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Yorodumi- PDB-3qq2: Crystal Structure of the Beta Domain of the Bordetella Autotransp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3qq2 | ||||||
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Title | Crystal Structure of the Beta Domain of the Bordetella Autotransporter Brka | ||||||
Components | BrkA autotransporter | ||||||
Keywords | MEMBRANE PROTEIN/PROTEIN TRANSPORT / BETA BARREL / TRANSMEMBRANE / MEMBRANE PROTEIN-PROTEIN TRANSPORT COMPLEX | ||||||
Function / homology | Function and homology information : / cell outer membrane / membrane => GO:0016020 / periplasmic space / cell surface / extracellular region Similarity search - Function | ||||||
Biological species | Bordetella pertussis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Zhai, Y. / Zhang, K. / Huo, Y. / Sun, F. | ||||||
Citation | Journal: Biochem.J. / Year: 2011 Title: Autotransporter passenger domain secretion requires a hydrophobic cavity at the extracellular entrance of the beta-domain pore Authors: Zhai, Y. / Zhang, K. / Huo, Y. / Zhu, Y. / Zhou, Q. / Lu, J. / Black, I. / Pang, X. / Roszak, A.W. / Zhang, X. / Isaacs, N.W. / Sun, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3qq2.cif.gz | 295.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3qq2.ent.gz | 247.2 KB | Display | PDB format |
PDBx/mmJSON format | 3qq2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3qq2_validation.pdf.gz | 453.9 KB | Display | wwPDB validaton report |
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Full document | 3qq2_full_validation.pdf.gz | 483.4 KB | Display | |
Data in XML | 3qq2_validation.xml.gz | 28.9 KB | Display | |
Data in CIF | 3qq2_validation.cif.gz | 39 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qq/3qq2 ftp://data.pdbj.org/pub/pdb/validation_reports/qq/3qq2 | HTTPS FTP |
-Related structure data
Related structure data | 2qomS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 30988.332 Da / Num. of mol.: 3 / Fragment: BETA DOMAIN, UNP RESIDUES 727-1010 / Mutation: L727M Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bordetella pertussis (bacteria) / Gene: BP3494, brkA / Plasmid: PET11A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q45340 |
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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: 4.04 Å3/Da / Density % sol: 69.54 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 100MM TIS-HCL, 10MM SPERMIDINE, 200MM LICL, 25% PEG 2000, PH8.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1.07176 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 26, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.07176 Å / Relative weight: 1 |
Reflection | Resolution: 3→15 Å / Num. all: 30635 / Num. obs: 29563 / % possible obs: 96.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.4 % / Biso Wilson estimate: 97.3 Å2 / Rmerge(I) obs: 0.145 / Net I/σ(I): 35.4 |
Reflection shell | Resolution: 3→3.11 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.315 / Mean I/σ(I) obs: 3.268 / % possible all: 75 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2QOM Resolution: 3→15 Å / Cor.coef. Fo:Fc: 0.895 / Cor.coef. Fo:Fc free: 0.848 / SU B: 41.812 / SU ML: 0.343 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.454 / 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: 92.81 Å2
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Refinement step | Cycle: LAST / Resolution: 3→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3→3.08 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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