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

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Basic information

Entry
Database: PDB / ID: 3osg
TitleThe structure of protozoan parasite Trichomonas vaginalis Myb2 in complex with MRE-1-12 DNA
Components
  • 5'-D(*AP*AP*AP*TP*AP*TP*CP*GP*TP*TP*AP*T)-3'
  • 5'-D(*AP*TP*AP*AP*CP*GP*AP*TP*AP*TP*TP*T)-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
DNA / DNA (> 10) / MYB21
Similarity search - Component
Biological speciesTrichomonas vaginalis (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.997 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
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MYB21
B: 5'-D(*AP*AP*AP*TP*AP*TP*CP*GP*TP*TP*AP*T)-3'
C: 5'-D(*AP*TP*AP*AP*CP*GP*AP*TP*AP*TP*TP*T)-3'
D: MYB21
E: 5'-D(*AP*AP*AP*TP*AP*TP*CP*GP*TP*TP*AP*T)-3'
F: 5'-D(*AP*TP*AP*AP*CP*GP*AP*TP*AP*TP*TP*T)-3'


Theoretical massNumber of molelcules
Total (without water)44,4126
Polymers44,4126
Non-polymers00
Water5,405300
1
A: MYB21
B: 5'-D(*AP*AP*AP*TP*AP*TP*CP*GP*TP*TP*AP*T)-3'
C: 5'-D(*AP*TP*AP*AP*CP*GP*AP*TP*AP*TP*TP*T)-3'


Theoretical massNumber of molelcules
Total (without water)22,2063
Polymers22,2063
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3640 Å2
ΔGint-16 kcal/mol
Surface area9590 Å2
MethodPISA
2
D: MYB21
E: 5'-D(*AP*AP*AP*TP*AP*TP*CP*GP*TP*TP*AP*T)-3'
F: 5'-D(*AP*TP*AP*AP*CP*GP*AP*TP*AP*TP*TP*T)-3'


Theoretical massNumber of molelcules
Total (without water)22,2063
Polymers22,2063
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3550 Å2
ΔGint-15 kcal/mol
Surface area9040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.115, 127.532, 41.473
Angle α, β, γ (deg.)90.00, 100.23, 90.00
Int Tables number4
Space group name H-MP1211

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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(*AP*AP*AP*TP*AP*TP*CP*GP*TP*TP*AP*T)-3' / MRE-2f


Mass: 3660.428 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: DNA chain 5'-D(*AP*TP*AP*AP*CP*GP*AP*TP*AP*TP*TP*T)-3' / MRE-2f


Mass: 3660.428 Da / Num. of mol.: 2 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 300 / 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: 2.35 Å3/Da / Density % sol: 47.68 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1M HEPES, 1.5-1.7M ammonium sulfate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 0.97622 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 6, 2008
RadiationMonochromator: LN2-cooled fixed-exit double crystl Si(111) monochromator
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97622 Å / Relative weight: 1
ReflectionResolution: 1.997→30 Å / Num. all: 27657 / Num. obs: 26911 / % possible obs: 97.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shell
Resolution (Å)Diffraction-ID% possible all
2-2.07193.7
2.07-2.15195.3
2.15-2.25195.7
2.25-2.37197.6
2.37-2.52198.9
2.52-2.71199.2
2.71-2.99199.2
2.99-3.42197.9
3.42-4.31197.4
4.31-30197.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
PHENIX(phenix.refine: 1.6_289)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.997→24.193 Å / SU ML: 0.31 / σ(F): 0.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2334 1293 4.97 %RANDOM
Rwork0.1905 ---
all0.1928 27657 --
obs0.1928 26024 93.81 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.221 Å2 / ksol: 0.363 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--10.2183 Å20 Å20.0687 Å2
2--7.6964 Å20 Å2
3---2.5218 Å2
Refinement stepCycle: LAST / Resolution: 1.997→24.193 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1762 972 0 300 3034
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082895
X-RAY DIFFRACTIONf_angle_d1.4074111
X-RAY DIFFRACTIONf_dihedral_angle_d24.4641139
X-RAY DIFFRACTIONf_chiral_restr0.082441
X-RAY DIFFRACTIONf_plane_restr0.005358
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.9973-2.07720.32261280.2388233980
2.0772-2.17170.25531280.2237257488
2.1717-2.28610.2991250.2141267391
2.2861-2.42920.30291410.2229279395
2.4292-2.61650.27981580.2167285097
2.6165-2.87950.26631450.214289599
2.8795-3.29520.26721470.2107286698
3.2952-4.14820.21091520.1542286197
4.1482-24.19510.17471690.1596288098

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