+Open data
-Basic information
Entry | Database: PDB / ID: 1k7j | ||||||
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Title | Structural Genomics, protein TF1 | ||||||
Components | Protein yciO | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / yciO / putative translation factor / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.4 Å | ||||||
Authors | Zhang, R. / Dementieva, I. / Thorn, J. / Donnelly, M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: Structural Genomics, protein TF1 Authors: Zhang, R. / Dementieva, I. / Thorn, J. / Donnelly, M. / Joachimiak, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1k7j.cif.gz | 54.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1k7j.ent.gz | 42.4 KB | Display | PDB format |
PDBx/mmJSON format | 1k7j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1k7j_validation.pdf.gz | 375.8 KB | Display | wwPDB validaton report |
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Full document | 1k7j_full_validation.pdf.gz | 377.7 KB | Display | |
Data in XML | 1k7j_validation.xml.gz | 5.9 KB | Display | |
Data in CIF | 1k7j_validation.cif.gz | 9.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k7/1k7j ftp://data.pdbj.org/pub/pdb/validation_reports/k7/1k7j | 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: 23568.027 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: MC1061 / Gene: yciO / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / 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: 2.62 Å3/Da / Density % sol: 53.07 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 30% Ammonium sulfate, 0.1M Na citrate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9795, 0.9798, 0.94656 | ||||||||||||
Detector | Type: SBC-2 / Detector: CCD / Date: Aug 22, 2001 / Details: mirrors | ||||||||||||
Radiation | Monochromator: Si 111 CHANNEL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.4→50 Å / Num. all: 49767 / Num. obs: 49419 / % possible obs: 99.3 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 2 / Redundancy: 12.57 % / Biso Wilson estimate: 11.1 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 27.03 | ||||||||||||
Reflection shell | Resolution: 1.4→1.45 Å / Redundancy: 4.28 % / Rmerge(I) obs: 0.293 / Mean I/σ(I) obs: 2.63 / Num. unique all: 4679 / % possible all: 95.2 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.4→45.84 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 409500.45 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 Details: Used mlhl:maximum likelihood target using amplitudes in CNS
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 45.435 Å2 / ksol: 0.394199 e/Å3 | ||||||||||||||||||||
Displacement parameters | Biso mean: 15.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.4→45.84 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.4→1.49 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
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Xplor file |
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