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Yorodumi- PDB-3hcz: The crystal structure of a domain of possible thiol-disulfide iso... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3hcz | ||||||
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Title | The crystal structure of a domain of possible thiol-disulfide isomerase from Cytophaga hutchinsonii ATCC 33406. | ||||||
Components | Possible thiol-disulfide isomerase | ||||||
Keywords | structural genomics / unknown function / APC61559.2 / thiol-disulfide isomerase / Cytophaga hutchinsonii ATCC / PSI-2 / protein structure initiative / midwest center for structural genomics / MCSG / Isomerase | ||||||
Function / homology | Function and homology information : / antioxidant activity / isomerase activity / cell redox homeostasis / oxidoreductase activity Similarity search - Function | ||||||
Biological species | Cytophaga hutchinsonii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.88 Å | ||||||
Authors | Tan, K. / Marshall, N. / Cobb, G. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: The crystal structure of a domain of possible thiol-disulfide isomerase from Cytophaga hutchinsonii ATCC 33406. Authors: Tan, K. / Marshall, N. / Cobb, G. / Joachimiak, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3hcz.cif.gz | 44.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3hcz.ent.gz | 34.4 KB | Display | PDB format |
PDBx/mmJSON format | 3hcz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hc/3hcz ftp://data.pdbj.org/pub/pdb/validation_reports/hc/3hcz | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Details | Experimentally unknown. It is predicted that the domain is monomeric. |
-Components
#1: Protein | Mass: 17620.074 Da / Num. of mol.: 1 / Fragment: residues 330-474 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cytophaga hutchinsonii (bacteria) / Strain: ATCC 33406 / Gene: CHU_0134, Cytophaga hutchinsonii / Plasmid: pMCSG19 / Production host: Escherichia coli (E. coli) / Strain (production host): pPK1037 / References: UniProt: Q11YT9 | ||||
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#2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-FMT / | #4: 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: 2.71 Å3/Da / Density % sol: 54.55 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.2 M Ammonium Sulfate, 0.1 M MES, 30% Peg 5000 MME, 3% 1,6-diaminohexane, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97926 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 10, 2008 / Details: mirror |
Radiation | Monochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97926 Å / Relative weight: 1 |
Reflection | Resolution: 1.88→33.4 Å / Num. all: 16600 / Num. obs: 16600 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 40.6 |
Reflection shell | Resolution: 1.88→1.91 Å / Redundancy: 12 % / Rmerge(I) obs: 0.876 / Mean I/σ(I) obs: 3.3 / Num. unique all: 816 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.88→33.39 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.95 / SU B: 6.498 / SU ML: 0.086 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.129 / ESU R Free: 0.126 / 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: 21.056 Å2
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Refinement step | Cycle: LAST / Resolution: 1.88→33.39 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.876→1.925 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 11.728 Å / Origin y: -4.878 Å / Origin z: 15.215 Å
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