+Open data
-Basic information
Entry | Database: PDB / ID: 7vmi | |||||||||
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Title | Crystal structure of Arabidopsis thaliana HDT3 | |||||||||
Components | Histone deacetylase HDT3 | |||||||||
Keywords | CHAPERONE / HDT / HD-tuin / Nucleoplasmin / Histone chaperone / HD2C / HDT3 | |||||||||
Function / homology | Function and homology information seed dormancy process / response to water deprivation / response to abscisic acid / response to salt stress / response to cold / chromatin organization / hydrolase activity / transcription cis-regulatory region binding / negative regulation of DNA-templated transcription / nucleolus ...seed dormancy process / response to water deprivation / response to abscisic acid / response to salt stress / response to cold / chromatin organization / hydrolase activity / transcription cis-regulatory region binding / negative regulation of DNA-templated transcription / nucleolus / metal ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Arabidopsis thaliana (thale cress) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | |||||||||
Authors | Bobde, R.C. / Kumar, A. / 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 | 7vmi.cif.gz | 201 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7vmi.ent.gz | 163.2 KB | Display | PDB format |
PDBx/mmJSON format | 7vmi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vm/7vmi ftp://data.pdbj.org/pub/pdb/validation_reports/vm/7vmi | HTTPS FTP |
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-Related structure data
Related structure data | 7vmfSC 7vmhC 7vrrC 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: 10778.290 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: HDT3, HD2C, At5g03740, F17C15_160, MED24.1 / Plasmid: pET22b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9LZR5 #2: Water | ChemComp-HOH / | |
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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: 2.18 Å3/Da / Density % sol: 43.69 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.1 M succinic acid pH 7.0, 0.1 M bicine, 30% V/V PEG MME 550 |
-Data collection
Diffraction | Mean temperature: 103 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: RRCAT INDUS-2 / Beamline: PX-BL21 / Wavelength: 0.97947 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 16, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97947 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→45.13 Å / Num. obs: 46503 / % possible obs: 99.5 % / Redundancy: 3.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.037 / Rrim(I) all: 0.051 / Net I/σ(I): 16.9 |
Reflection shell | Resolution: 1.75→1.78 Å / Redundancy: 4 % / Rmerge(I) obs: 0.495 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 2562 / CC1/2: 0.869 / Rrim(I) all: 0.678 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7VMF Resolution: 1.8→35.26 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.961 / SU B: 9.812 / SU ML: 0.136 / Cross valid method: THROUGHOUT / ESU R: 0.138 / ESU R Free: 0.12 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.76 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→35.26 Å
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