+Open data
-Basic information
Entry | Database: PDB / ID: 5hyz | ||||||
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Title | Crystal Structure of SCL7 in Oryza sativa | ||||||
Components | GRAS family transcription factor containing protein, expressed | ||||||
Keywords | TRANSCRIPTION FACTOR / Rossmann fold helix bundle | ||||||
Function / homology | Transcription factor GRAS / GRAS domain family / GRAS family profile. / sequence-specific DNA binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription / nucleus / SCARECROW-LIKE protein 7 Function and homology information | ||||||
Biological species | Oryza sativa Japonica Group (Japanese rice) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.822 Å | ||||||
Authors | Wu, Y. / Li, S. / Zhao, Y. / Sun, L. | ||||||
Citation | Journal: Plant Cell / Year: 2016 Title: Crystal Structure of the GRAS Domain of SCARECROW-LIKE7 in Oryza sativa. Authors: Li, S. / Zhao, Y. / Zhao, Z. / Wu, X. / Sun, L. / Liu, Q. / Wu, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5hyz.cif.gz | 89.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5hyz.ent.gz | 70.7 KB | Display | PDB format |
PDBx/mmJSON format | 5hyz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hy/5hyz ftp://data.pdbj.org/pub/pdb/validation_reports/hy/5hyz | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 41530.418 Da / Num. of mol.: 1 / Fragment: GRAS domain, UNP residues 204-578 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Oryza sativa Japonica Group (Japanese rice) Gene: Os03g0723000, LOC_Os03g51330, OSNPB_030723000 / Plasmid: pET32a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q53K16 |
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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: 2.87 Å3/Da / Density % sol: 57.13 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 10% PEG 4000, 10% isopropanol, 0.1M HEPES |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 29, 2014 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.82→50 Å / Num. obs: 43031 / % possible obs: 99.8 % / Redundancy: 10.8 % / Biso Wilson estimate: 21.66 Å2 / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.027 / Rrim(I) all: 0.087 / Χ2: 3.211 / Net I/av σ(I): 56.967 / Net I/σ(I): 15.9 / Num. measured all: 465093 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.822→33.181 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 20.56 / Stereochemistry target values: MLHL
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.822→33.181 Å
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Refine LS restraints |
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LS refinement shell |
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