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- PDB-3osf: The structure of protozoan parasite Trichomonas vaginalis Myb2 in... -

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Basic information

Entry
Database: PDB / ID: 3osf
TitleThe structure of protozoan parasite Trichomonas vaginalis Myb2 in complex with MRE-2f-13 DNA
Components
  • 5'-D(*CP*AP*AP*GP*AP*CP*GP*AP*TP*AP*CP*AP*G)-3'
  • 5'-D(*CP*TP*GP*TP*AP*TP*CP*GP*TP*CP*TP*TP*G)-3'
  • MYB21
Keywordstranscription/DNA / transcription-DNA complex / Myb2 / R2R3 Domain / DNA binding protein / transcription factor / Nucleus
Function / homology
Function and homology information


DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / regulation of DNA-templated transcription / nucleus
Similarity search - Function
Myb-like domain profile. / Myb-like DNA-binding domain / Myb-type HTH DNA-binding domain profile. / Myb domain / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / SANT/Myb domain / Homeodomain-like / Homeobox-like domain superfamily / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ISOPROPYL ALCOHOL / DNA / DNA (> 10) / MYB21
Similarity search - Component
Biological speciesTrichomonas vaginalis (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.032 Å
AuthorsJiang, I. / Tsai, C.K. / Chen, S.C. / Wang, S.H. / Amiraslanov, I. / Chang, C.F. / Wu, W.J. / Tai, J.H. / Liaw, Y.C. / Huang, T.H.
CitationJournal: Nucleic Acids Res. / Year: 2011
Title: Molecular basis of the recognition of the ap65-1 gene transcription promoter elements by a Myb protein from the protozoan parasite Trichomonas vaginalis.
Authors: Jiang, I. / Tsai, C.K. / Chen, S.C. / Wang, S.H. / Amiraslanov, I. / Chang, C.F. / Wu, W.J. / Tai, J.H. / Liaw, Y.C. / Huang, T.H.
History
DepositionSep 9, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 3, 2011Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2013Group: Database references
Revision 1.2Mar 20, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MYB21
B: 5'-D(*CP*TP*GP*TP*AP*TP*CP*GP*TP*CP*TP*TP*G)-3'
C: 5'-D(*CP*AP*AP*GP*AP*CP*GP*AP*TP*AP*CP*AP*G)-3'
D: MYB21
E: 5'-D(*CP*TP*GP*TP*AP*TP*CP*GP*TP*CP*TP*TP*G)-3'
F: 5'-D(*CP*AP*AP*GP*AP*CP*GP*AP*TP*AP*CP*AP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,7157
Polymers45,6556
Non-polymers601
Water6,485360
1
A: MYB21
B: 5'-D(*CP*TP*GP*TP*AP*TP*CP*GP*TP*CP*TP*TP*G)-3'
C: 5'-D(*CP*AP*AP*GP*AP*CP*GP*AP*TP*AP*CP*AP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8874
Polymers22,8273
Non-polymers601
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3790 Å2
ΔGint-19 kcal/mol
Surface area9480 Å2
MethodPISA
2
D: MYB21
E: 5'-D(*CP*TP*GP*TP*AP*TP*CP*GP*TP*CP*TP*TP*G)-3'
F: 5'-D(*CP*AP*AP*GP*AP*CP*GP*AP*TP*AP*CP*AP*G)-3'


Theoretical massNumber of molelcules
Total (without water)22,8273
Polymers22,8273
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3790 Å2
ΔGint-18 kcal/mol
Surface area9550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.941, 77.352, 84.410
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: Protein MYB21 / Myb-like DNA-binding domain containing protein


Mass: 14885.064 Da / Num. of mol.: 2 / Fragment: Myb2 R2R3 Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trichomonas vaginalis (eukaryote) / Gene: TVAG_211210 / Plasmid: pET-22b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(de3) / References: UniProt: Q58HP3
#2: DNA chain 5'-D(*CP*TP*GP*TP*AP*TP*CP*GP*TP*CP*TP*TP*G)-3' / MRE-2f


Mass: 3948.569 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: DNA chain 5'-D(*CP*AP*AP*GP*AP*CP*GP*AP*TP*AP*CP*AP*G)-3' / MRE-2f


Mass: 3993.639 Da / Num. of mol.: 2 / Source method: obtained synthetically
#4: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL / Isopropyl alcohol


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 360 / 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: 2.64 Å3/Da / Density % sol: 53.47 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1M sodium cacodylate, 15% isopropanol, 25% PEG 4000, 10% glycerol, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.97622, 0.9788, 0.9790, 0.9686
DetectorType: Bruker DIP-6040 / Detector: CCD / Date: Jan 30, 2010
RadiationMonochromator: double-crystal monochromato / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.976221
20.97881
30.9791
40.96861
ReflectionResolution: 2.03→50 Å / Num. all: 31872 / Num. obs: 31586 / % possible obs: 99.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.9 % / Rmerge(I) obs: 0.047
Reflection shell
Resolution (Å)Diffraction-ID% possible all
2.03-2.07193.1
2.07-2.1195.9
2.1-2.14199.3
2.14-2.19199.9
2.19-2.231100
2.23-2.291100
2.29-2.341100
2.34-2.411100
2.41-2.481100
2.48-2.561100
2.56-2.651100
2.65-2.761100
2.76-2.881100
2.88-3.031100
3.03-3.22199.5
3.22-3.47199.1
3.47-3.82199.8
3.82-4.37199.8
4.37-5.51199.9
5.51-50195.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
RESOLVEmodel building
PHENIX(phenix.refine: 1.6_289)refinement
HKL-2000data reduction
HKL-2000data scaling
RESOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.032→36.654 Å / SU ML: 0.29 / σ(F): 0.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2579 1581 5.03 %RANDOM
Rwork0.2064 ---
all0.209 31872 --
obs0.209 31422 98.67 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.515 Å2 / ksol: 0.341 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.5957 Å2-0 Å20 Å2
2---0.2088 Å20 Å2
3---1.8044 Å2
Refinement stepCycle: LAST / Resolution: 2.032→36.654 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1712 1054 4 360 3130
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072941
X-RAY DIFFRACTIONf_angle_d1.3974191
X-RAY DIFFRACTIONf_dihedral_angle_d25.1621162
X-RAY DIFFRACTIONf_chiral_restr0.067448
X-RAY DIFFRACTIONf_plane_restr0.005354
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.0322-2.10480.31671520.2575275793
2.1048-2.1890.26291420.2277297499
2.189-2.28870.26341430.23013008100
2.2887-2.40930.31791460.23082972100
2.4093-2.56020.29351830.22472975100
2.5602-2.75780.27281650.22612973100
2.7578-3.03520.32991590.24123014100
3.0352-3.47410.29241650.2086297899
3.4741-4.37590.20611850.16393040100
4.3759-36.66020.20161410.1813315098

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