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Yorodumi- PDB-2axo: X-Ray Crystal Structure of Protein AGR_C_4864 from Agrobacterium ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2axo | ||||||
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Title | X-Ray Crystal Structure of Protein AGR_C_4864 from Agrobacterium tumefaciens. Northeast Structural Genomics Consortium Target AtR35. | ||||||
Components | hypothetical protein Atu2684Hypothesis | ||||||
Keywords | UNKNOWN FUNCTION / alpha beta protein. / Structural Genomics / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG | ||||||
Function / homology | Protein of unknown function DUF1223 / Protein of unknown function (DUF1223) / Thioredoxin-like superfamily / Uncharacterized protein / : Function and homology information | ||||||
Biological species | Agrobacterium tumefaciens str. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å | ||||||
Authors | Forouhar, F. / Abashidze, M. / Benach, J. / Xiao, R. / Janjua, H. / Conover, K. / 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 Hypothetical Protein AGR_C_4864 from Agrobacterium tumefaciens, NESG target AtR35 Authors: Forouhar, F. / Abashidze, M. / Benach, J. / Xiao, R. / Janjua, H. / Conover, K. / 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 | 2axo.cif.gz | 54.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2axo.ent.gz | 42.4 KB | Display | PDB format |
PDBx/mmJSON format | 2axo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ax/2axo ftp://data.pdbj.org/pub/pdb/validation_reports/ax/2axo | HTTPS FTP |
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-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 | possibly dimer. |
-Components
#1: Protein | Mass: 29822.830 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Agrobacterium tumefaciens str. (bacteria) Species: Agrobacterium tumefaciens / Strain: C58 / Gene: MDK4.6 / Plasmid: BL21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+ Magic / References: UniProt: Q8UC14, UniProt: A9CHH7*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: 1.6 Å3/Da / Density % sol: 23.1 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 20 mM Tris (pH 7.5), 18% PEG 2kMME, 200 mM sodium formate, and 5 mM DTT., VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97923 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 24, 2005 / Details: mirrors |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97923 Å / Relative weight: 1 |
Reflection | Resolution: 1.72→20 Å / Num. all: 37482 / Num. obs: 37295 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Biso Wilson estimate: 10.5 Å2 / Rmerge(I) obs: 0.084 / Rsym value: 0.064 / Net I/σ(I): 23.4 |
Reflection shell | Resolution: 1.72→1.75 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.452 / Mean I/σ(I) obs: 2.3 / Num. unique all: 1837 / Rsym value: 0.429 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.8→20 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 228678.5 / Data cutoff low absF: 0 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber Details: XtalView and SnB were also used in the refinement and solution of this structure.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 43.9 Å2 / ksol: 0.36423 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.91 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
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