+Open data
-Basic information
Entry | Database: PDB / ID: 1x6j | ||||||
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Title | Crystal structure of ygfY from Escherichia coli | ||||||
Components | Hypothetical protein ygfY | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / ygfY / hypothetical protein / transcriptional regulation / Structure 2 Function Project / S2F | ||||||
Function / homology | Function and homology information respiratory chain complex II assembly / succinate metabolic process / cytoplasm Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Lim, K. / Doseeva, V. / Sarikaya Demirkan, E. / Pullalarevu, S. / Krajewski, W. / Galkin, A. / Howard, A. / Herzberg, O. / Structure 2 Function Project (S2F) | ||||||
Citation | Journal: Proteins / Year: 2005 Title: Crystal structure of the YgfY from Escherichia coli, a protein that may be involved in transcriptional regulation Authors: Lim, K. / Doseeva, V. / Sarikaya Demirkan, E. / Pullalarevu, S. / Krajewski, W. / Galkin, A. / Howard, A. / Herzberg, O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1x6j.cif.gz | 30.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1x6j.ent.gz | 19.8 KB | Display | PDB format |
PDBx/mmJSON format | 1x6j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1x6j_validation.pdf.gz | 425.7 KB | Display | wwPDB validaton report |
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Full document | 1x6j_full_validation.pdf.gz | 425.8 KB | Display | |
Data in XML | 1x6j_validation.xml.gz | 5.9 KB | Display | |
Data in CIF | 1x6j_validation.cif.gz | 7.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x6/1x6j ftp://data.pdbj.org/pub/pdb/validation_reports/x6/1x6j | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | monomer in solution |
-Components
#1: Protein | Mass: 10845.427 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ygfY / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Star (DE3) / References: UniProt: P64559 |
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#2: 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: 1.75 Å3/Da / Density % sol: 33.5 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 1.1 M sodium Malonate, 0.1 M Tris HCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.54179 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 1, 2003 |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54179 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 5225 / % possible obs: 97.1 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.059 / Net I/σ(I): 7.8 |
Reflection shell | Resolution: 2→2.07 Å / Rmerge(I) obs: 0.328 / Mean I/σ(I) obs: 2 / % possible all: 95.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→8 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 28 Å2 | ||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.07 Å / Rfactor Rfree: 0.297 / Rfactor Rwork: 0.185 |