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Yorodumi- PDB-2icu: Crystal Structure of Hypothetical Protein YedK From Escherichia coli -
+Open data
-Basic information
Entry | Database: PDB / ID: 2icu | ||||||
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Title | Crystal Structure of Hypothetical Protein YedK From Escherichia coli | ||||||
Components | Hypothetical protein yedKHypothesis | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / HYPOTHETICAL PROTEIN YEDK / PSI / PROTEIN STRUCTURE INITIATIVE / SOUTHEAST COLLABORATORY FOR STRUCTURAL GENOMICS / SECSG / RIKEN / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information protein-DNA covalent cross-linking activity / Lyases / Hydrolases; Acting on peptide bonds (peptidases) / SOS response / single-stranded DNA binding / peptidase activity / DNA damage response / proteolysis Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å | ||||||
Authors | Chen, L. / Liu, Z.J. / Li, Y. / Zhao, M. / Rose, J. / Ebihara, A. / Yokoyama, S. / Wang, B.C. / Southeast Collaboratory for Structural Genomics (SECSG) / RIKEN Structural Genomics/Proteomics Initiative / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Crystal Structure of Hypothetical Protein YedK From Escherichia coli Authors: Chen, L. / Liu, Z.J. / Li, Y. / Zhao, M. / Rose, J. / Ebihara, A. / Yokoyama, S. / 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 | 2icu.cif.gz | 108.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2icu.ent.gz | 87.2 KB | Display | PDB format |
PDBx/mmJSON format | 2icu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ic/2icu ftp://data.pdbj.org/pub/pdb/validation_reports/ic/2icu | 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: 25715.273 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: yedK / Plasmid: PCR2.1-TOPO / Production host: Escherichia coli (E. coli) / References: UniProt: P76318 #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: 2.27 Å3/Da / Density % sol: 45.82 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.4 Details: 0.5 MICROLITER DROPS CONTAINING EQUAL VOLUMES OF PROTEIN CONCENTRATE (9.9 MG/ML) AND RESERVOIR SOLUTION CONTAINING 50% PEG 3350, 0.1M BIS-TRIS PH 6.4, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-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: Aug 24, 2006 / Details: ROSENBAUM |
Radiation | Monochromator: SI CHANNEL 220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9724 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→50 Å / Num. all: 56919 / Num. obs: 53997 / % possible obs: 94.1 % / Observed criterion σ(I): 2 / Redundancy: 6.8 % / Rsym value: 0.081 / Net I/σ(I): 27.09 |
Reflection shell | Resolution: 1.6→1.66 Å / Redundancy: 5.2 % / Mean I/σ(I) obs: 4.5 / Num. unique all: 4019 / Rsym value: 0.24 / % possible all: 67 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.6→18.59 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.94 / SU B: 1.518 / SU ML: 0.055 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.093 / ESU R Free: 0.091 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.729 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→18.59 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.64 Å / Total num. of bins used: 20
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