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Yorodumi- PDB-2o0q: X-ray Crystal Structure of Protein CC0527 from Caulobacter cresce... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2o0q | ||||||
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Title | X-ray Crystal Structure of Protein CC0527 from Caulobacter crescentus. Northeast Structural Genomics Consortium Target CcR55 | ||||||
Components | Hypothetical protein CC0527Hypothesis | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / PSI / PROTEIN STRUCTURE INITIATIVE / NORTHEAST STRUCTURAL GENOMICS CONSORTIUM / NESG / Hypothetical protein CC0527 | ||||||
Function / homology | Protein of unknown function DUF952 / Protein of unknown function DUF952 / Protein of unknown function (DUF952) / ADP-ribosylation fold / Alpha-Beta Barrel / Alpha Beta / DUF952 domain-containing protein Function and homology information | ||||||
Biological species | Caulobacter vibrioides (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Seetharaman, J. / Su, M. / Wang, D. / Fang, Y. / Cunningham, K. / Ma, L. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T.B. ...Seetharaman, J. / Su, M. / Wang, D. / Fang, Y. / Cunningham, K. / Ma, L. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG) | ||||||
Citation | Journal: TO BE PUBLISHED Title: Crystal Structure of the Hypothetical Protein from Caulobacter Crescentus. Authors: Seetharaman, J. / Su, M. / Wang, D. / Fang, Y. / Cunningham, K. / Ma, L. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2o0q.cif.gz | 37.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2o0q.ent.gz | 25 KB | Display | PDB format |
PDBx/mmJSON format | 2o0q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o0/2o0q ftp://data.pdbj.org/pub/pdb/validation_reports/o0/2o0q | HTTPS FTP |
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-Related structure data
Related structure data | 2o0pSC S: Starting model for refinement C: citing same article (ref.) |
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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: 12571.089 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Caulobacter vibrioides (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9AAR9 |
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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: 4.07 Å3/Da / Density % sol: 69.79 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 0.2M Sodium acetate, 0.1M Sodium Citrate, PGE 4000 , pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.978 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 10, 2006 / Details: Mirrors |
Radiation | Monochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. obs: 31132 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Biso Wilson estimate: 9.9 Å2 / Rmerge(I) obs: 0.07 / Rsym value: 0.054 / Net I/σ(I): 11.4 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.369 / Mean I/σ(I) obs: 9.4 / Num. unique all: 3267 / Rsym value: 0.334 / % possible all: 88.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2O0P Resolution: 1.8→32.98 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 83262.25 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 41.6208 Å2 / ksol: 0.390814 e/Å3 | ||||||||||||||||||||
Displacement parameters | Biso mean: 21.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→32.98 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.91 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
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Xplor file |
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