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Yorodumi- PDB-3pea: Crystal structure of enoyl-CoA hydratase from Bacillus anthracis ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3pea | ||||||
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Title | Crystal structure of enoyl-CoA hydratase from Bacillus anthracis str. 'Ames Ancestor' | ||||||
Components | Enoyl-CoA hydratase/isomerase family protein | ||||||
Keywords | ISOMERASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / Fatty acid and phospholipid metabolism / enoyl-CoA / Bacillus anthracis | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Bacillus anthracis (anthrax bacterium) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.817 Å | ||||||
Authors | Filippova, E.V. / Wawrzak, Z. / Kudritska, M. / Edwards, A. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
Citation | Journal: To be Published Title: Crystal structure of enoyl-CoA hydratase from Bacillus anthracis str. 'Ames Ancestor' Authors: Filippova, E.V. / Wawrzak, Z. / Kudritska, M. / Edwards, A. / Savchenko, A. / 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 | 3pea.cif.gz | 619.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3pea.ent.gz | 519.4 KB | Display | PDB format |
PDBx/mmJSON format | 3pea.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3pea_validation.pdf.gz | 496.2 KB | Display | wwPDB validaton report |
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Full document | 3pea_full_validation.pdf.gz | 512.5 KB | Display | |
Data in XML | 3pea_validation.xml.gz | 65.9 KB | Display | |
Data in CIF | 3pea_validation.cif.gz | 92.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pe/3pea ftp://data.pdbj.org/pub/pdb/validation_reports/pe/3pea | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 28536.502 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Strain: Ames Ancestor / Gene: BAS4420, BA_4761, GBAA4761, GBAA_4761 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIPL / References: UniProt: Q81L70, UniProt: A0A6L7GYV0*PLUS #2: Chemical | ChemComp-FLC / #3: Chemical | ChemComp-PG4 / #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: 2.62 Å3/Da / Density % sol: 53.06 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 20% PEG3350, 0.2 M NH4 hydrogen Citrate, 2% PEG400, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.04006 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 23, 2010 / Details: MIRROR |
Radiation | Monochromator: Si(111) / Protocol: MOLECULAR REPLACEMENT / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.04006 Å / Relative weight: 1 |
Reflection | Resolution: 1.817→30 Å / Num. all: 151590 / Num. obs: 151590 / % possible obs: 97.3 % / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Biso Wilson estimate: 36.1 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 13.9 |
Reflection shell | Resolution: 1.817→1.85 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 2.2 / Num. unique all: 7431 / % possible all: 95.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: the starting model was the structure solved by SAD in a different space group Resolution: 1.817→29.016 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.958 / SU B: 5.135 / SU ML: 0.071 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.113 / ESU R Free: 0.108 / 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: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.282 Å2
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Refine analyze | Luzzati coordinate error obs: 0.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.817→29.016 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.817→1.864 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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