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Yorodumi- PDB-5vj4: Crystal structure of a putative surface protein encoded by BTA121 -
+Open data
-Basic information
Entry | Database: PDB / ID: 5vj4 | ||||||
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Title | Crystal structure of a putative surface protein encoded by BTA121 | ||||||
Components | Uncharacterized protein | ||||||
Keywords | LIPID BINDING PROTEIN / Relapsing fever | ||||||
Function / homology | Prokaryotic membrane lipoprotein lipid attachment site profile. / Uncharacterized protein Function and homology information | ||||||
Biological species | Borrelia turicatae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 Å | ||||||
Authors | Luo, Z. / Asojo, O. | ||||||
Citation | Journal: Sci Rep / Year: 2017 Title: Crystal Structure of Borrelia turicatae protein, BTA121, a differentially regulated gene in the tick-mammalian transmission cycle of relapsing fever spirochetes. Authors: Luo, Z. / Kelleher, A.J. / Darwiche, R. / Hudspeth, E.M. / Shittu, O.K. / Krishnavajhala, A. / Schneiter, R. / Lopez, J.E. / Asojo, O.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5vj4.cif.gz | 120.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5vj4.ent.gz | 97.7 KB | Display | PDB format |
PDBx/mmJSON format | 5vj4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5vj4_validation.pdf.gz | 453.6 KB | Display | wwPDB validaton report |
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Full document | 5vj4_full_validation.pdf.gz | 459.1 KB | Display | |
Data in XML | 5vj4_validation.xml.gz | 20.8 KB | Display | |
Data in CIF | 5vj4_validation.cif.gz | 28.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vj/5vj4 ftp://data.pdbj.org/pub/pdb/validation_reports/vj/5vj4 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 40695.973 Da / Num. of mol.: 2 / Fragment: residues 71-445 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Borrelia turicatae (bacteria) / Strain: 91E135 / Gene: BTA121 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0R9P931 #2: Chemical | ChemComp-SO4 / #3: 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: 3.4 Å3/Da / Density % sol: 63.85 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 1.8M lithium sulfate, 50mM sodium HEPES pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Feb 17, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. obs: 26628 / % possible obs: 100 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 20.3 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 5.7 % / Rmerge(I) obs: 1.16 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 2665 / CC1/2: 0.738 / Rpim(I) all: 0.037 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.8→39.8 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.949 / SU B: 12.405 / SU ML: 0.229 / Cross valid method: THROUGHOUT / ESU R: 0.422 / ESU R Free: 0.266
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 82.974 Å2
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Refinement step | Cycle: 1 / Resolution: 2.8→39.8 Å
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Refine LS restraints |
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