+Open data
-Basic information
Entry | Database: PDB / ID: 5hwh | ||||||
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Title | Structure of a cysteine hydrolase with a positive substrate | ||||||
Components | Isochorismatase | ||||||
Keywords | HYDROLASE / catalyic triad | ||||||
Function / homology | Isochorismatase-like / Isochorismatase-like superfamily / Isochorismatase family / hydrolase activity / (1~{S},4~{R})-3-azabicyclo[2.2.1]hept-5-en-2-one / Isochorismatase Function and homology information | ||||||
Biological species | Microbacterium hydrocarbonoxydans (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.79 Å | ||||||
Authors | Feng, Y. / Gao, S. | ||||||
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 | 5hwh.cif.gz | 52.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5hwh.ent.gz | 36.3 KB | Display | PDB format |
PDBx/mmJSON format | 5hwh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hw/5hwh ftp://data.pdbj.org/pub/pdb/validation_reports/hw/5hwh | HTTPS FTP |
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-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: 20425.797 Da / Num. of mol.: 1 / Mutation: C111A 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: Chemical | ChemComp-66Z / ( |
#3: 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: 2.96 Å3/Da / Density % sol: 58.5 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / Details: PEG 3350, sodium malonate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 8, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.79→50 Å / Num. obs: 26655 / % possible obs: 98.2 % / Redundancy: 11.1 % / Net I/σ(I): 32.7 |
-Processing
Software |
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Refinement | Resolution: 1.79→24.75 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.93 / Phase error: 20.71 / 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: 1.79→24.75 Å
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Refine LS restraints |
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LS refinement shell |
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