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- PDB-4m8b: Fungal Protein -

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Basic information

Entry
Database: PDB / ID: 4m8b
TitleFungal Protein
Components
  • Chain A of dsDNA containing the cis-regulatory element
  • Chain B of dsDNA containing the cis-regulatory element
  • YHR177W
KeywordsTRANSCRIPTION/DNA / WOPR fungal-pathogenesis transcription / WOPR domain / transcription factor / TRANSCRIPTION / TRANSCRIPTION-DNA complex
Function / homologyGti1/Pac2 family / Gti1/Pac2 family / positive regulation of transcription by RNA polymerase II / DNA binding / nucleus / DNA / DNA (> 10) / Uncharacterized protein YHR177W
Function and homology information
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.61 Å
AuthorsRosenberg, O.S. / Lohse, M.L. / Stroud, R.M. / Johnson, A.D.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Structure of a new DNA-binding domain which regulates pathogenesis in a wide variety of fungi.
Authors: Lohse, M.B. / Rosenberg, O.S. / Cox, J.S. / Stroud, R.M. / Finer-Moore, J.S. / Johnson, A.D.
History
DepositionAug 13, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 25, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 2, 2014Group: Database references
Revision 1.2Jul 23, 2014Group: Database references
Revision 1.3Aug 20, 2014Group: Database references
Revision 1.4Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chain A of dsDNA containing the cis-regulatory element
B: Chain B of dsDNA containing the cis-regulatory element
R: YHR177W
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7364
Polymers35,6743
Non-polymers621
Water1,65792
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4330 Å2
ΔGint-19 kcal/mol
Surface area16080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.293, 103.401, 73.178
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: DNA chain Chain A of dsDNA containing the cis-regulatory element


Mass: 6196.987 Da / Num. of mol.: 1 / Fragment: UNP residues 6-201 / Source method: obtained synthetically
Details: DNA synthesis through standard methods and annealing of double stranded DNA.
#2: DNA chain Chain B of dsDNA containing the cis-regulatory element


Mass: 6072.946 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: DNA synthesis through standard methods and annealing of double stranded DNA.
#3: Protein YHR177W


Mass: 23404.328 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: a pET21 based vector with an N-terminal 8-his tag followed by a 3C protease cleavage site
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: S288c / Gene: YHR177W, Yhr177wp / Plasmid: H3C / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3) / References: UniProt: P38867
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 92 / 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: 4.79 Å3/Da / Density % sol: 74.31 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 2 uL drops were a 1 to 1 mixture of protein with a well solution of 9 mM Calcium chloride, 10 mM Spermine, 50 mM Sodium cacodylate pH 7, 4.5% Isopropanol, 3.5% Ethylene glycol. ...Details: 2 uL drops were a 1 to 1 mixture of protein with a well solution of 9 mM Calcium chloride, 10 mM Spermine, 50 mM Sodium cacodylate pH 7, 4.5% Isopropanol, 3.5% Ethylene glycol. Cryoprotection involved a 4 to 6 mixture of 25% Glucose/Ethylene Glycol and well solution., VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.115869 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 10, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.115869 Å / Relative weight: 1
ReflectionResolution: 2.61→68.012 Å / Num. all: 19969 / Num. obs: 19969 / % possible obs: 93.6 % / Redundancy: 3.6 % / Rsym value: 0.057 / Net I/σ(I): 9.7
Reflection shellResolution: 2.61→2.75 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.512 / Mean I/σ(I) obs: 1.5 / Num. unique all: 2684 / Rsym value: 0.512 / % possible all: 87.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SOLVEphasing
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: The starting model was a poor initial model built from MAD phases of a SeMet derivative.

Resolution: 2.61→38.25 Å
RfactorNum. reflection
Rfree0.2354 2159
Rwork0.1977 -
all-19835
obs-18341
Refinement stepCycle: LAST / Resolution: 2.61→38.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1484 817 4 92 2397
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONfhenix_bonds0.003
X-RAY DIFFRACTIONfhenix_angles0.897
LS refinement shellResolution: 2.61→2.6753 Å
RfactorNum. reflection% reflection
Rfree0.3682 130 -
Rwork0.3228 --
obs-1168 85.9 %

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