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- PDB-4qtj: Complex of WOPR domain of Wor1 in Candida albicans with the 13bp dsDNA -

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Basic information

Entry
Database: PDB / ID: 4qtj
TitleComplex of WOPR domain of Wor1 in Candida albicans with the 13bp dsDNA
Components
  • DNA (5'-D(*AP*AP*AP*AP*GP*TP*TP*TP*AP*AP*CP*TP*T)-3')
  • DNA (5'-D(*AP*AP*GP*TP*TP*AP*AP*AP*CP*TP*TP*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: 2.1 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)38,7573
Polymers38,7573
Non-polymers00
Water1,964109
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2790 Å2
ΔGint-13 kcal/mol
Surface area12350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.628, 46.628, 215.499
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein White-opaque regulator 1


Mass: 30818.729 Da / Num. of mol.: 1 / 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(*AP*AP*AP*AP*GP*TP*TP*TP*AP*AP*CP*TP*T)-3')


Mass: 3973.635 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain DNA (5'-D(*AP*AP*GP*TP*TP*AP*AP*AP*CP*TP*TP*TP*T)-3')


Mass: 3964.621 Da / Num. of mol.: 1 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / 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: 1.74 Å3/Da / Density % sol: 29.51 %
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: 0.9791 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 29, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 16046 / % possible obs: 95.2 % / Redundancy: 7.6 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 18.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.1-2.187.80.446194
2.18-2.267.70.294195.2
2.26-2.377.60.211196
2.37-2.497.70.147196
2.49-2.657.50.1197
2.65-2.857.40.069198.4
2.85-3.147.50.053199.5
3.14-3.597.70.052195
3.59-4.527.10.059195.3
4.52-507.50.04186.6

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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: 2.1→24.49 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.941 / SU B: 9.485 / SU ML: 0.128 / Cross valid method: THROUGHOUT / ESU R: 0.22 / ESU R Free: 0.189 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24834 810 5.1 %RANDOM
Rwork0.20592 ---
obs0.20803 15172 95.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 59.62 Å2
Baniso -1Baniso -2Baniso -3
1-0.91 Å20.91 Å20 Å2
2--0.91 Å20 Å2
3----2.96 Å2
Refinement stepCycle: LAST / Resolution: 2.1→24.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1229 527 0 109 1865
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0171838
X-RAY DIFFRACTIONr_bond_other_d0.0020.021512
X-RAY DIFFRACTIONr_angle_refined_deg1.8191.6832595
X-RAY DIFFRACTIONr_angle_other_deg1.13133502
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8935152
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.12523.81855
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.25915228
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.691159
X-RAY DIFFRACTIONr_chiral_restr0.1070.2271
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.021681
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02389
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.101→2.156 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.28 59 -
Rwork0.285 1082 -
obs--93.22 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
13.0822-1.7366-1.07252.05350.36681.92420.0755-0.39330.10850.127-0.09210.23090.06920.0250.01660.0673-0.09270.02160.2-0.11910.18140.961721.1469-13.7231
24.42161.2151.05912.14480.40983.61550.01780.0983-0.1408-0.47830.0088-0.19950.12910.2341-0.02660.13660.00620.04490.2737-0.04570.167513.646915.3023-28.4046
32.41011.13742.05030.9340.93021.9380.09730.3203-0.0092-0.18880.0402-0.07510.09220.338-0.13750.1990.0243-0.00040.3195-0.04740.185514.625116.9771-29.6965
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 270
2X-RAY DIFFRACTION2B1 - 13
3X-RAY DIFFRACTION3C1 - 13

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