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Yorodumi- PDB-3cyv: Crystal structure of uroporphyrinogen decarboxylase from Shigella... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3cyv | ||||||
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Title | Crystal structure of uroporphyrinogen decarboxylase from Shigella flexineri: new insights into its catalytic mechanism | ||||||
Components | Uroporphyrinogen decarboxylase | ||||||
Keywords | LYASE / alpha/beta barrel / Cytoplasm / Decarboxylase / Porphyrin biosynthesis | ||||||
Function / homology | Function and homology information uroporphyrinogen decarboxylase / uroporphyrinogen decarboxylase activity / protoporphyrinogen IX biosynthetic process / cytoplasm Similarity search - Function | ||||||
Biological species | Shigella flexneri (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Liu, H. / Zhou, H. / Bi, R. | ||||||
Citation | Journal: To be Published Title: Crystal structure of uroporphyrinogen III decarboxylase from Shigella flexineri: new insights into its catalytic mechanism Authors: Liu, H. / Zhou, H. / Bi, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3cyv.cif.gz | 84.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3cyv.ent.gz | 63.3 KB | Display | PDB format |
PDBx/mmJSON format | 3cyv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3cyv_validation.pdf.gz | 415.9 KB | Display | wwPDB validaton report |
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Full document | 3cyv_full_validation.pdf.gz | 434.2 KB | Display | |
Data in XML | 3cyv_validation.xml.gz | 19.1 KB | Display | |
Data in CIF | 3cyv_validation.cif.gz | 27.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cy/3cyv ftp://data.pdbj.org/pub/pdb/validation_reports/cy/3cyv | HTTPS FTP |
-Related structure data
Related structure data | 1uroS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 39274.988 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Shigella flexneri (bacteria) / Strain: 2a str. 301 / Gene: urod / Plasmid: pET22b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q83PB7, uroporphyrinogen decarboxylase |
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#2: 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: 2.31 Å3/Da / Density % sol: 46.7 % |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BSRF / Beamline: 3W1A / Wavelength: 0.97954 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Mar 26, 2005 |
Radiation | Monochromator: SI(111) DOUBLE-CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97954 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. all: 9336 / Num. obs: 9240 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Biso Wilson estimate: 31.1 Å2 / Rmerge(I) obs: 0.113 / Net I/σ(I): 17.9 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.309 / Mean I/σ(I) obs: 6 / Num. unique all: 853 / % possible all: 92.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1URO Resolution: 2.8→50 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 1764582.51 / Data cutoff low absF: 0 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 33.2071 Å2 / ksol: 0.337117 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.8→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.98 Å / Rfactor Rfree error: 0.036 / Total num. of bins used: 6
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Xplor file |
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