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Yorodumi- PDB-2cjw: Crystal structure of the small GTPase Gem (GemDNDCaM) in complex ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2cjw | ||||||
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Title | Crystal structure of the small GTPase Gem (GemDNDCaM) in complex to Mg.GDP | ||||||
Components | (GTP-BINDING PROTEIN GEM) x 2 | ||||||
Keywords | G-PROTEIN / NUCLEOTIDE-BINDING / GTP-BINDING / SMALL GTPASE / CONFORMATIONAL CHANGE / CYSTEINE-MODIFIED / G-PROTEIN HYDROLASE | ||||||
Function / homology | Function and homology information metaphase chromosome alignment / calcium channel regulator activity / chromosome organization / spindle midzone / NPAS4 regulates expression of target genes / cytoplasmic side of plasma membrane / mitotic spindle / GDP binding / mitotic cell cycle / midbody ...metaphase chromosome alignment / calcium channel regulator activity / chromosome organization / spindle midzone / NPAS4 regulates expression of target genes / cytoplasmic side of plasma membrane / mitotic spindle / GDP binding / mitotic cell cycle / midbody / cell surface receptor signaling pathway / calmodulin binding / immune response / GTPase activity / GTP binding / magnesium ion binding / signal transduction / nucleus / plasma membrane Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Splingard, A. / Menetrey, J. / Perderiset, M. / Cicolari, J. / Hamoudi, F. / Cabanie, L. / El Marjou, A. / Wells, A. / Houdusse, A. / de Gunzburg, J. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2007 Title: Biochemical and Structural Characterization of the Gem Gtpase. Authors: Splingard, A. / Menetrey, J. / Perderiset, M. / Cicolari, J. / Regazzoni, K. / Hamoudi, F. / Cabanie, L. / El Marjou, A. / Wells, A. / Houdusse, A. / De Gunzburg, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2cjw.cif.gz | 92.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2cjw.ent.gz | 68.6 KB | Display | PDB format |
PDBx/mmJSON format | 2cjw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cj/2cjw ftp://data.pdbj.org/pub/pdb/validation_reports/cj/2cjw | HTTPS FTP |
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-Related structure data
Related structure data | 1kaoS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 22431.904 Da / Num. of mol.: 1 / Fragment: G DOMAIN, RESIDUES 74-261 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P55040 | ||||||
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#2: Protein | Mass: 22431.904 Da / Num. of mol.: 1 / Fragment: G DOMAIN, RESIDUES 74-261 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P55040 | ||||||
#3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Sequence details | RESIDUES 70-72 (EFG) IN MOLECULE B BELONG TO THE REMAINING PART OF THE TAG. | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.65 Å3/Da / Density % sol: 66.3 % |
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Crystal grow | Details: 0.1M NACACODYLATE PH6.5, 0.9M NAACETATE, 5MM MGCL2 AND 2MM DTT |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.96115 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Sep 8, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.96115 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→60 Å / Num. obs: 36826 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 7.7 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 19 |
Reflection shell | Resolution: 2.1→2.21 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.342 / Mean I/σ(I) obs: 5.3 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1KAO Resolution: 2.1→60 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.918 / SU B: 3.452 / SU ML: 0.096 / Cross valid method: THROUGHOUT / ESU R: 0.168 / ESU R Free: 0.156 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 102-105 AND 136-139 IN MOLECULE A AND RESIDUES 99-110 AND 136-142 IN MOLECULE B WERE DISORDERED AND NOT MODELED. SOME SIDE-CHAINS ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 102-105 AND 136-139 IN MOLECULE A AND RESIDUES 99-110 AND 136-142 IN MOLECULE B WERE DISORDERED AND NOT MODELED. SOME SIDE-CHAINS WERE MODELED WITH 0.0 OR PARTIAL OCCUPANCY RATE.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.22 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→60 Å
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