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- PDB-5z28: AtVAL2 PHD-Like domain -

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Basic information

Entry
Database: PDB / ID: 5z28
TitleAtVAL2 PHD-Like domain
ComponentsB3 domain-containing transcription repressor VAL2
KeywordsTRANSCRIPTION / transcriptional factor / Val2 / PHD-Like domain / FLC / plant
Function / homology
Function and homology information


transcription cis-regulatory region binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription / 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 VAL2
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.245 Å
AuthorsWu, B.X. / Zhang, M.M.
CitationJournal: To Be Published
Title: Crystal structure of AtVAL12 PHD-Like domain
Authors: Wu, B.X. / Zhang, M.M.
History
DepositionDec 30, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 2, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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 VAL2
B: B3 domain-containing transcription repressor VAL2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,7979
Polymers22,3122
Non-polymers4857
Water39622
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2300 Å2
ΔGint-15 kcal/mol
Surface area11020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.558, 76.022, 76.046
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein B3 domain-containing transcription repressor VAL2 / Protein HIGH-LEVEL EXPRESSION OF SUGAR-INDUCIBLE-LIKE 1 / Protein VP1/ABI3-LIKE 2


Mass: 11156.031 Da / Num. of mol.: 2 / Fragment: PHD-Like domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: VAL2, HSL1, At4g32010, F10N7.180 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5CCK4
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / 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: 2.32 Å3/Da / Density % sol: 46.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1M Bis-Tris pH6.5, 28% PEG MME 2000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 29, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.244→52.11 Å / Num. obs: 10184 / % possible obs: 99.6 % / Redundancy: 9.6 % / Rmerge(I) obs: 0.147 / Net I/σ(I): 17.94
Reflection shellResolution: 2.25→2.33 Å / Redundancy: 6.6 %

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5YUG

5yug


Resolution: 2.245→26.882 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 23.75
RfactorNum. reflection% reflection
Rfree0.2372 514 5.33 %
Rwork0.1837 --
obs0.1865 9650 94.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.245→26.882 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1445 0 12 22 1479
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091474
X-RAY DIFFRACTIONf_angle_d1.121966
X-RAY DIFFRACTIONf_dihedral_angle_d21.672885
X-RAY DIFFRACTIONf_chiral_restr0.058206
X-RAY DIFFRACTIONf_plane_restr0.006248
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2446-2.47040.26581190.20761872X-RAY DIFFRACTION80
2.4704-2.82750.27541300.20482335X-RAY DIFFRACTION98
2.8275-3.56110.26981290.19192416X-RAY DIFFRACTION100
3.5611-26.8840.20231360.16692513X-RAY DIFFRACTION100

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