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Yorodumi- PDB-1gl6: Plasmid coupling protein TrwB in complex with the non-hydrolysabl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1gl6 | ||||||
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Title | Plasmid coupling protein TrwB in complex with the non-hydrolysable GTP analogue GDPNP | ||||||
Components | ATPASE | ||||||
Keywords | COUPLING PROTEIN / TYPE IV SECRETION SYSTEM / BACTERIAL CONJUG PROTEIN / RING HELICASE | ||||||
Function / homology | Function and homology information nucleotide binding / identical protein binding / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | ESCHERICHIA COLI (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Gomis-Ruth, F.X. / Moncalian, G. / De La cruz, F. / Coll, M. | ||||||
Citation | Journal: Nature / Year: 2001 Title: The Bacterial Conjugation Protein Trwb Resembles Ring Helicases and F1-ATPase Authors: Gomis-Ruth, F.X. / Moncalian, G. / Perez-Luque, R. / Gonzalez, A. / Cabezon, E. / De La Cruz, F. / Coll, M. #1: Journal: J.Biol.Chem. / Year: 2002 Title: Conjugative Plasmid Protein Trwb, an Integral Membrane Type Iv Secretion System Coupling Protein. Detailed Structural Features and Mapping of the Active Site Cleft. Authors: Gomis-Ruth, F.X. / Moncalian, G. / De La Cruz, F. / Coll, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1gl6.cif.gz | 500.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1gl6.ent.gz | 411.4 KB | Display | PDB format |
PDBx/mmJSON format | 1gl6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1gl6_validation.pdf.gz | 843.2 KB | Display | wwPDB validaton report |
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Full document | 1gl6_full_validation.pdf.gz | 927.1 KB | Display | |
Data in XML | 1gl6_validation.xml.gz | 60.4 KB | Display | |
Data in CIF | 1gl6_validation.cif.gz | 87 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gl/1gl6 ftp://data.pdbj.org/pub/pdb/validation_reports/gl/1gl6 | HTTPS FTP |
-Related structure data
Related structure data | 1e9rSC 1e9sC 1gkiC 1gl7C S: Starting model for refinement C: citing same article (ref.) |
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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: 48558.312 Da / Num. of mol.: 6 / Fragment: CYTOSOLIC FRAGMENT / Mutation: YES Source method: isolated from a genetically manipulated source Details: COMPLEX WITH GDPNP. / Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q04230 #2: Chemical | ChemComp-GNP / #3: Chemical | ChemComp-CL / | #4: Chemical | ChemComp-EPE / | #5: Water | ChemComp-HOH / | Compound details | CHAIN A, B, D, E, F, G FIRST 70 RESIDUES DELETED | |
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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: 2.9 Å3/Da / Density % sol: 57 % |
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Crystal grow | pH: 7.5 / Details: pH 7.50 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.842 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.842 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. obs: 81160 / % possible obs: 98 % / Redundancy: 5.3 % / Biso Wilson estimate: 76.7 Å2 / Rmerge(I) obs: 0.093 / Net I/σ(I): 6.1 |
Reflection shell | Resolution: 2.8→2.95 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.453 / Mean I/σ(I) obs: 1.7 / % possible all: 92 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1E9R Resolution: 2.8→50 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 Details: FREE RFACTOR USED UNTIL PENULTIMATE REFINEMENT CYCLE. SAME INDICES AS IN 1E9R, 1GKI AND 1GL7.
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Displacement parameters | Biso mean: 56 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→50 Å
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Refine LS restraints |
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