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Yorodumi- PDB-1zce: X-Ray Crystal Structure of Protein Atu2648 from Agrobacterium tum... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1zce | ||||||
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Title | X-Ray Crystal Structure of Protein Atu2648 from Agrobacterium tumefaciens. Northeast Structural Genomics Consortium Target AtR33. | ||||||
Components | hypothetical protein Atu2648 | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / alpha-beta protein. / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG | ||||||
Function / homology | EVE domain / EVE domain / ph1033 like fold / ph1033 like domains / PUA-like superfamily / Roll / Alpha Beta / EVE domain-containing protein / : Function and homology information | ||||||
Biological species | Agrobacterium tumefaciens str. C58 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.3 Å | ||||||
Authors | Forouhar, F. / Chen, Y. / Conover, K. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG) | ||||||
Citation | Journal: Proteins / Year: 2009 Title: Structural genomics reveals EVE as a new ASCH/PUA-related domain. Authors: Bertonati, C. / Punta, M. / Fischer, M. / Yachdav, G. / Forouhar, F. / Zhou, W. / Kuzin, A.P. / Seetharaman, J. / Abashidze, M. / Ramelot, T.A. / Kennedy, M.A. / Cort, J.R. / Belachew, A. / ...Authors: Bertonati, C. / Punta, M. / Fischer, M. / Yachdav, G. / Forouhar, F. / Zhou, W. / Kuzin, A.P. / Seetharaman, J. / Abashidze, M. / Ramelot, T.A. / Kennedy, M.A. / Cort, J.R. / Belachew, A. / Hunt, J.F. / Tong, L. / Montelione, G.T. / Rost, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1zce.cif.gz | 45.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1zce.ent.gz | 34.8 KB | Display | PDB format |
PDBx/mmJSON format | 1zce.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1zce_validation.pdf.gz | 424.2 KB | Display | wwPDB validaton report |
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Full document | 1zce_full_validation.pdf.gz | 426.4 KB | Display | |
Data in XML | 1zce_validation.xml.gz | 11.1 KB | Display | |
Data in CIF | 1zce_validation.cif.gz | 17 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zc/1zce ftp://data.pdbj.org/pub/pdb/validation_reports/zc/1zce | HTTPS FTP |
-Related structure data
Related structure data | 2eveC 2g2xC 2gbsC C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 18083.438 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Agrobacterium tumefaciens str. C58 (bacteria) Species: Agrobacterium tumefaciens / Strain: C58 / ATCC 33970 / Gene: locus_tag="Atu2648" / Plasmid: BL21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: Q8UC50, UniProt: A9CHJ4*PLUS |
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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: 2.1 Å3/Da / Density % sol: 40 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 100 mM MES (pH 6), 40% PEG 20K, 100 mM magnesium acetate, 5 mM DTT, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97914 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 7, 2005 / Details: mirrors |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97914 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→30 Å / Num. all: 66474 / Num. obs: 63550 / % possible obs: 95.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 9.5 Å2 / Rmerge(I) obs: 0.058 / Rsym value: 0.079 / Net I/σ(I): 16.75 |
Reflection shell | Resolution: 1.3→1.35 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.107 / Mean I/σ(I) obs: 7.53 / Num. unique all: 6561 / Rsym value: 0.108 / % possible all: 98.8 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.3→27.18 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 1300233.25 / Data cutoff low absF: 0 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 48.8842 Å2 / ksol: 0.371491 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 12.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.3→27.18 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.3→1.38 Å / Rfactor Rfree error: 0.007 / Total num. of bins used: 6
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