+Open data
-Basic information
Entry | Database: PDB / ID: 1kk9 | ||||||
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Title | CRYSTAL STRUCTURE OF E. COLI YCIO | ||||||
Components | probable translation factor yciO | ||||||
Keywords | UNKNOWN FUNCTION / alpha/beta open twisted sheet / Montreal-Kingston Bacterial Structural Genomics Initiative / BSGI / Structural Genomics | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å | ||||||
Authors | Jia, J. / Lunin, V.V. / Sauve, V. / Huang, L.-W. / Matte, A. / Cygler, M. / Montreal-Kingston Bacterial Structural Genomics Initiative (BSGI) | ||||||
Citation | Journal: PROTEINS: STRUCT.,FUNCT.,GENET. / Year: 2002 Title: Crystal structure of the YciO protein from Escherichia coli Authors: Jia, J. / Lunin, V.V. / Sauve, V. / Huang, L.-W. / Matte, A. / Cygler, M. #1: Journal: Protein Sci. / Year: 2000 Title: The structure of the Yrdc gene product from E.coli Authors: Teplova, M. / Tereshko, R. / Sanishvili, A. / Joachimiak, A. / Bushueva, T. / Anderson, W.F. / Egli, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1kk9.cif.gz | 53.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1kk9.ent.gz | 40.8 KB | Display | PDB format |
PDBx/mmJSON format | 1kk9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1kk9_validation.pdf.gz | 442.7 KB | Display | wwPDB validaton report |
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Full document | 1kk9_full_validation.pdf.gz | 445.9 KB | Display | |
Data in XML | 1kk9_validation.xml.gz | 11.5 KB | Display | |
Data in CIF | 1kk9_validation.cif.gz | 15.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kk/1kk9 ftp://data.pdbj.org/pub/pdb/validation_reports/kk/1kk9 | HTTPS FTP |
-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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Unit cell |
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-Components
#1: Protein | Mass: 25190.631 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ycio / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P45847, UniProt: P0AFR4*PLUS |
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#2: Chemical | ChemComp-SO4 / |
#3: 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: 3.47 Å3/Da / Density % sol: 64.6 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: PEG 3350, MES, magnesium acetate, ethylene glycol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 0.97921,0.97942,0.95369 | ||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 2, 2001 | ||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.1→50 Å / Num. all: 19133 / Num. obs: 18736 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Redundancy: 10.7 % / Rsym value: 0.068 / Net I/σ(I): 10.4 | ||||||||||||
Reflection shell | Resolution: 2.1→2.18 Å / Num. unique all: 1869 / Rsym value: 0.422 / % possible all: 100 | ||||||||||||
Reflection | *PLUS Lowest resolution: 50 Å / Num. obs: 19133 / Num. measured all: 205748 / Rmerge(I) obs: 0.068 | ||||||||||||
Reflection shell | *PLUS Highest resolution: 2.1 Å / % possible obs: 99.9 % / Rmerge(I) obs: 0.422 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.1→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh and Huber
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Refinement step | Cycle: LAST / Resolution: 2.1→50 Å
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Refine LS restraints |
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Refinement | *PLUS Lowest resolution: 50 Å / Rfactor Rfree: 0.229 / Rfactor Rwork: 0.211 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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