+Open data
-Basic information
Entry | Database: PDB / ID: 5ha8 | |||||||||
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Title | Structure of a cysteine hydrolase | |||||||||
Components | Isochorismatase | |||||||||
Keywords | HYDROLASE / catalyic triad | |||||||||
Function / homology | : / Isochorismatase-like / Isochorismatase-like superfamily / Isochorismatase family / hydrolase activity / Isochorismatase Function and homology information | |||||||||
Biological species | Microbacterium hydrocarbonoxydans (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.054 Å | |||||||||
Authors | Gao, S. / Feng, Y. | |||||||||
Funding support | China, 2items
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Citation | Journal: To Be Published Title: Structure of a cysteine hydrolase Authors: Gao, S. / Feng, Y. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ha8.cif.gz | 49.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ha8.ent.gz | 33.9 KB | Display | PDB format |
PDBx/mmJSON format | 5ha8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ha8_validation.pdf.gz | 402.5 KB | Display | wwPDB validaton report |
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Full document | 5ha8_full_validation.pdf.gz | 402.5 KB | Display | |
Data in XML | 5ha8_validation.xml.gz | 9.6 KB | Display | |
Data in CIF | 5ha8_validation.cif.gz | 13.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ha/5ha8 ftp://data.pdbj.org/pub/pdb/validation_reports/ha/5ha8 | 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 20457.863 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Microbacterium hydrocarbonoxydans (bacteria) Production host: Escherichia coli (E. coli) / References: UniProt: A0A0K0XHU0 |
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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: 3 Å3/Da / Density % sol: 58.96 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion / pH: 6 / Details: sodium malonate (pH 6.0), polyethylene glycol 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17B1 / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 22, 2015 |
Radiation | Protocol: LAUE / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→50 Å / Num. obs: 15793 / % possible obs: 100 % / Redundancy: 13.1 % / Net I/σ(I): 39.75 |
-Processing
Software |
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Refinement | Resolution: 2.054→35.526 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 19.41 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.054→35.526 Å
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Refine LS restraints |
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LS refinement shell |
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