+Open data
-Basic information
Entry | Database: PDB / ID: 1ni3 | ||||||
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Title | Structure of the Schizosaccharomyces pombe YchF GTPase | ||||||
Components | YchF GTP-binding protein | ||||||
Keywords | HYDROLASE / STRUCTURAL GENOMICS / G-protein / GTPase / YCHF / GTP1OBG / PSI / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC | ||||||
Function / homology | Function and homology information Platelet degranulation / : / ribosomal large subunit binding / ribosome binding / GTP binding / ATP binding / metal ion binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Schizosaccharomyces pombe (fission yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / single wavelength / Resolution: 2.8 Å | ||||||
Authors | Kniewel, R.K. / Buglino, J.A. / Lima, C.D. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
Citation | Journal: To be Published Title: Structure of the S. pombe YchF GTP-binding protein Authors: Kniewel, R.K. / Buglino, J.A. / Lima, C.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ni3.cif.gz | 88.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ni3.ent.gz | 71.5 KB | Display | PDB format |
PDBx/mmJSON format | 1ni3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ni/1ni3 ftp://data.pdbj.org/pub/pdb/validation_reports/ni/1ni3 | 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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Unit cell |
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-Components
#1: Protein | Mass: 44770.051 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast) Gene: SPAC27E2.03C / Plasmid: pSUMO (pSMT3) / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: O13998 |
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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: 3.62 Å3/Da / Density % sol: 66.03 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 15% PEG 4000, 0.1M Sodium, Citrate pH 5.6, 0.1M Ammonium, Sulfate, 5%, Glycerol, Water , VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X9A / Wavelength: 0.979 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Nov 15, 2001 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→19.76 Å / Num. all: 15900 / Num. obs: 15709 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Biso Wilson estimate: 55.9 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 16.9 |
Reflection shell | Resolution: 2.8→2.9 Å / Rmerge(I) obs: 0.329 / Mean I/σ(I) obs: 3.5 / % possible all: 95.7 |
-Processing
Software |
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Refinement | Method to determine structure: single wavelength / Resolution: 2.8→19.76 Å / Rfactor Rfree error: 0.009 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 24.0602 Å2 / ksol: 0.281342 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 59.2 Å2
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Refine analyze | Luzzati coordinate error free: 0.44 Å / Luzzati sigma a free: 0.68 Å | ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→19.76 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.9 Å / Rfactor Rfree error: 0.047 / Total num. of bins used: 10
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Xplor file |
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