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- PDB-5yug: AtVAL1 PHD-Like domain in the P31 space group -

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Basic information

Entry
Database: PDB / ID: 5yug
TitleAtVAL1 PHD-Like domain in the P31 space group
ComponentsB3 domain-containing transcription repressor VAL1
KeywordsSTRUCTURAL PROTEIN / H3K27me3 / PHD / VAL1 / PHD-Like domain / Histone modification
Function / homology
Function and homology information


response to sucrose / response to abscisic acid / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / mitochondrion / DNA binding / zinc ion binding / nucleus
Similarity search - Function
B3 DNA binding domain / B3 DNA binding domain / B3 DNA-binding domain profile. / B3 DNA binding domain / DNA-binding pseudobarrel domain superfamily / Zinc finger, CW-type / CW-type Zinc Finger / Zinc finger CW-type profile.
Similarity search - Domain/homology
B3 domain-containing transcription repressor VAL1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.57 Å
AuthorsZhang, M.M. / Wu, B.X.
CitationJournal: To Be Published
Title: AtVAL1 PHD-Like domain in the P31 space group
Authors: Zhang, M.M. / Wu, B.X.
History
DepositionNov 22, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 2, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Data collection / Database references ...Data collection / Database references / Source and taxonomy / Structure summary
Category: citation / entity_src_gen / struct
Item: _citation.title / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id ..._citation.title / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _struct.title
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: B3 domain-containing transcription repressor VAL1
B: B3 domain-containing transcription repressor VAL1
E: B3 domain-containing transcription repressor VAL1
G: B3 domain-containing transcription repressor VAL1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,01418
Polymers49,0454
Non-polymers96914
Water2,504139
1
G: B3 domain-containing transcription repressor VAL1
hetero molecules

A: B3 domain-containing transcription repressor VAL1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0079
Polymers24,5222
Non-polymers4857
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Buried area2520 Å2
ΔGint-16 kcal/mol
Surface area10860 Å2
MethodPISA
2
B: B3 domain-containing transcription repressor VAL1
E: B3 domain-containing transcription repressor VAL1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0079
Polymers24,5222
Non-polymers4857
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2810 Å2
ΔGint-17 kcal/mol
Surface area10760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.228, 52.228, 121.674
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein
B3 domain-containing transcription repressor VAL1 / Protein HIGH-LEVEL EXPRESSION OF SUGAR-INDUCIBLE 2 / Protein VP1/ABI3-LIKE 1


Mass: 12261.192 Da / Num. of mol.: 4 / Fragment: PHD-Like domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: VAL1, HSI2, At2g30470, T6B20.17 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8W4L5
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.95 Å3/Da / Density % sol: 37.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2M Ammonium citrate tribasic pH 7.0, 20% w/v Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97737 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97737 Å / Relative weight: 1
ReflectionResolution: 1.57→50 Å / Num. obs: 51823 / % possible obs: 99.8 % / Redundancy: 10.3 % / Rmerge(I) obs: 0.142 / Net I/σ(I): 16
Reflection shellResolution: 1.57→1.63 Å

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
SHELXCDphasing
RefinementMethod to determine structure: SAD / Resolution: 1.57→26.114 Å / SU ML: 0.18 / Cross valid method: NONE / σ(F): 1.98 / Phase error: 22.79
RfactorNum. reflection% reflection
Rfree0.2544 2595 5.02 %
Rwork0.2203 --
obs0.222 51702 99.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.57→26.114 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2956 0 24 139 3119
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063033
X-RAY DIFFRACTIONf_angle_d0.9154070
X-RAY DIFFRACTIONf_dihedral_angle_d15.1881792
X-RAY DIFFRACTIONf_chiral_restr0.05429
X-RAY DIFFRACTIONf_plane_restr0.005509
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5698-1.59830.25041070.20782441X-RAY DIFFRACTION93
1.5983-1.62910.2921300.20492646X-RAY DIFFRACTION100
1.6291-1.66230.23511520.19672539X-RAY DIFFRACTION100
1.6623-1.69850.23511530.19632613X-RAY DIFFRACTION100
1.6985-1.7380.19221400.18722596X-RAY DIFFRACTION100
1.738-1.78140.26441340.20152556X-RAY DIFFRACTION100
1.7814-1.82960.23911400.20922585X-RAY DIFFRACTION100
1.8296-1.88340.22221780.20162582X-RAY DIFFRACTION100
1.8834-1.94420.2941690.22632591X-RAY DIFFRACTION100
1.9442-2.01360.25421440.21562546X-RAY DIFFRACTION100
2.0136-2.09420.23231480.21922624X-RAY DIFFRACTION100
2.0942-2.18950.28011100.21652591X-RAY DIFFRACTION100
2.1895-2.30480.30331360.23242572X-RAY DIFFRACTION100
2.3048-2.44920.2654920.23672630X-RAY DIFFRACTION100
2.4492-2.63810.25471660.24392571X-RAY DIFFRACTION100
2.6381-2.90330.28231220.23342615X-RAY DIFFRACTION100
2.9033-3.32260.28251180.24272590X-RAY DIFFRACTION100
3.3226-4.18340.25911260.21632613X-RAY DIFFRACTION100
4.1834-26.11760.20591300.20912606X-RAY DIFFRACTION100

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