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Yorodumi- PDB-3cv2: Atomic Resolution Structures of Escherichia coli and Bacillis ant... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3cv2 | ||||||
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Title | Atomic Resolution Structures of Escherichia coli and Bacillis anthracis Malate Synthase A: Comparison with Isoform G and Implications for Structure Based Drug Design | ||||||
Components | Malate synthase A | ||||||
Keywords | TRANSFERASE / malate synthase / TIM barrel / Cytoplasm / Glyoxylate bypass / Tricarboxylic acid cycle | ||||||
Function / homology | Function and homology information malate synthase / malate synthase activity / glyoxylate cycle / peroxisomal matrix / tricarboxylic acid cycle / cytoplasm Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å | ||||||
Authors | Lohman, J.R. / Remington, S.J. | ||||||
Citation | Journal: Protein Sci. / Year: 2008 Title: Atomic resolution structures of Escherichia coli and Bacillus anthracis malate synthase A: comparison with isoform G and implications for structure-based drug discovery Authors: Lohman, J.R. / Olson, A.C. / Remington, S.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3cv2.cif.gz | 454.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3cv2.ent.gz | 386.4 KB | Display | PDB format |
PDBx/mmJSON format | 3cv2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3cv2_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 3cv2_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 3cv2_validation.xml.gz | 49 KB | Display | |
Data in CIF | 3cv2_validation.cif.gz | 75.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cv/3cv2 ftp://data.pdbj.org/pub/pdb/validation_reports/cv/3cv2 | HTTPS FTP |
-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
#1: Protein | Mass: 60227.148 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: TEV cleavable / Source: (gene. exp.) Escherichia coli (E. coli) / Gene: aceB, mas / Plasmid: pBAD / Production host: Escherichia coli (E. coli) / Strain (production host): TOP10 / References: UniProt: P08997, malate synthase #2: Chemical | #3: Chemical | #4: Chemical | #5: 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: 2.3 Å3/Da / Density % sol: 46.61 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1M PIPES pH 6.5, 0.1M ammonium sulfate, 27% PEG 8K. Data collected 3 months after set-up, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: May 6, 2007 |
Radiation | Monochromator: Single crystal, cylindrically bent, Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→30 Å / Num. obs: 229489 / % possible obs: 97.1 % / Observed criterion σ(I): 1 |
Reflection shell | Resolution: 1.4→1.45 Å / % possible all: 94.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→25.01 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.961 / SU B: 2.704 / SU ML: 0.047 / Cross valid method: THROUGHOUT / ESU R: 0.072 / ESU R Free: 0.063 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.284 Å2
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Refinement step | Cycle: LAST / Resolution: 1.4→25.01 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.4→1.437 Å / Total num. of bins used: 20
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