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Yorodumi- PDB-3qh7: 2.5 A resolution structure of Se-Met labeled CT296 from Chlamydia... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3qh7 | ||||||
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Title | 2.5 A resolution structure of Se-Met labeled CT296 from Chlamydia trachomatis | ||||||
Components | CT296 | ||||||
Keywords | UNKNOWN FUNCTION / CT296 / Iron / modeling / Chlamydia | ||||||
Function / homology | Domain of unknown function (DUF5070) / Protein of unknown function DUF5070 / Domain of unknown function (DUF5070) / Thiol Ester Dehydrase; Chain A / Roll / Alpha Beta / Uncharacterized protein / Uncharacterized protein Function and homology information | ||||||
Biological species | Chlamydia trachomatis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.497 Å | ||||||
Authors | Kemege, K. / Hickey, J. / Lovell, S. / Battaile, K.P. / Zhang, Y. / Hefty, P.S. | ||||||
Citation | Journal: J. Bacteriol. / Year: 2011 Title: Ab initio structural modeling of and experimental validation for Chlamydia trachomatis protein CT296 reveal structural similarity to Fe(II) 2-oxoglutarate-dependent enzymes. Authors: Kemege, K.E. / Hickey, J.M. / Lovell, S. / Battaile, K.P. / Zhang, Y. / Hefty, P.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3qh7.cif.gz | 37.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3qh7.ent.gz | 27.7 KB | Display | PDB format |
PDBx/mmJSON format | 3qh7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3qh7_validation.pdf.gz | 423.1 KB | Display | wwPDB validaton report |
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Full document | 3qh7_full_validation.pdf.gz | 426.3 KB | Display | |
Data in XML | 3qh7_validation.xml.gz | 7.7 KB | Display | |
Data in CIF | 3qh7_validation.cif.gz | 9.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qh/3qh7 ftp://data.pdbj.org/pub/pdb/validation_reports/qh/3qh7 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 18216.473 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chlamydia trachomatis (bacteria) / Strain: L2/434/Bu / Gene: CTL0548 / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B0B7L2, UniProt: A0A0H3MBY2*PLUS |
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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: 2.05 Å3/Da / Density % sol: 40.11 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion / pH: 7 Details: 0.1 M HEPES, 15 % PEG 20000, pH 7.0, VAPOR DIFFUSION, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 0.9793 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 1, 2010 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.497→63.663 Å / Num. all: 5585 / Num. obs: 5585 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 11.8 % / Rsym value: 0.118 / Net I/σ(I): 18 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: SAD |
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.497→39.721 Å / Occupancy max: 1 / Occupancy min: 0.79 / SU ML: 0.29 / σ(F): 1.46 / Phase error: 28.36 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.65 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 20 Å2 / ksol: 0.382 e/Å3 | ||||||||||||||||||||||||||||
Displacement parameters | Biso max: 68.97 Å2 / Biso mean: 34.0823 Å2 / Biso min: 16.13 Å2
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Refinement step | Cycle: LAST / Resolution: 2.497→39.721 Å
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Refine LS restraints |
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