+Open data
-Basic information
Entry | Database: PDB / ID: 5gzl | ||||||
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Title | Cyclodeaminase_PA | ||||||
Components | Lysine cyclodeaminase | ||||||
Keywords | LYASE / dimer / complex / cyclization / deamination | ||||||
Function / homology | Function and homology information ornithine cyclodeaminase activity / ornithine cyclodeaminase / thyroid hormone metabolic process / thyroid hormone binding / nucleotide binding / cytoplasm Similarity search - Function | ||||||
Biological species | Streptomyces pristinaespiralis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2 Å | ||||||
Authors | Ying, H. / Chen, K. | ||||||
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 | 5gzl.cif.gz | 156.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5gzl.ent.gz | 122.8 KB | Display | PDB format |
PDBx/mmJSON format | 5gzl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5gzl_validation.pdf.gz | 991.4 KB | Display | wwPDB validaton report |
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Full document | 5gzl_full_validation.pdf.gz | 996.2 KB | Display | |
Data in XML | 5gzl_validation.xml.gz | 32.7 KB | Display | |
Data in CIF | 5gzl_validation.cif.gz | 48.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gz/5gzl ftp://data.pdbj.org/pub/pdb/validation_reports/gz/5gzl | 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: Escherichia coli (E. coli) / References: UniProt: D9UBW0, ornithine cyclodeaminase #2: Chemical | #3: Chemical | #4: 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: 2.31 Å3/Da / Density % sol: 46.7 % |
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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: 1.54178 Å |
Detector | Type: RIGAKU SATURN 944 / Detector: IMAGE PLATE / Date: Sep 1, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 47575 / % possible obs: 99.9 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.102 / Net I/σ(I): 18.68 |
Reflection shell | Resolution: 2→2.03 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.491 / Mean I/σ(I) obs: 4.4 / % possible all: 100 |
-Processing
Software |
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Refinement | Resolution: 2→49.76 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.95 / SU B: 2.684 / SU ML: 0.079 / Cross valid method: THROUGHOUT / ESU R: 0.147 / ESU R Free: 0.136 / 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: 22.733 Å2
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Refinement step | Cycle: 1 / Resolution: 2→49.76 Å
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Refine LS restraints |
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