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Yorodumi- PDB-2e12: The crystal structure of XC5848 from Xanthomonas campestris adopt... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2000000000000 | ||||||
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Title | The crystal structure of XC5848 from Xanthomonas campestris adopting a novel variant of Sm-like motif | ||||||
Components | Hypothetical protein XCC3642Hypothesis | ||||||
Keywords | TRANSLATION / novel Sm-like motif / Lsm motif / Xanthomonas campestris | ||||||
Function / homology | Protein of unknown function (DUF3247) / Protein of unknown function DUF3247 / Protein of unknown function (DUF3247) / SH3 type barrels. / Roll / Mainly Beta / Uncharacterized protein Function and homology information | ||||||
Biological species | Xanthomonas campestris pv. campestris (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å | ||||||
Authors | Chin, K.-H. / Ruan, S.-K. / Wang, A.H.-J. / Chou, S.-H. | ||||||
Citation | Journal: Proteins / Year: 2007 Title: XC5848, an ORFan protein from Xanthomonas campestris, adopts a novel variant of Sm-like motif Authors: Chin, K.-H. / Ruan, S.-K. / Wang, A.H.-J. / Chou, S.-H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2e12.cif.gz | 45.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2e12.ent.gz | 32.5 KB | Display | PDB format |
PDBx/mmJSON format | 2e12.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e1/2e12 ftp://data.pdbj.org/pub/pdb/validation_reports/e1/2e12 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 11571.090 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xanthomonas campestris pv. campestris (bacteria) Species: Xanthomonas campestris / Strain: pv. campestris / Production host: Escherichia coli (E. coli) / References: UniProt: Q8P4R5 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 10 |
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-Sample preparation
Crystal | Density Matthews: 2.29 Å3/Da / Density % sol: 46.26 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8 Details: pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 0.96437, 0.97983 | |||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 28, 2006 | |||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 1.7→30 Å / Num. obs: 6937 / % possible obs: 99.7 % / Observed criterion σ(F): 5 / Observed criterion σ(I): 2 / Redundancy: 4.5 % / Biso Wilson estimate: 24 Å2 / Rmerge(I) obs: 0.24 / Rsym value: 0.06 / Net I/σ(I): 8 | |||||||||
Reflection shell | Highest resolution: 1.7 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 7.9 / Num. unique all: 6937 / Rsym value: 0.24 / % possible all: 97.5 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.7→30 Å / Cross valid method: THROUGHOUT / σ(F): 5 / σ(I): 2
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Refinement step | Cycle: LAST / Resolution: 1.7→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.75 Å / Rfactor Rfree error: 0.012
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