+Open data
-Basic information
Entry | Database: PDB / ID: 3pug | ||||||
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Title | Haloferax volcanii Malate Synthase Native at 3mM Glyoxylate | ||||||
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 / SIRAS / Resolution: 2.7 Å | ||||||
Authors | Howard, B.R. / Bracken, C.D. / Neighbor, A.M. / Thomas, G.C. / 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 | 3pug.cif.gz | 87.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3pug.ent.gz | 64.7 KB | Display | PDB format |
PDBx/mmJSON format | 3pug.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pu/3pug ftp://data.pdbj.org/pub/pdb/validation_reports/pu/3pug | 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 / Details: ATCC / Source: (natural) Haloferax volcanii (archaea) / Strain: ATCC 29605, DS2 / References: UniProt: D4GTL2, malate synthase |
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-Non-polymers , 5 types, 81 molecules
#2: Chemical | ChemComp-GLV / | ||||
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#3: Chemical | ChemComp-MG / | ||||
#4: Chemical | ChemComp-CL / #5: Chemical | ChemComp-K / #6: 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: 3.46 Å3/Da / Density % sol: 64.45 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 4.4 Details: PEG 4500, glycerol, 2M KCl,13 mM MgCl2, 3mM Glyoxylate, pH 4.4, 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 / Detector: IMAGE PLATE / Date: Mar 18, 2009 / Details: R-axis IV, confocal optics | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: graphite / Protocol: SIRAS / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Redundancy: 3.7 % / Av σ(I) over netI: 14.23 / Number: 271479 / Rmerge(I) obs: 0.103 / Χ2: 1.11 / D res high: 2.1 Å / D res low: 30 Å / Num. obs: 73241 / % possible obs: 99.5 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Diffraction reflection shell |
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Reflection | Resolution: 2.7→30 Å / Num. obs: 18255 / % possible obs: 100 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.09 / Χ2: 1.022 / Net I/σ(I): 15.6 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: SIRAS | |||||||||||||||||||||||||||||||||||||||||||||||||
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Phasing dm | FOM : 0.71 / FOM acentric: 0.7 / FOM centric: 0.74 / Reflection: 17020 / Reflection acentric: 15865 / Reflection centric: 1155 | |||||||||||||||||||||||||||||||||||||||||||||||||
Phasing dm shell |
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-Processing
Software |
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Refinement | Method to determine structure: SIRAS / Resolution: 2.7→30 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.868 / WRfactor Rfree: 0.269 / WRfactor Rwork: 0.2062 / Occupancy max: 1 / Occupancy min: 0.33 / FOM work R set: 0.8252 / SU B: 9.058 / SU ML: 0.192 / SU R Cruickshank DPI: 0.3801 / SU Rfree: 0.2939 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.294 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 118.89 Å2 / Biso mean: 58.3396 Å2 / Biso min: 18.09 Å2
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Refinement step | Cycle: LAST / Resolution: 2.7→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.703→2.773 Å / Total num. of bins used: 20
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