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Yorodumi- PDB-3cpk: Crystal structure of the Q7W7N7_BORPA protein from Bordetella par... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3cpk | ||||||
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Title | Crystal structure of the Q7W7N7_BORPA protein from Bordetella parapertussis. Northeast Structural Genomics Consortium target BeR31 | ||||||
Components | Uncharacterized protein Q7W7N7_BORPA | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / Q7W7N7_BORPA / BPP2477 / BeR31 / NESG / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium | ||||||
Function / homology | Hypothetical Protein Mth938; Chain: A, / MTH938-like / NDUFAF3/Mth938 domain-containing protein / MTH938-like superfamily / Protein of unknown function (DUF498/DUF598) / 3-Layer(aba) Sandwich / Alpha Beta / Xcc1710-like domain-containing protein Function and homology information | ||||||
Biological species | Bordetella parapertussis 12822 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å | ||||||
Authors | Vorobiev, S.M. / Abashidze, M. / Seetharaman, J. / Zhao, L. / Janjua, H. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG) | ||||||
Citation | Journal: To be Published Title: Crystal structure of the Q7W7N7_BORPA protein from Bordetella parapertussis. Authors: Vorobiev, S.M. / Abashidze, M. / Seetharaman, J. / Zhao, L. / Janjua, H. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3cpk.cif.gz | 31.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3cpk.ent.gz | 23.7 KB | Display | PDB format |
PDBx/mmJSON format | 3cpk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3cpk_validation.pdf.gz | 421.7 KB | Display | wwPDB validaton report |
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Full document | 3cpk_full_validation.pdf.gz | 425.5 KB | Display | |
Data in XML | 3cpk_validation.xml.gz | 7.6 KB | Display | |
Data in CIF | 3cpk_validation.cif.gz | 9.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cp/3cpk ftp://data.pdbj.org/pub/pdb/validation_reports/cp/3cpk | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | AUTHORS STATE THAT THE BIOLOGICAL UNIT IS A MONOMER ACCORDING TO AGGREGATION SCREENING |
-Components
#1: Protein | Mass: 15990.487 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bordetella parapertussis 12822 (bacteria) Species: Bordetella parapertussis / Strain: 12822 / NCTC 13253 / Gene: BPP2477 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: Q7W7N7 |
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#2: 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: 1.75 Å3/Da / Density % sol: 29.7 % Description: The structure factor file contains Friedel pairs |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 15-20% PEG 8000, 0.1M Manganese chloride, 0.1M MOPS pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97901, 0.97928, 0.96785 | ||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 30, 2008 | ||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.5→50 Å / Num. all: 15148 / Num. obs: 15148 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.6 % / Biso Wilson estimate: 28.1 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 20.4 | ||||||||||||
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.565 / Mean I/σ(I) obs: 2.95 / Num. unique all: 1546 / % possible all: 96.6 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.5→40.83 Å / Rfactor Rfree error: 0.014 / Data cutoff high absF: 372303.38 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber / Details: The Bijvoet differences were used in phasing
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 57.2715 Å2 / ksol: 0.351461 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→40.83 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.66 Å / Rfactor Rfree error: 0.042 / Total num. of bins used: 6
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Xplor file |
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