+Open data
-Basic information
Entry | Database: PDB / ID: 2qpq | ||||||
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Title | Structure of Bug27 from Bordetella pertussis | ||||||
Components | protein Bug27 | ||||||
Keywords | TRANSPORT PROTEIN / ALPHA/BETA DOMAIN / VENUS FLYTRAP | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Bordetella pertussis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.92 Å | ||||||
Authors | Herrou, J. / Bompard, C. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2007 Title: Structure-based mechanism of ligand binding for periplasmic solute-binding protein of the Bug family. Authors: Herrou, J. / Bompard, C. / Antoine, R. / Leroy, A. / Rucktooa, P. / Hot, D. / Huvent, I. / Locht, C. / Villeret, V. / Jacob-Dubuisson, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2qpq.cif.gz | 345 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2qpq.ent.gz | 295.4 KB | Display | PDB format |
PDBx/mmJSON format | 2qpq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2qpq_validation.pdf.gz | 467.3 KB | Display | wwPDB validaton report |
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Full document | 2qpq_full_validation.pdf.gz | 506.1 KB | Display | |
Data in XML | 2qpq_validation.xml.gz | 44.5 KB | Display | |
Data in CIF | 2qpq_validation.cif.gz | 63.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qp/2qpq ftp://data.pdbj.org/pub/pdb/validation_reports/qp/2qpq | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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3 |
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Unit cell |
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Details | The biological assembly is a monomer |
-Components
#1: Protein | Mass: 31728.287 Da / Num. of mol.: 3 / Fragment: residues 30-330 (no signal peptide) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bordetella pertussis (bacteria) / Gene: 2667749 / Plasmid: pQE-30 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q7W019 #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.72 Å3/Da / Density % sol: 54.85 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.2 Details: 0.1 M Na-citrate, 25% (w/v) PEG 2000, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction |
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Diffraction source |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 1.9→6.56 Å / Num. obs: 78417 / % possible obs: 97.3 % / Redundancy: 3.89 % / Rsym value: 0.057 / Net I/σ(I): 0.1484 | |||||||||||||||
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 3.87 % / Mean I/σ(I) obs: 4.64 / Rsym value: 0.273 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.92→6.56 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.912 / SU B: 7.755 / SU ML: 0.104 / Cross valid method: THROUGHOUT / ESU R: 0.368 / ESU R Free: 0.156 / 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: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.617 Å2
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Refinement step | Cycle: LAST / Resolution: 1.92→6.56 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.92→1.965 Å / Total num. of bins used: 20
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