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Yorodumi- PDB-2xtm: Crystal structure of GDP-bound human GIMAP2, amino acid residues ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2xtm | ||||||
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Title | Crystal structure of GDP-bound human GIMAP2, amino acid residues 1- 234 | ||||||
Components | GTPASE IMAP FAMILY MEMBER 2 | ||||||
Keywords | IMMUNE SYSTEM / G PROTEIN | ||||||
Function / homology | Function and homology information lipid droplet / GTP binding / endoplasmic reticulum / nucleoplasm / identical protein binding Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Schwefel, D. / Froehlich, C. / Daumke, O. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2010 Title: Structural Basis of Oligomerization in Septin-Like Gtpase of Immunity-Associated Protein 2 (Gimap2) Authors: Schwefel, D. / Froehlich, C. / Eichhorst, J. / Wiesner, B. / Behlke, J. / Aravind, L. / Daumke, O. #1: Journal: Acta Crystallogr.,Sect.F / Year: 2010 Title: Purification, Crystallization and Preliminary X- Ray Analysis of Human Gimap2. Authors: Schwefel, D. / Frohlich, C. / Daumke, O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2xtm.cif.gz | 176.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2xtm.ent.gz | 140.9 KB | Display | PDB format |
PDBx/mmJSON format | 2xtm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xt/2xtm ftp://data.pdbj.org/pub/pdb/validation_reports/xt/2xtm | HTTPS FTP |
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-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: 25887.150 Da / Num. of mol.: 2 / Fragment: RESIDUES 1-234 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PGEX6P1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ROSETTA / References: UniProt: Q9UG22 #2: Chemical | #3: Chemical | #4: Chemical | #5: 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: 2.35 Å3/Da / Density % sol: 48.15 % / Description: NONE |
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Crystal grow | pH: 7.5 / Details: 12.5% 2-PROPANOL, 30% GLYCEROL, PH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Aug 7, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→50 Å / Num. obs: 54984 / % possible obs: 99.2 % / Observed criterion σ(I): 1 / Redundancy: 4.1 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 15.8 |
Reflection shell | Resolution: 1.7→1.8 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 3 / % possible all: 98.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→92.85 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.951 / SU B: 3.598 / SU ML: 0.058 / Cross valid method: THROUGHOUT / ESU R: 0.095 / ESU R Free: 0.091 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.7 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→92.85 Å
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Refine LS restraints |
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