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Yorodumi- PDB-3ulx: Crystal structural of the conserved domain of Rice Stress-respons... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ulx | ||||||
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Title | Crystal structural of the conserved domain of Rice Stress-responsive NAC1 | ||||||
Components | Stress-induced transcription factor NAC1 | ||||||
Keywords | DNA BINDING PROTEIN / NAC family / Stress-responsive | ||||||
Function / homology | Function and homology information positive regulation of response to salt stress / positive regulation of response to water deprivation / sequence-specific DNA binding / regulation of DNA-templated transcription / protein homodimerization activity / nucleus Similarity search - Function | ||||||
Biological species | Oryza sativa subsp. japonica (Japanese rice) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Lou, Z.Y. / Chen, Q.F. / Wang, Q. / Xiong, L.Z. | ||||||
Citation | Journal: To be Published Title: A structural view of the conserved domain of Rice Stress-responsive NAC1 Authors: Lou, Z.Y. / Chen, Q.F. / Wang, Q. / Xiong, L.Z. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ulx.cif.gz | 43.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ulx.ent.gz | 29.9 KB | Display | PDB format |
PDBx/mmJSON format | 3ulx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ulx_validation.pdf.gz | 422 KB | Display | wwPDB validaton report |
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Full document | 3ulx_full_validation.pdf.gz | 430.2 KB | Display | |
Data in XML | 3ulx_validation.xml.gz | 9.2 KB | Display | |
Data in CIF | 3ulx_validation.cif.gz | 11.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ul/3ulx ftp://data.pdbj.org/pub/pdb/validation_reports/ul/3ulx | HTTPS FTP |
-Related structure data
Related structure data | 1ut4S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 20028.951 Da / Num. of mol.: 1 / Fragment: UNP residues 1-174 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Oryza sativa subsp. japonica (Japanese rice) Gene: snac1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q27JE5, UniProt: Q75HE5*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: 2.33 Å3/Da / Density % sol: 47.16 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1M HEPES, 1.5M ammonium sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 7, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→50 Å / Num. all: 6433 / Num. obs: 6435 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 57.3 Å2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1UT4 Resolution: 2.6→32.507 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7813 / SU ML: 0.59 / σ(F): 1.35 / Phase error: 26.5 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 63.391 Å2 / ksol: 0.373 e/Å3 | ||||||||||||||||||||||||
Displacement parameters | Biso max: 104.28 Å2 / Biso mean: 55.8857 Å2 / Biso min: 20 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→32.507 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 2 / % reflection obs: 100 %
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