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- PDB-2p6y: X-ray structure of the protein Q9KM02_VIBCH from Vibrio cholerae ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2p6y | ||||||
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Title | X-ray structure of the protein Q9KM02_VIBCH from Vibrio cholerae at the resolution 1.63 A. Northeast Structural Genomics Consortium target VcR80. | ||||||
![]() | Hypothetical protein VCA0587 | ||||||
![]() | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / NESG / Q9KM02_VIBCH / VcR80 / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium | ||||||
Function / homology | PPC domain / Plants and Prokaryotes Conserved (PCC) domain / PPC domain profile profile. / Hypothetical protein, similar to alpha- acetolactate decarboxylase; domain 2 / 60s Ribosomal Protein L30; Chain: A; / 2-Layer Sandwich / metal ion binding / Alpha Beta / PPC domain-containing protein![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kuzin, A.P. / Abashidze, M. / Jayaraman, S. / Chen, C.X. / Wang, C. / Fang, Y. / Cunningham, K. / Owens, L. / Xiao, R. / Liu, J. ...Kuzin, A.P. / Abashidze, M. / Jayaraman, S. / Chen, C.X. / Wang, C. / Fang, Y. / Cunningham, K. / Owens, L. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J. / Northeast Structural Genomics Consortium (NESG) | ||||||
![]() | ![]() Title: X-ray structure of the protein Q9KM02_VIBCH from Vibrio cholerae at the resolution 1.63 A. Authors: Kuzin, A.P. / Abashidze, M. / Jayaraman, S. / Chen, C.X. / Wang, C. / Fang, Y. / Cunningham, K. / Owens, L. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J. | ||||||
History |
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Remark 300 | BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 ... BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). THE TRIMERIC ASSEMBLY OF THE BIOLOGICAL UNIT, SHOWN IN REMARK 350, HAS BEEN EXPERIMENTALLY DETERMINED BY THE AUTHORS. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 39.1 KB | Display | ![]() |
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PDB format | ![]() | 31.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 419.5 KB | Display | ![]() |
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Full document | ![]() | 421.2 KB | Display | |
Data in XML | ![]() | 8.7 KB | Display | |
Data in CIF | ![]() | 11.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data | |
Other databases |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 16018.817 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-ZN / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.36 Å3/Da / Density % sol: 63.41 % Description: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 10 mM MgSO4, 50 mM Cacodylic acid, 200 mM (NH4)2SO4, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 7, 2007 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.63→50 Å / Num. obs: 51743 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 21.9 % / Biso Wilson estimate: 16 Å2 / Rsym value: 0.064 / Net I/σ(I): 56 |
Reflection shell | Resolution: 1.63→1.69 Å / Mean I/σ(I) obs: 8.1 / Rsym value: 0.5 / % possible all: 92.1 |
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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: 45.4679 Å2 / ksol: 0.380998 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.63→19.97 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.63→1.73 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
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Xplor file |
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