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- PDB-5yuh: AtVAL1 PHD-Like domain in the P6122 space group -

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Basic information

Entry
Database: PDB / ID: 5yuh
TitleAtVAL1 PHD-Like domain in the P6122 space group
ComponentsB3 domain-containing transcription repressor VAL1
KeywordsSTRUCTURAL PROTEIN / AtVAL1 / PHD-Like domain / PHD
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: 1.801 Å
AuthorsZhang, M.M. / Wu, B.X.
CitationJournal: To Be Published
Title: AtVAL1 PHD-Like domain in the P6122 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 / Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,4574
Polymers12,2611
Non-polymers1963
Water30617
1
A: B3 domain-containing transcription repressor VAL1
hetero molecules

A: B3 domain-containing transcription repressor VAL1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9158
Polymers24,5222
Non-polymers3926
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555x,x-y,-z+1/61
Buried area2190 Å2
ΔGint-12 kcal/mol
Surface area9950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.743, 52.743, 125.030
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-313-

HOH

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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.: 1 / 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.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / 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: 2.05 Å3/Da / Density % sol: 39.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.15M DL-Malic acid 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: 1.8→30 Å / Num. obs: 10206 / % possible obs: 99.9 % / Redundancy: 33.7 % / Rmerge(I) obs: 0.094 / Net I/σ(I): 48.25
Reflection shellResolution: 1.8→1.86 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: 1.801→26.371 Å / SU ML: 0.22 / Cross valid method: NONE / σ(F): 1.38 / Phase error: 29.06
RfactorNum. reflection% reflection
Rfree0.2782 501 4.99 %
Rwork0.2457 --
obs0.2473 10038 98.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.801→26.371 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms685 0 3 17 705
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008699
X-RAY DIFFRACTIONf_angle_d0.888938
X-RAY DIFFRACTIONf_dihedral_angle_d15.579412
X-RAY DIFFRACTIONf_chiral_restr0.0599
X-RAY DIFFRACTIONf_plane_restr0.004116
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8007-1.98190.33621100.31852220X-RAY DIFFRACTION95
1.9819-2.26860.34231320.28082345X-RAY DIFFRACTION100
2.2686-2.85760.2931150.25672411X-RAY DIFFRACTION100
2.8576-26.37430.23761440.21282561X-RAY DIFFRACTION100

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