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- PDB-3dkz: Crystal structure of the Q7W9W5_BORPA protein from Bordetella par... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3dkz | ||||||
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Title | Crystal structure of the Q7W9W5_BORPA protein from Bordetella parapertussis. Northeast Structural Genomics Consortium target BpR208C. | ||||||
![]() | Thioesterase superfamily protein | ||||||
![]() | HYDROLASE / Q7W9W5 / BORPA / thioesterase superfamily / PF03061 / NESG / BpR208C / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium | ||||||
Function / homology | Phenylacetic acid degradation-related domain / Thioesterase domain / Thioesterase superfamily / Hotdog Thioesterase / Thiol Ester Dehydrase; Chain A / HotDog domain superfamily / Roll / Alpha Beta / 4HBT domain-containing protein![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Vorobiev, S.M. / Su, M. / Seetharaman, J. / Wang, D. / Ciccosanti, C. / Foote, E.L. / Mao, L. / Xiao, R. / Acton, T.B. / Montelione, G.T. ...Vorobiev, S.M. / Su, M. / Seetharaman, J. / Wang, D. / Ciccosanti, C. / Foote, E.L. / Mao, L. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG) | ||||||
![]() | ![]() Title: Crystal structure of the Q7W9W5_BORPA protein from Bordetella parapertussis. Authors: Vorobiev, S.M. / Su, M. / Seetharaman, J. / Wang, D. / Ciccosanti, C. / Foote, E.L. / Mao, L. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 55.8 KB | Display | ![]() |
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PDB format | ![]() | 44.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 439.9 KB | Display | ![]() |
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Full document | ![]() | 448.6 KB | Display | |
Data in XML | ![]() | 12.6 KB | Display | |
Data in CIF | ![]() | 16.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 15581.942 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 49.21 % |
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Crystal grow | Temperature: 291 K / Method: microbatch-under-oil crystallization Details: 26% PEG 4000, 0.17M ammonium sulfate, 15% glycerol, microbatch-under-oil crystallization , temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Jun 19, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97907 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. all: 45637 / Num. obs: 44952 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Biso Wilson estimate: 45.2 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 30.1 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.306 / Mean I/σ(I) obs: 2.5 / Num. unique all: 4595 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 47.7959 Å2 / ksol: 0.347748 e/Å3 | |||||||||||||||||||||
Displacement parameters | Biso mean: 59.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.4→35.93 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.55 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 6
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Xplor file |
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