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- PDB-5z00: AtVAL1 B3 domain in complex with 15bp-DNA -

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Basic information

Entry
Database: PDB / ID: 5z00
TitleAtVAL1 B3 domain in complex with 15bp-DNA
Components
  • B3 domain-containing transcription repressor VAL1
  • DNA (5'-D(*AP*AP*TP*TP*CP*TP*GP*CP*AP*TP*GP*GP*AP*TP*T)-3')
  • DNA (5'-D(*TP*AP*AP*TP*CP*CP*AP*TP*GP*CP*AP*GP*AP*AP*T)-3')
  • DNA (5'-D(*TP*AP*AP*TP*CP*CP*AP*TP*GP*CP*AP*GP*AP*AP*TP*T)-3')
KeywordsTRANSCRIPTION/DNA / transcriptional factor / Val1 / B3 domain / DNA complex / FLC / plant / TRANSCRIPTION / TRANSCRIPTION-DNA complex
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
DNA-binding pseudobarrel domain / At1g16640 B3 domain / 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. ...DNA-binding pseudobarrel domain / At1g16640 B3 domain / 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. / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / B3 domain-containing transcription repressor VAL1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.587 Å
AuthorsWu, B.X. / Zhang, M.M.
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2018
Title: Structural insight into the role of VAL1 B3 domain for targeting to FLC locus in Arabidopsis thaliana.
Authors: Wu, B.X. / Zhang, M.M. / Su, S.C. / Liu, H.H. / Gan, J.H. / Ma, J.B.
History
DepositionDec 17, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 2, 2018Provider: repository / Type: Initial release
Revision 1.1May 30, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
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: DNA (5'-D(*AP*AP*TP*TP*CP*TP*GP*CP*AP*TP*GP*GP*AP*TP*T)-3')
B: DNA (5'-D(*TP*AP*AP*TP*CP*CP*AP*TP*GP*CP*AP*GP*AP*AP*T)-3')
C: B3 domain-containing transcription repressor VAL1
E: DNA (5'-D(*AP*AP*TP*TP*CP*TP*GP*CP*AP*TP*GP*GP*AP*TP*T)-3')
F: DNA (5'-D(*TP*AP*AP*TP*CP*CP*AP*TP*GP*CP*AP*GP*AP*AP*TP*T)-3')
G: B3 domain-containing transcription repressor VAL1
I: DNA (5'-D(*AP*AP*TP*TP*CP*TP*GP*CP*AP*TP*GP*GP*AP*TP*T)-3')
J: DNA (5'-D(*TP*AP*AP*TP*CP*CP*AP*TP*GP*CP*AP*GP*AP*AP*T)-3')
K: B3 domain-containing transcription repressor VAL1
M: B3 domain-containing transcription repressor VAL1


Theoretical massNumber of molelcules
Total (without water)84,60910
Polymers84,60910
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13050 Å2
ΔGint-73 kcal/mol
Surface area34430 Å2
Unit cell
Length a, b, c (Å)68.223, 97.416, 71.149
Angle α, β, γ (deg.)90.00, 110.19, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: DNA chain DNA (5'-D(*AP*AP*TP*TP*CP*TP*GP*CP*AP*TP*GP*GP*AP*TP*T)-3')


Mass: 4599.007 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (5'-D(*TP*AP*AP*TP*CP*CP*AP*TP*GP*CP*AP*GP*AP*AP*T)-3')


Mass: 4577.012 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Protein
B3 domain-containing transcription repressor VAL1 / Protein HIGH-LEVEL EXPRESSION OF SUGAR-INDUCIBLE 2 / Protein VP1/ABI3-LIKE 1


Mass: 14194.220 Da / Num. of mol.: 4 / Fragment: B3 domain, DNA binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: VAL1, HSI2, At2g30470, T6B20.17 / Production host: Arabidopsis thaliana (thale cress) / References: UniProt: Q8W4L5
#4: DNA chain DNA (5'-D(*TP*AP*AP*TP*CP*CP*AP*TP*GP*CP*AP*GP*AP*AP*TP*T)-3')


Mass: 4881.205 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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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: 2.62 Å3/Da / Density % sol: 53.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1M Bicine pH 8.5, 30% (w/v) PEG 6000

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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 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.587→66.78 Å / Num. obs: 27090 / % possible obs: 77 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 12.2
Reflection shellResolution: 2.6→2.69 Å

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementResolution: 2.587→29.202 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 29.88
RfactorNum. reflection% reflection
Rfree0.2676 1012 4.8 %
Rwork0.2162 --
obs0.2186 21086 77.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.587→29.202 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3464 1830 0 0 5294
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0135589
X-RAY DIFFRACTIONf_angle_d1.5397943
X-RAY DIFFRACTIONf_dihedral_angle_d23.3883033
X-RAY DIFFRACTIONf_chiral_restr0.079879
X-RAY DIFFRACTIONf_plane_restr0.011714
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5875-2.72380.3874690.30821130X-RAY DIFFRACTION31
2.7238-2.89430.30671060.29281781X-RAY DIFFRACTION49
2.8943-3.11750.32951090.29642628X-RAY DIFFRACTION70
3.1175-3.43080.29071610.25483340X-RAY DIFFRACTION90
3.4308-3.92630.31321790.24173712X-RAY DIFFRACTION100
3.9263-4.94280.25121910.1873717X-RAY DIFFRACTION100
4.9428-29.20430.21221970.16863766X-RAY DIFFRACTION100

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