+Open data
-Basic information
Entry | Database: PDB / ID: 2cxx | ||||||
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Title | Crystal structure of a probable GTP-binding protein engB | ||||||
Components | Probable GTP-binding protein engB | ||||||
Keywords | CELL CYCLE / GTP-binding protein / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Pyrococcus horikoshii (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å | ||||||
Authors | Kukimoto-Niino, M. / Murayama, K. / Shirouzu, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Crystal structure of a probable GTP-binding protein engB Authors: Kukimoto-Niino, M. / Murayama, K. / Shirouzu, M. / Yokoyama, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2cxx.cif.gz | 130.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2cxx.ent.gz | 107.7 KB | Display | PDB format |
PDBx/mmJSON format | 2cxx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cx/2cxx ftp://data.pdbj.org/pub/pdb/validation_reports/cx/2cxx | 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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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 22250.543 Da / Num. of mol.: 3 / Fragment: residues 1-190 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Strain: OT3 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: O57939 #2: Chemical | #3: 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: 36.667076 % |
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Crystal grow | Temperature: 300 K / Method: vapor diffusion, hanging drop / pH: 6 Details: PEG4000, magnesium sulfate, MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 300K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 0.979117 Å |
Detector | Detector: CCD / Date: May 25, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979117 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→50 Å / Num. obs: 55008 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 7.3918 % / Biso Wilson estimate: 15.4 Å2 / Rsym value: 0.077 / Net I/σ(I): 23.9457 |
Reflection shell | Resolution: 1.7→1.76 Å / Mean I/σ(I) obs: 3.52895 / Rsym value: 0.302 / % possible all: 95 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.7→19.06 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 864960.61 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 39.1108 Å2 / ksol: 0.329702 e/Å3 | ||||||||||||||||||||
Displacement parameters | Biso mean: 18.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.7→19.06 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.81 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
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Xplor file |
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