |
PDBx/mmJSON format | 3oyz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oy/3oyz ftp://data.pdbj.org/pub/pdb/validation_reports/oy/3oyz | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 48066.848 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloferax volcanii (archaea) / Strain: ATCC 29605, DS2 / References: UniProt: D4GTL2, malate synthase |
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-Non-polymers , 7 types, 187 molecules
#2: Chemical | ChemComp-ACO / | ||||||
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#3: Chemical | ChemComp-PYR / | ||||||
#4: Chemical | ChemComp-MG / | ||||||
#5: Chemical | #6: Chemical | ChemComp-CL / #7: Chemical | ChemComp-PO4 / | #8: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.41 Å3/Da / Density % sol: 63.9 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 4.4 Details: PEG 4500, glycerol, 2M KCl,MgCl2 , pH 4.4, supplemented with 0.07M pyruvate, 0.15M acetyl-coa, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Dec 30, 2009 / Details: confocal |
Radiation | Monochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→30 Å / Num. all: 47508 / Num. obs: 47508 / % possible obs: 100 % / Redundancy: 8.4 % / Rmerge(I) obs: 0.099 / Net I/σ(I): 15.25 |
Reflection shell | Resolution: 1.95→2.02 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.806 / Mean I/σ(I) obs: 2.35 / Num. unique all: 47508 / Rsym value: 0.806 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Model built into a lower resolution dataset from a crystal soaked under different conditions, phased with a lead derivative using the SIRAS method and SOLVE. Resolution: 1.95→30 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.936 / SU B: 3.205 / SU ML: 0.091 / Cross valid method: THROUGHOUT / ESU R Free: 0.126 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 47.651 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.951→2.001 Å / Total num. of bins used: 20
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