+Open data
-Basic information
Entry | Database: PDB / ID: 2cx6 | ||||||
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Title | Crystal structure of ribonuclease inhibitor Barstar | ||||||
Components | Hypothetical protein yhcOHypothesis | ||||||
Keywords | HYDROLASE INHIBITOR / Barstar / ribonuclease inhibitor / RSGI / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative | ||||||
Function / homology | Barstar-like / Barstar (barnase inhibitor) / Barstar (barnase inhibitor) / Barstar-like superfamily / Barnase; Chain D / 2-Layer Sandwich / Alpha Beta / Uncharacterized protein YhcO Function and homology information | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.43 Å | ||||||
Authors | Murayama, K. / Kawazoe, M. / Shirouzu, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Crystal structure of ribonuclease inhibitor Barstar Authors: Murayama, K. / Kawazoe, M. / Shirouzu, M. / Yokoyama, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2cx6.cif.gz | 45.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2cx6.ent.gz | 36.8 KB | Display | PDB format |
PDBx/mmJSON format | 2cx6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cx/2cx6 ftp://data.pdbj.org/pub/pdb/validation_reports/cx/2cx6 | 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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-Components
#1: Protein | Mass: 10902.902 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: O157:H7 / Gene: yhcO / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: P64618 #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: 2.69 Å3/Da / Density % sol: 54.29 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 1.7M Sodium formate, 0.1M Sodium acetate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 0.9792, 0.9795, 0.964 | ||||||||||||
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Jul 24, 2004 | ||||||||||||
Radiation | Monochromator: Si 111 CHANNEL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.43→50 Å / Num. obs: 9619 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 8.9 % / Biso Wilson estimate: 29.4 Å2 / Rsym value: 0.062 / Net I/σ(I): 27.7 | ||||||||||||
Reflection shell | Resolution: 2.43→2.52 Å / Rsym value: 0.232 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.43→49.13 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 1287230.85 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 36.8107 Å2 / ksol: 0.362069 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 45.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.43→49.13 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.43→2.58 Å / Rfactor Rfree error: 0.035 / Total num. of bins used: 6
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Xplor file |
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