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Yorodumi- PDB-5vfb: 1.36 Angstrom Resolution Crystal Structure of Malate Synthase G f... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5vfb | |||||||||
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Title | 1.36 Angstrom Resolution Crystal Structure of Malate Synthase G from Pseudomonas aeruginosa in Complex with Glycolic Acid. | |||||||||
Components | Malate synthase G | |||||||||
Keywords | TRANSFERASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / Malate Synthase G / Glycolic Acid | |||||||||
Function / homology | Function and homology information malate synthase / malate synthase activity / glyoxylate catabolic process / glyoxylate cycle / tricarboxylic acid cycle / magnesium ion binding / cytosol Similarity search - Function | |||||||||
Biological species | Pseudomonas aeruginosa (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.36 Å | |||||||||
Authors | Minasov, G. / Shuvalova, L. / Dubrovska, I. / Kiryukhina, O. / Grimshaw, S. / Kwon, K. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID) | |||||||||
Citation | Journal: To Be Published Title: 1.36 Angstrom Resolution Crystal Structure of Malate Synthase G from Pseudomonas aeruginosa in Complex with Glycolic Acid. Authors: Minasov, G. / Shuvalova, L. / Dubrovska, I. / Kiryukhina, O. / Grimshaw, S. / Kwon, K. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID) | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5vfb.cif.gz | 621.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5vfb.ent.gz | 505.6 KB | Display | PDB format |
PDBx/mmJSON format | 5vfb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vf/5vfb ftp://data.pdbj.org/pub/pdb/validation_reports/vf/5vfb | HTTPS FTP |
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-Related structure data
Related structure data | 3s9zS S: Starting model for refinement |
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Similar structure data | |
Other databases |
-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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 79025.125 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (strain PAO1) (bacteria) Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1 Gene: glcB, PA0482 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) magic / References: UniProt: Q9I636, malate synthase |
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-Non-polymers , 5 types, 2263 molecules
#2: Chemical | #3: Chemical | ChemComp-CL / #4: Chemical | #5: Chemical | #6: 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: 2.06 Å3/Da / Density % sol: 40.4 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5 Details: Protein: 14.6 mg/ml, 0.01M Tris HCl (pH 8.3); Screen: PACT (A7), 0.2M Sodium chloride, 0.1M Sodium acetate pH (5.0), 20% (w/v) PEG 6000. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 28, 2017 / Details: C(111) |
Radiation | Monochromator: Be / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 1.36→30 Å / Num. obs: 280381 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 4.3 % / Biso Wilson estimate: 10.5 Å2 / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.047 / Rsym value: 0.087 / Χ2: 1.003 / Net I/σ(I): 15.4 |
Reflection shell | Resolution: 1.36→1.38 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.715 / Mean I/σ(I) obs: 2.07 / Num. unique obs: 13617 / CC1/2: 0.607 / Rpim(I) all: 0.426 / Rsym value: 0.715 / Χ2: 1.003 / % possible all: 96.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3S9Z Resolution: 1.36→29.62 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.965 / SU B: 1.697 / SU ML: 0.036 / Cross valid method: THROUGHOUT / ESU R: 0.052 / ESU R Free: 0.054 / 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: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 11.977 Å2
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Refinement step | Cycle: 1 / Resolution: 1.36→29.62 Å
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Refine LS restraints |
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