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Yorodumi- PDB-5eu0: FIC domain of Bep1 from Bartonella rochalimae in complex with BiaA -
+Open data
-Basic information
Entry | Database: PDB / ID: 5eu0 | ||||||
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Title | FIC domain of Bep1 from Bartonella rochalimae in complex with BiaA | ||||||
Components |
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Keywords | TOXIN / AMPylation / adenylylation / Fic proteins / toxin-antitoxin complex | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Bartonella rochalimae ATCC BAA-1498 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 Å | ||||||
Authors | Goepfert, A. | ||||||
Funding support | Switzerland, 1items
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Citation | Journal: to be published Title: Molecular basis for Rho-family GTPase discrimination by a bacterial virulence factor Authors: Dietz, N. / Harms, A. / Sorg, I. / Mas, G. / Goepfert, A. / Hiller, S. / Schirmer, T. / Dehio, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5eu0.cif.gz | 132.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5eu0.ent.gz | 103.7 KB | Display | PDB format |
PDBx/mmJSON format | 5eu0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5eu0_validation.pdf.gz | 421.3 KB | Display | wwPDB validaton report |
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Full document | 5eu0_full_validation.pdf.gz | 421.3 KB | Display | |
Data in XML | 5eu0_validation.xml.gz | 14.1 KB | Display | |
Data in CIF | 5eu0_validation.cif.gz | 20.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eu/5eu0 ftp://data.pdbj.org/pub/pdb/validation_reports/eu/5eu0 | HTTPS FTP |
-Related structure data
Related structure data | 3shgS 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: 25997.557 Da / Num. of mol.: 1 / Fragment: FIC domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bartonella rochalimae ATCC BAA-1498 (bacteria) Gene: BARRO_10061 / Plasmid: pRSFDuet1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: E6YJU0 | ||
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#2: Protein | Mass: 7447.257 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bartonella rochalimae ATCC BAA-1498 (bacteria) Gene: BARRO_50056, O99_01280 / Plasmid: pRSFDuet1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: E6YLF5 | ||
#3: Chemical | #4: 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: 2.82 Å3/Da / Density % sol: 56.46 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.2M HEPES pH7.5, 2.3M AMMONIUM SULFATE, 2% v/v PEG 400 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 14, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→73.1 Å / Num. obs: 47293 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 11.6 % / Biso Wilson estimate: 21 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.14 / Rrim(I) all: 0.146 / Χ2: 1.013 / Net I/σ(I): 16.29 / Num. measured all: 547927 |
Reflection shell | Resolution: 1.6→1.64 Å / Redundancy: 9.1 % / Rmerge(I) obs: 0.027 / Mean I/σ(I) obs: 1.31 / Num. measured obs: 6418 / Num. possible: 634 / Num. unique obs: 633 / CC1/2: 1 / Rrim(I) all: 0.028 / Rejects: 0 / % possible all: 98.5 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3SHG Resolution: 1.6→30 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.948 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.077 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.083 / SU Rfree Blow DPI: 0.08 / SU Rfree Cruickshank DPI: 0.077
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Displacement parameters | Biso max: 97.71 Å2 / Biso mean: 25.19 Å2 / Biso min: 8.58 Å2
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Refine analyze | Luzzati coordinate error obs: 0.22 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.6→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.64 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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