+Open data
-Basic information
Entry | Database: PDB / ID: 2hiq | ||||||
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Title | Crystal structure of JW1657 from Escherichia coli | ||||||
Components | Hypothetical protein ydhR | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / HYPOTHETICAL PROTEIN JW1657 / PSI / Protein Structure Initiative / Southeast Collaboratory for Structural Genomics / SECSG | ||||||
Function / homology | Function and homology information Oxidoreductases / oxidoreductase activity / protein homodimerization activity / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å | ||||||
Authors | Chen, L.Q. / Chen, L.R. / Liu, Z.-J. / Temple, W. / Lee, D. / Chang, S.-H. / Rose, J.P. / Ebihara, A. / Wang, B.-C. / Southeast Collaboratory for Structural Genomics (SECSG) | ||||||
Citation | Journal: To be Published Title: Crystal structure of JW1657 from Escherichia coli at 2.0A resolution Authors: Chen, L.Q. / Chen, L.R. / Liu, Z.-J. / Temple, W. / Lee, D. / Chang, S.-H. / Rose, J.P. / Ebihara, A. / Wang, B.-C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2hiq.cif.gz | 50.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2hiq.ent.gz | 36.9 KB | Display | PDB format |
PDBx/mmJSON format | 2hiq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2hiq_validation.pdf.gz | 423.6 KB | Display | wwPDB validaton report |
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Full document | 2hiq_full_validation.pdf.gz | 426.7 KB | Display | |
Data in XML | 2hiq_validation.xml.gz | 10.5 KB | Display | |
Data in CIF | 2hiq_validation.cif.gz | 13.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hi/2hiq ftp://data.pdbj.org/pub/pdb/validation_reports/hi/2hiq | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 12513.216 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ydhR / Plasmid: PCA24N / Production host: Escherichia coli (E. coli) / References: UniProt: Q2MB61, UniProt: P0ACX3*PLUS #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: 3.99 Å3/Da / Density % sol: 69.19 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 6.6 Details: 100 mM Sodium Cacodylate, 2.5 M Ammonium Sulfate, pH 6.6, VAPOR DIFFUSION, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.9724 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 2, 2006 / Details: Rosenbaum |
Radiation | Monochromator: SI220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9724 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. all: 27533 / Num. obs: 27533 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.1 % / Biso Wilson estimate: 15.5 Å2 / Rmerge(I) obs: 0.074 / Rsym value: 0.074 / Net I/σ(I): 17.9 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 11.8 % / Rmerge(I) obs: 0.476 / Mean I/σ(I) obs: 7.2 / Num. unique all: 2721 / Rsym value: 0.476 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2→19.96 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 251092.76 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 42.8365 Å2 / ksol: 0.360105 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→19.96 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
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Xplor file |
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