+Open data
-Basic information
Entry | Database: PDB / ID: 5gzj | ||||||
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Title | Cyclodeaminase_PA | ||||||
Components | Lysine cyclodeaminase | ||||||
Keywords | LYASE / dimer / complexes / cyclization / deamination | ||||||
Function / homology | Function and homology information ornithine cyclodeaminase activity / ornithine cyclodeaminase / nucleotide binding / cytoplasm Similarity search - Function | ||||||
Biological species | Streptomyces pristinaespiralis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 1.87 Å | ||||||
Authors | Ying, H. / Chen, K. | ||||||
Funding support | China, 1items
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Citation | Journal: To Be Published Title: Cyclodeaminase_PA Authors: Ying, H. / Chen, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5gzj.cif.gz | 154.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5gzj.ent.gz | 122 KB | Display | PDB format |
PDBx/mmJSON format | 5gzj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5gzj_validation.pdf.gz | 985 KB | Display | wwPDB validaton report |
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Full document | 5gzj_full_validation.pdf.gz | 995.6 KB | Display | |
Data in XML | 5gzj_validation.xml.gz | 32.7 KB | Display | |
Data in CIF | 5gzj_validation.cif.gz | 47.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gz/5gzj ftp://data.pdbj.org/pub/pdb/validation_reports/gz/5gzj | HTTPS FTP |
-Related 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: 38106.141 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces pristinaespiralis (bacteria) Gene: pipA, SPRI_0308, SPRI_7045 / Plasmid: pET-28a / Production host: Eschirchia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: D9UBW0, ornithine cyclodeaminase #2: Chemical | #3: 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: 2.36 Å3/Da / Density % sol: 47.88 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 2%(v/v) polyethylene glycol 400, 0.1M HEPES |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5417 Å |
Detector | Type: RIGAKU SATURN 944 / Detector: IMAGE PLATE / Date: Aug 21, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5417 Å / Relative weight: 1 |
Reflection | Resolution: 1.87→50 Å / Num. obs: 59165 / % possible obs: 100 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 19.48 |
Reflection shell | Resolution: 1.87→1.9 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.481 / Mean I/σ(I) obs: 3.31 / % possible all: 100 |
-Processing
Software |
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Refinement | Resolution: 1.87→29.63 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.947 / SU B: 2.32 / SU ML: 0.072 / Cross valid method: THROUGHOUT / ESU R: 0.123 / ESU R Free: 0.119 / 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: 25.937 Å2
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Refinement step | Cycle: 1 / Resolution: 1.87→29.63 Å
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Refine LS restraints |
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