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Yorodumi- PDB-2ppx: Crystal structure of a HTH XRE-family like protein from Agrobacte... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ppx | ||||||
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Title | Crystal structure of a HTH XRE-family like protein from Agrobacterium tumefaciens | ||||||
Components | Uncharacterized protein Atu1735 | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / Agrobacterium tumefaciens / HTH-motif / XRE-family / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Agrobacterium tumefaciens str. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å | ||||||
Authors | Cuff, M.E. / Skarina, T. / Onopriyenko, O. / Edwards, A. / Savchenko, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: TO BE PUBLISHED Title: Structure of a HTH XRE-family like protein from Agrobacterium tumefaciens. Authors: Cuff, M.E. / Skarina, T. / Onopriyenko, O. / Edwards, A. / Savchenko, A. / Joachimiak, A. | ||||||
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). AUTHORS STATE THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS UNKNOWN. THE POTENTIAL TETRAMERIC ASSEMBLY SHOWN IN REMARK 350 IS PREDICTED BY THE ANALYSIS OF PROTEIN INTERFACES BASED ON THIS CRYSTAL STRUCTURE. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ppx.cif.gz | 26.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ppx.ent.gz | 19.4 KB | Display | PDB format |
PDBx/mmJSON format | 2ppx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2ppx_validation.pdf.gz | 415.2 KB | Display | wwPDB validaton report |
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Full document | 2ppx_full_validation.pdf.gz | 415.3 KB | Display | |
Data in XML | 2ppx_validation.xml.gz | 3.6 KB | Display | |
Data in CIF | 2ppx_validation.cif.gz | 4.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pp/2ppx ftp://data.pdbj.org/pub/pdb/validation_reports/pp/2ppx | 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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2 |
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Unit cell |
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Components on special symmetry positions |
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Details | potential tetramer |
-Components
#1: Protein | Mass: 10927.922 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: Atu1735, AGR_C_3184 / Plasmid: modified p11 / Production host: Escherichia coli (E. coli) / Strain (production host): modified BL21(DE3) / References: UniProt: Q8UEM2, UniProt: A9CIQ1*PLUS | ||||
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#2: Chemical | ChemComp-SO4 / #3: Chemical | #4: 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: 3.42 Å3/Da / Density % sol: 64.05 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 2M Ammonium sulfate, 0.2M K/Na tartrate, 0.1M Na citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97948, 0.97935 | |||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 5, 2006 | |||||||||
Radiation | Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 1.95→35.35 Å / Num. all: 10649 / Num. obs: 10649 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 38.6 Å2 / Rsym value: 0.049 / Net I/σ(I): 11.9 | |||||||||
Reflection shell | Resolution: 1.95→2.05 Å / Redundancy: 5.9 % / Mean I/σ(I) obs: 2 / Rsym value: 0.347 / % possible all: 81.3 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2→35.35 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.93 / SU B: 5.095 / SU ML: 0.075 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -3 / ESU R: 0.118 / ESU R Free: 0.126 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 65.677 Å2
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Refinement step | Cycle: LAST / Resolution: 2→35.35 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 44.6426 Å / Origin y: 3.0189 Å / Origin z: 11.9951 Å
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