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- PDB-6fas: Crystal structure of VAL1 B3 domain in complex with cognate DNA -

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Basic information

Entry
Database: PDB / ID: 6fas
TitleCrystal structure of VAL1 B3 domain in complex with cognate DNA
Components
  • B3 domain-containing transcription repressor VAL1
  • DNA (5'-D(*AP*GP*CP*CP*AP*TP*GP*CP*AP*CP*CP*G)-3')
  • DNA (5'-D(*CP*GP*GP*TP*GP*CP*AP*TP*GP*GP*CP*T)-3')
KeywordsDNA BINDING PROTEIN / B3 DNA binding domain / VAL1 transcriptional regulator / epigenome reader / Complex / Specific DNA recognition / Sph/RY sequence
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 / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsSasnauskas, G.
Funding supportLithuania, 1items
OrganizationGrant numberCountry
Research Council of LithuaniaMIP-106/2015Lithuania
CitationJournal: Nucleic Acids Res. / Year: 2018
Title: Structural basis of DNA target recognition by the B3 domain of Arabidopsis epigenome reader VAL1.
Authors: Sasnauskas, G. / Kauneckaite, K. / Siksnys, V.
History
DepositionDec 17, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 18, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 25, 2018Group: Data collection / Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2May 16, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3May 1, 2024Group: 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
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
C: DNA (5'-D(*AP*GP*CP*CP*AP*TP*GP*CP*AP*CP*CP*G)-3')
D: DNA (5'-D(*CP*GP*GP*TP*GP*CP*AP*TP*GP*GP*CP*T)-3')
E: DNA (5'-D(*AP*GP*CP*CP*AP*TP*GP*CP*AP*CP*CP*G)-3')
F: DNA (5'-D(*CP*GP*GP*TP*GP*CP*AP*TP*GP*GP*CP*T)-3')


Theoretical massNumber of molelcules
Total (without water)41,4486
Polymers41,4486
Non-polymers00
Water3,477193
1
A: B3 domain-containing transcription repressor VAL1
C: DNA (5'-D(*AP*GP*CP*CP*AP*TP*GP*CP*AP*CP*CP*G)-3')
D: DNA (5'-D(*CP*GP*GP*TP*GP*CP*AP*TP*GP*GP*CP*T)-3')


Theoretical massNumber of molelcules
Total (without water)20,7243
Polymers20,7243
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2660 Å2
ΔGint-18 kcal/mol
Surface area9570 Å2
MethodPISA
2
B: B3 domain-containing transcription repressor VAL1
E: DNA (5'-D(*AP*GP*CP*CP*AP*TP*GP*CP*AP*CP*CP*G)-3')
F: DNA (5'-D(*CP*GP*GP*TP*GP*CP*AP*TP*GP*GP*CP*T)-3')


Theoretical massNumber of molelcules
Total (without water)20,7243
Polymers20,7243
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2680 Å2
ΔGint-19 kcal/mol
Surface area9500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.091, 86.577, 65.160
Angle α, β, γ (deg.)90.00, 94.14, 90.00
Int Tables number4
Space group name H-MP1211

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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: 13397.412 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: One cysteine forms an adduct with 2-mercaptoethanol. The resultant adduct is CME S,S-(2-HYDROXYETHYL)THIOCYSTEINE
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: VAL1, HSI2, At2g30470, T6B20.17 / Production host: Escherichia coli (E. coli) / Strain (production host): ER2566 / References: UniProt: Q8W4L5
#2: DNA chain DNA (5'-D(*AP*GP*CP*CP*AP*TP*GP*CP*AP*CP*CP*G)-3')


Mass: 3632.382 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*CP*GP*GP*TP*GP*CP*AP*TP*GP*GP*CP*T)-3')


Mass: 3694.402 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 193 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.72 Å3/Da / Density % sol: 54.8 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.17 M Ammonium acetate 0.085 M Sodium citrate tribasic dihydrate pH 5.6 25.5% w/v Polyethylene glycol 4,000 15% v/v glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.976 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 29, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.9→43.29 Å / Num. obs: 66958 / % possible obs: 99 % / Redundancy: 3.5 % / Biso Wilson estimate: 39.11 Å2 / Rmerge(I) obs: 0.0294 / Net I/σ(I): 18.81
Reflection shellResolution: 1.9→1.968 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.524 / Mean I/σ(I) obs: 2.69 / Num. unique obs: 3404 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Structural models of VAL1-B3

Resolution: 1.9→43.289 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 0.86 / Phase error: 23.43
RfactorNum. reflection% reflection
Rfree0.2166 6729 10.05 %
Rwork0.1695 --
obs0.1742 66958 97.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.9→43.289 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1710 972 0 193 2875
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0132845
X-RAY DIFFRACTIONf_angle_d1.3224049
X-RAY DIFFRACTIONf_dihedral_angle_d23.811535
X-RAY DIFFRACTIONf_chiral_restr0.07447
X-RAY DIFFRACTIONf_plane_restr0.008356
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.92160.30982170.23831999X-RAY DIFFRACTION97
1.9216-1.94420.33671680.25441992X-RAY DIFFRACTION96
1.9442-1.96790.28372090.23882043X-RAY DIFFRACTION97
1.9679-1.99280.27532220.22492012X-RAY DIFFRACTION96
1.9928-2.0190.24062140.20942004X-RAY DIFFRACTION97
2.019-2.04670.29012170.21161966X-RAY DIFFRACTION96
2.0467-2.07590.27882230.20571989X-RAY DIFFRACTION97
2.0759-2.10690.25062570.19242028X-RAY DIFFRACTION97
2.1069-2.13980.26312530.19481919X-RAY DIFFRACTION97
2.1398-2.17490.26232390.1892001X-RAY DIFFRACTION96
2.1749-2.21240.26262240.17152019X-RAY DIFFRACTION97
2.2124-2.25270.24262210.17591978X-RAY DIFFRACTION97
2.2527-2.2960.24542050.18181959X-RAY DIFFRACTION97
2.296-2.34280.29111990.18392106X-RAY DIFFRACTION98
2.3428-2.39380.23032490.1771987X-RAY DIFFRACTION97
2.3938-2.44950.24652420.17791970X-RAY DIFFRACTION97
2.4495-2.51070.27162090.18672107X-RAY DIFFRACTION98
2.5107-2.57860.27792240.1941956X-RAY DIFFRACTION98
2.5786-2.65450.24432210.18952064X-RAY DIFFRACTION98
2.6545-2.74010.24992210.19481999X-RAY DIFFRACTION98
2.7401-2.8380.26722360.18721994X-RAY DIFFRACTION96
2.838-2.95160.22522280.18092006X-RAY DIFFRACTION98
2.9516-3.08590.24452490.19552060X-RAY DIFFRACTION99
3.0859-3.24860.22992240.17611943X-RAY DIFFRACTION97
3.2486-3.45210.21222300.17361977X-RAY DIFFRACTION95
3.4521-3.71850.21081980.14942009X-RAY DIFFRACTION97
3.7185-4.09240.18812240.15042028X-RAY DIFFRACTION98
4.0924-4.6840.16412260.1372048X-RAY DIFFRACTION99
4.684-5.89890.16542120.13982067X-RAY DIFFRACTION99
5.8989-43.29970.18962680.171999X-RAY DIFFRACTION99

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