+Open data
-Basic information
Entry | Database: PDB / ID: 2vy3 | ||||||
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Title | Type IV secretion system effector protein BepA | ||||||
Components | CELL FILAMENTATION PROTEIN | ||||||
Keywords | CELL ADHESION / T4SS / OB FOLD / FIC DOMAIN / SUBSTRATE PROTEIN / PROTEIN TRANSLOCATION | ||||||
Function / homology | Function and homology information AMPylase activity / protein adenylyltransferase / protein adenylylation / extracellular region / ATP binding Similarity search - Function | ||||||
Biological species | BARTONELLA HENSELAE (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 Å | ||||||
Authors | Palanivelu, D.V. / Schirmer, T. | ||||||
Citation | Journal: Protein Sci. / Year: 2011 Title: Fic Domain Catalyzed Adenylylation: Insight Provided by the Structural Analysis of the Type Iv Secretion System Effector Bepa. Authors: Palanivelu, D.V. / Goepfert, A. / Meury, M. / Guye, P. / Dehio, C. / Schirmer, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2vy3.cif.gz | 124.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2vy3.ent.gz | 103.8 KB | Display | PDB format |
PDBx/mmJSON format | 2vy3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vy/2vy3 ftp://data.pdbj.org/pub/pdb/validation_reports/vy/2vy3 | 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
NCS oper:
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-Components
#1: Protein | Mass: 34851.102 Da / Num. of mol.: 2 / Fragment: RESIDUES 1-302 Source method: isolated from a genetically manipulated source Details: N-TERMINAL (HIS)6-TAG WITH THROMBIN CLEAVAGE SITE / Source: (gene. exp.) BARTONELLA HENSELAE (bacteria) / Plasmid: PRUN / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS / References: UniProt: Q6G2A9 #2: Chemical | ChemComp-NI / #3: Chemical | #4: Water | ChemComp-HOH / | Sequence details | IN BOTH CHAINS, RESIDUES 1 TO 11 ARE MISSING DUE TO DISORDER AND RESIDUES 303 TO 544 ARE MISSING ...IN BOTH CHAINS, RESIDUES 1 TO 11 ARE MISSING DUE TO DISORDER AND RESIDUES 303 TO 544 ARE MISSING DUE TO PROTEOLYTI | |
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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 % / Description: NONE |
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Crystal grow | pH: 8.7 Details: 17 MG/ML PROTEIN IN 20 MM TRIS-HCL (PH 8.0), 500 MM NACL AND 2 MM BETA-MERCAPTOETHANOL MIXED WITH 22 % POLYETHYLENE GLYCOL 4000, 0.1 M TRIS PH 8.7, 5 MM NICL2 IN A 1:1 (V:V) RATIO |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.97935 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Dec 1, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97935 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→85.13 Å / Num. obs: 18356 / % possible obs: 91.6 % / Observed criterion σ(I): 0 / Redundancy: 5.56 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 6.25 |
Reflection shell | Resolution: 2.8→2.95 Å / Redundancy: 2.58 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 2.37 / % possible all: 60.9 |
-Processing
Software |
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Refinement | Method to determine structure: SAD Starting model: NONE Resolution: 2.8→30 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.889 / SU B: 39.143 / SU ML: 0.321 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.411 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY.
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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: 47.03 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→30 Å
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Refine LS restraints |
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