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- PDB-4qtk: Complex of WOPR domain of Wor1 in Candida albicans with the 17bp dsDNA -

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Basic information

Entry
Database: PDB / ID: 4qtk
TitleComplex of WOPR domain of Wor1 in Candida albicans with the 17bp dsDNA
Components
  • DNA (5'-D(*AP*AP*GP*TP*TP*AP*AP*AP*CP*TP*TP*TP*TP*TP*TP*GP*A)-3')
  • DNA (5'-D(*TP*CP*AP*AP*AP*AP*AP*AP*GP*TP*TP*TP*AP*AP*CP*TP*T)-3')
  • White-opaque regulator 1
KeywordsTRANSCRIPTION/DNA / Wor1 / WOPR domain / white-opaque switching / protein-DNA recognition / transcriptional regulation / DNA binding domain / TRANSCRIPTION-DNA complex
Function / homology
Function and homology information


positive regulation of phenotypic switching / parasexual reproduction with cellular fusion / regulation of single-species biofilm formation on inanimate substrate / regulation of phenotypic switching / biological process involved in symbiotic interaction / filamentous growth of a population of unicellular organisms / mating / single-species biofilm formation on inanimate substrate / phenotypic switching / adhesion of symbiont to host ...positive regulation of phenotypic switching / parasexual reproduction with cellular fusion / regulation of single-species biofilm formation on inanimate substrate / regulation of phenotypic switching / biological process involved in symbiotic interaction / filamentous growth of a population of unicellular organisms / mating / single-species biofilm formation on inanimate substrate / phenotypic switching / adhesion of symbiont to host / sequence-specific DNA binding / cell adhesion / DNA-binding transcription factor activity / regulation of DNA-templated transcription / chromatin / positive regulation of transcription by RNA polymerase II / DNA binding / nucleus
Similarity search - Function
Gti1/Pac2 family / Gti1/Pac2 family
Similarity search - Domain/homology
DNA / DNA (> 10) / White-opaque regulator 1
Similarity search - Component
Biological speciesCandida albicans SC5314 (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.99 Å
AuthorsZhang, S. / Zhang, T. / Ding, J.
CitationJournal: Cell Res. / Year: 2014
Title: Crystal structure of the WOPR-DNA complex and implications for Wor1 function in white-opaque switching of Candida albicans.
Authors: Zhang, S. / Zhang, T. / Yan, M. / Ding, J. / Chen, J.
History
DepositionJul 8, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 13, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 20, 2014Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Aug 24, 2022Group: Database references / Category: citation / database_2 / struct_ref_seq_dif
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: White-opaque regulator 1
B: White-opaque regulator 1
C: DNA (5'-D(*TP*CP*AP*AP*AP*AP*AP*AP*GP*TP*TP*TP*AP*AP*CP*TP*T)-3')
D: DNA (5'-D(*AP*AP*GP*TP*TP*AP*AP*AP*CP*TP*TP*TP*TP*TP*TP*GP*A)-3')
E: DNA (5'-D(*TP*CP*AP*AP*AP*AP*AP*AP*GP*TP*TP*TP*AP*AP*CP*TP*T)-3')
F: DNA (5'-D(*AP*AP*GP*TP*TP*AP*AP*AP*CP*TP*TP*TP*TP*TP*TP*GP*A)-3')


Theoretical massNumber of molelcules
Total (without water)82,4556
Polymers82,4556
Non-polymers00
Water905
1
A: White-opaque regulator 1
C: DNA (5'-D(*TP*CP*AP*AP*AP*AP*AP*AP*GP*TP*TP*TP*AP*AP*CP*TP*T)-3')
D: DNA (5'-D(*AP*AP*GP*TP*TP*AP*AP*AP*CP*TP*TP*TP*TP*TP*TP*GP*A)-3')


Theoretical massNumber of molelcules
Total (without water)41,2283
Polymers41,2283
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3090 Å2
ΔGint-17 kcal/mol
Surface area12880 Å2
MethodPISA
2
B: White-opaque regulator 1
E: DNA (5'-D(*TP*CP*AP*AP*AP*AP*AP*AP*GP*TP*TP*TP*AP*AP*CP*TP*T)-3')
F: DNA (5'-D(*AP*AP*GP*TP*TP*AP*AP*AP*CP*TP*TP*TP*TP*TP*TP*GP*A)-3')


Theoretical massNumber of molelcules
Total (without water)41,2283
Polymers41,2283
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3080 Å2
ΔGint-18 kcal/mol
Surface area13170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.713, 49.910, 84.307
Angle α, β, γ (deg.)90.000, 97.960, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein White-opaque regulator 1


Mass: 30818.729 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 6-272
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida albicans SC5314 (yeast) / Gene: WOR1, EAP2, TOS9, CaO19.12348, CaO19.4884 / Plasmid: pETDuet / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) codon plus / References: UniProt: Q5AP80
#2: DNA chain DNA (5'-D(*TP*CP*AP*AP*AP*AP*AP*AP*GP*TP*TP*TP*AP*AP*CP*TP*T)-3')


Mass: 5193.423 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: DNA chain DNA (5'-D(*AP*AP*GP*TP*TP*AP*AP*AP*CP*TP*TP*TP*TP*TP*TP*GP*A)-3')


Mass: 5215.419 Da / Num. of mol.: 2 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / 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: 1.91 Å3/Da / Density % sol: 35.71 % / Mosaicity: 1.254 °
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.7
Details: 0.10M Bis-Tris, 0.2M ammonnuim sulfate, 20% PEG 3350, pH 5.7, temperature 289K, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 29, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.99→50 Å / Num. obs: 12474 / % possible obs: 97.7 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.107 / Χ2: 1.943 / Net I/σ(I): 15.7
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
3-3.117.40.45612531.14298.5
3.11-3.237.30.24112191.4297.4
3.23-3.387.20.17612451.67797.6
3.38-3.567.30.14112311.96798.6
3.56-3.787.30.13212582.09898.4
3.78-4.077.30.11912372.29198.3
4.07-4.487.20.10212682.38998.7
4.48-5.137.10.0912461.81498.3
5.13-6.467.20.08312542.15996.4
6.46-5070.09312632.49894.6

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACT3.14data extraction
REFMAC5.7.0029refinement
RefinementMethod to determine structure: SAD / Resolution: 2.99→38.86 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.911 / SU B: 22.974 / SU ML: 0.415 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.469 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2711 609 4.9 %RANDOM
Rwork0.2209 ---
obs0.2232 12453 96.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 207.4 Å2 / Biso mean: 84.634 Å2 / Biso min: 40.46 Å2
Baniso -1Baniso -2Baniso -3
1-7.96 Å2-0 Å25.43 Å2
2---2.42 Å20 Å2
3----6.07 Å2
Refinement stepCycle: LAST / Resolution: 2.99→38.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2351 1382 0 5 3738
LS refinement shellResolution: 2.994→3.072 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 38 -
Rwork0.33 786 -
all-824 -
obs--87.47 %

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