+Open data
-Basic information
Entry | Database: PDB / ID: 1nmn | ||||||
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Title | Structure of yqgF from Escherichia coli, a hypothetical protein | ||||||
Components | Hypothetical protein yqgF | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / hypothetical protein / yqgF / Structure 2 Function Project / S2F | ||||||
Function / homology | Function and homology information rRNA 5'-end processing / 3'-5'-DNA exonuclease activity / ribosome biogenesis / Hydrolases; Acting on ester bonds / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.3 Å | ||||||
Authors | Galkin, A. / Sarikaya, E. / Krajewski, W. / Howard, A. / Herzberg, O. / Structure 2 Function Project (S2F) | ||||||
Citation | Journal: To be Published Title: Structure of yqgF from Escherichia coli, a hypothetical protein Authors: Galkin, A. / Sarikaya, E. / Krajewski, W. / 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 | 1nmn.cif.gz | 59.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1nmn.ent.gz | 44.4 KB | Display | PDB format |
PDBx/mmJSON format | 1nmn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1nmn_validation.pdf.gz | 429.3 KB | Display | wwPDB validaton report |
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Full document | 1nmn_full_validation.pdf.gz | 434.9 KB | Display | |
Data in XML | 1nmn_validation.xml.gz | 13.3 KB | Display | |
Data in CIF | 1nmn_validation.cif.gz | 18.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nm/1nmn ftp://data.pdbj.org/pub/pdb/validation_reports/nm/1nmn | HTTPS FTP |
-Related structure data
-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: 15205.271 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: YQGF / Plasmid: pYQGF / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Star / References: UniProt: P0A8I1 #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: 2.1 Å3/Da / Density % sol: 41.38 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4 Details: 0.8 M sodium malonate, 0.1 M sodium acetate, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 0.9724 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 7, 2002 |
Radiation | Monochromator: Si(111) double crystal system / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9724 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→30 Å / Num. all: 11857 / Num. obs: 11857 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.043 / Net I/σ(I): 27.4 |
Reflection shell | Resolution: 2.3→2.38 Å / Rmerge(I) obs: 0.071 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 2.3→30 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 27 Å2 | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.38 Å
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