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Yorodumi- PDB-5jzo: Structure of wild type amidase at high temperature at 2.5 Angstro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5jzo | ||||||
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Title | Structure of wild type amidase at high temperature at 2.5 Angstrom resolution | ||||||
Components | Intracellular protease/amidase | ||||||
Keywords | LYASE / Heat Shock Protein | ||||||
Function / homology | Function and homology information D-lactate dehydratase / glyoxalase III activity / methylglyoxal catabolic process to D-lactate via S-lactoyl-glutathione / protein deglycase activity / DNA repair / cytoplasm Similarity search - Function | ||||||
Biological species | Vibrio cholerae serotype O1 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Chowdhury, S.R. / Sen, U. | ||||||
Citation | Journal: To Be Published Title: Structure of wild type amidase at high temperature at 2.5 Angstrom resolution Authors: Chowdhury, S.R. / Sen, U. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5jzo.cif.gz | 330.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5jzo.ent.gz | 269.5 KB | Display | PDB format |
PDBx/mmJSON format | 5jzo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5jzo_validation.pdf.gz | 469.4 KB | Display | wwPDB validaton report |
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Full document | 5jzo_full_validation.pdf.gz | 488.1 KB | Display | |
Data in XML | 5jzo_validation.xml.gz | 61.8 KB | Display | |
Data in CIF | 5jzo_validation.cif.gz | 85.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jz/5jzo ftp://data.pdbj.org/pub/pdb/validation_reports/jz/5jzo | HTTPS FTP |
-Related structure data
Related structure data | 1n57S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 31511.557 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio cholerae serotype O1 (strain ATCC 39541 / Classical Ogawa 395 / O395) (bacteria) Strain: ATCC 39541 / Classical Ogawa 395 / O395 / Gene: VC0395_0351, VC395_A0912 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0H3AFW5, D-lactate dehydratase #2: 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: 2.07 Å3/Da / Density % sol: 40.55 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 5% PEG 6000, 0.1M sodium citrate, 8% MPD against a reservoir solution of 15% PEG 6000, 0.1M tris-HCl, pH-8.5, 5% MPD. |
-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 7, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→29.668 Å / Num. obs: 49277 / % possible obs: 92.32 % / Redundancy: 1.94 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 1.39 |
Reflection shell | Resolution: 2.5→2.67 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1N57 Resolution: 2.5→29.668 Å / SU ML: 0.38 / Cross valid method: NONE / σ(F): 1.39 / Phase error: 28.09 / 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: 2.5→29.668 Å
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Refine LS restraints |
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LS refinement shell |
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