+Open data
-Basic information
Entry | Database: PDB / ID: 1lnz | ||||||
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Title | Structure of the Obg GTP-binding protein | ||||||
Components | SPO0B-associated GTP-binding protein | ||||||
Keywords | CELL CYCLE / GTPase / Obg / stringent factor / stress response / sporulation / large G-protein / Structural Genomics / PSI / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC | ||||||
Function / homology | Function and homology information sporulation resulting in formation of a cellular spore / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / ribosome biogenesis / GTPase activity / GTP binding / magnesium ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Bacillus subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.6 Å | ||||||
Authors | Buglino, J. / Shen, V. / Hakimian, P. / Lima, C.D. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
Citation | Journal: Structure / Year: 2002 Title: Structural and biochemical analysis of the Obg GTP binding protein Authors: Buglino, J. / Shen, V. / Hakimian, P. / 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 | 1lnz.cif.gz | 149.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1lnz.ent.gz | 122.9 KB | Display | PDB format |
PDBx/mmJSON format | 1lnz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ln/1lnz ftp://data.pdbj.org/pub/pdb/validation_reports/ln/1lnz | 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 38109.434 Da / Num. of mol.: 2 / Fragment: residues 1- 342 of P20964 / Mutation: selenomethionine substituted Source method: isolated from a genetically manipulated source Details: Full-length protein, residues 1-428, was purified and prepartively proteolyzed with subtilisin to obtain the 1-342 fragment Source: (gene. exp.) Bacillus subtilis (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P20964 #2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-G4P / | #4: 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: 2.55 Å3/Da / Density % sol: 51.68 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 7-12% isopropanol, 0.1M magnesium chloride, 0.05M sodium cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP at 291K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: APS / Beamline: 19-ID / Wavelength: 0.9794 Å |
Detector | Type: CUSTOM-MADE / Detector: CCD / Date: Apr 24, 2000 / Details: undulator, mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→25 Å / Num. all: 24613 / Num. obs: 24465 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 27 Å2 |
Reflection | *PLUS Lowest resolution: 25 Å / Num. obs: 38652 / % possible obs: 82.5 % / Num. measured all: 70639 / Rmerge(I) obs: 0.079 |
Reflection shell | *PLUS % possible obs: 46.5 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 2.3 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.6→19.89 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 3009010.75 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: BULK SOLVENT MODEL USED. Structure factors obtained from SHARP, no experimental sigmas
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 33.681 Å2 / ksol: 0.254047 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.6 Å2
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Refine analyze | Luzzati coordinate error free: 0.44 Å / Luzzati sigma a free: 0.69 Å | ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→19.89 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.76 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 2.6 Å / Lowest resolution: 25 Å / % reflection Rfree: 5 % / Rfactor obs: 0.203 / Rfactor Rfree: 0.293 / Rfactor Rwork: 0.204 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.387 / Rfactor Rwork: 0.309 |