+Open data
-Basic information
Entry | Database: PDB / ID: 7vmf | |||||||||
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Title | Crystal structure of Arabidopsis thaliana HDT2 | |||||||||
Components | Histone deacetylase HDT2 | |||||||||
Keywords | CHAPERONE / HDT / HD-tuin / Nucleoplasmin / Histone chaperone / HD2B / HDT2 | |||||||||
Function / homology | Function and homology information polarity specification of adaxial/abaxial axis / seed dormancy process / DNA-mediated transformation / plant-type cell wall / root development / plant-type vacuole / plastid / histone deacetylase activity / chromatin organization / negative regulation of DNA-templated transcription ...polarity specification of adaxial/abaxial axis / seed dormancy process / DNA-mediated transformation / plant-type cell wall / root development / plant-type vacuole / plastid / histone deacetylase activity / chromatin organization / negative regulation of DNA-templated transcription / nucleolus / mitochondrion / nucleus Similarity search - Function | |||||||||
Biological species | Arabidopsis thaliana (thale cress) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.32 Å | |||||||||
Authors | Kumar, A. / Bobde, R.C. / Vasudevan, D. | |||||||||
Funding support | India, 2items
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Citation | Journal: Plant Cell / Year: 2022 Title: Plant-specific HDT family histone deacetylases are nucleoplasmins. Authors: Bobde, R.C. / Kumar, A. / Vasudevan, D. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7vmf.cif.gz | 203 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7vmf.ent.gz | 162.8 KB | Display | PDB format |
PDBx/mmJSON format | 7vmf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7vmf_validation.pdf.gz | 449 KB | Display | wwPDB validaton report |
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Full document | 7vmf_full_validation.pdf.gz | 450.9 KB | Display | |
Data in XML | 7vmf_validation.xml.gz | 21.8 KB | Display | |
Data in CIF | 7vmf_validation.cif.gz | 31.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vm/7vmf ftp://data.pdbj.org/pub/pdb/validation_reports/vm/7vmf | HTTPS FTP |
-Related structure data
Related structure data | 7vmhC 7vmiC 7vrrC 6j2zS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 10365.731 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: HDT2, HD2, HD2B, HDA4, At5g22650, MDJ22.7 / Plasmid: pET22b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q56WH4 #2: Chemical | ChemComp-NA / | #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.44 Å3/Da / Density % sol: 49.6 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 0.2M ammonium phosphate dibasic pH-8.0, 20%W/V PEG 3350 |
-Data collection
Diffraction | Mean temperature: 103 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.07227 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 1, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.07227 Å / Relative weight: 1 |
Reflection | Resolution: 1.32→49.07 Å / Num. obs: 111734 / % possible obs: 95 % / Redundancy: 3.6 % / CC1/2: 0.999 / Net I/σ(I): 13.9 |
Reflection shell | Resolution: 1.32→1.34 Å / Redundancy: 2.4 % / Mean I/σ(I) obs: 2.1 / Num. unique obs: 4443 / CC1/2: 0.853 / % possible all: 77.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6J2Z Resolution: 1.32→46.77 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.968 / SU B: 1.786 / SU ML: 0.033 / Cross valid method: THROUGHOUT / ESU R: 0.052 / ESU R Free: 0.05 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 1.1 Å / Shrinkage radii: 1.1 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.148 Å2
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Refinement step | Cycle: LAST / Resolution: 1.32→46.77 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.32→1.354 Å / Total num. of bins used: 20
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