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Yorodumi- PDB-3btp: Crystal structure of Agrobacterium tumefaciens VirE2 in complex w... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3btp | ||||||
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Title | Crystal structure of Agrobacterium tumefaciens VirE2 in complex with its chaperone VirE1: a novel fold and implications for DNA binding | ||||||
Components |
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Keywords | DNA BINDING PROTEIN / CHAPERONE / TIM BARREL / unique topology / novel fold / Structural Genomics / Israel Structural Proteomics Center / ISPC / Crown gall tumor / DNA-binding / Secreted / Virulence | ||||||
Function / homology | Function and homology information DNA-mediated transformation / : / protein folding / host cell nucleus / DNA binding / extracellular region / identical protein binding Similarity search - Function | ||||||
Biological species | Agrobacterium tumefaciens str. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å | ||||||
Authors | Dym, O. / Albeck, S. / Unger, T. / Elbaum, M. / Israel Structural Proteomics Center (ISPC) | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.Usa / Year: 2008 Title: Crystal structure of the Agrobacterium virulence complex VirE1-VirE2 reveals a flexible protein that can accommodate different partners. Authors: Dym, O. / Albeck, S. / Unger, T. / Jacobovitch, J. / Branzburg, A. / Michael, Y. / Frenkiel-Krispin, D. / Wolf, S.G. / Elbaum, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3btp.cif.gz | 102.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3btp.ent.gz | 77 KB | Display | PDB format |
PDBx/mmJSON format | 3btp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3btp_validation.pdf.gz | 453.3 KB | Display | wwPDB validaton report |
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Full document | 3btp_full_validation.pdf.gz | 466.1 KB | Display | |
Data in XML | 3btp_validation.xml.gz | 19 KB | Display | |
Data in CIF | 3btp_validation.cif.gz | 25.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bt/3btp ftp://data.pdbj.org/pub/pdb/validation_reports/bt/3btp | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 63433.484 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Agrobacterium tumefaciens str. (bacteria) Strain: C58 / Gene: virE2, Atu6190, AGR_pTi_28 / Plasmid: pACYCDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P08062 | ||||
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#2: Protein | Mass: 7157.181 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Agrobacterium tumefaciens str. (bacteria) Strain: C58 / Gene: virE1, Atu6189, AGR_pTi_26 / Plasmid: pACYCDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P08063 | ||||
#3: Chemical | #4: Chemical | ChemComp-PEG / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.96 Å3/Da / Density % sol: 37.14 % |
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Crystal grow | Temperature: 292 K / Method: microbatch under oil / pH: 7 Details: 20% PEG 6000, 0.2M NH4Cl, 1% Triton X-405, pH 7.0, MICROBATCH UNDER OIL, temperature 292K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.97900, 0.98000, 0.97600 | ||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 4, 2006 Details: Single Silicon (111) monochromator and toroidal focusing mirror | ||||||||||||
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.3→50 Å / Num. obs: 23980 / % possible obs: 99.8 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.109 / Rsym value: 0.099 / Net I/σ(I): 16.8 | ||||||||||||
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.386 / Mean I/σ(I) obs: 4.6 / Rsym value: 0.403 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.3→48.14 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.899 / SU B: 6.216 / SU ML: 0.156 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.289 / ESU R Free: 0.229 / 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: 32.3 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→48.14 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.36 Å / Total num. of bins used: 20
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