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- PDB-1bja: ACTIVATION DOMAIN OF THE PHAGE T4 TRANSCRIPTION FACTOR MOTA -

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Basic information

Entry
Database: PDB / ID: 1bja
TitleACTIVATION DOMAIN OF THE PHAGE T4 TRANSCRIPTION FACTOR MOTA
ComponentsTRANSCRIPTION REGULATORY PROTEIN MOTA
KeywordsACTIVATION DOMAIN / PHAGE T4 / MIDDLE MODE TRANSCRIPTION / ALPHA HELICAL STRUCTURE / TRANSCRIPTION REGULATION
Function / homology
Function and homology information


Bacteriophage T4, MotA, transcription regulator N-terminal / Transcription regulator MotA, C-terminal / Transcription regulator MotA, C-terminal domain superfamily / Transcription factor MotA, activation domain / Bacteriophage T4 MotA, C-terminal / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Middle transcription regulatory protein motA
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2.19 Å
AuthorsFinnin, M.S. / Cicero, M.P. / Davies, C. / Porter, S.J. / White, S.W. / Kreuzer, K.N.
CitationJournal: EMBO J. / Year: 1997
Title: The activation domain of the MotA transcription factor from bacteriophage T4.
Authors: Finnin, M.S. / Cicero, M.P. / Davies, C. / Porter, S.J. / White, S.W. / Kreuzer, K.N.
History
DepositionJun 23, 1998Processing site: BNL
Revision 1.0Nov 4, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _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: TRANSCRIPTION REGULATORY PROTEIN MOTA
B: TRANSCRIPTION REGULATORY PROTEIN MOTA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,3253
Polymers20,2292
Non-polymers961
Water1,08160
1
A: TRANSCRIPTION REGULATORY PROTEIN MOTA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,2112
Polymers10,1151
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: TRANSCRIPTION REGULATORY PROTEIN MOTA


Theoretical massNumber of molelcules
Total (without water)10,1151
Polymers10,1151
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.700, 46.700, 139.600
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
33
44
/ NCS ensembles :
ID
1
2
3
4

NCS oper: (Code: given
Matrix: (0.9042, -0.381, 0.1928), (-0.3928, -0.9193, 0.0255), (0.1675, -0.0988, -0.9809)
Vector: -12.7108, 50.6938, 245.6096)
DetailsIT IS UNCERTAIN WHETHER THE DIMER IN THE CRYSTAL STRUCTURE HAS BIOLOGICAL SIGNIFICANCE. A POSSIBILITY IS THAT THE DIMERIC STRUCTURE IS ALSO FORMED WHEN THE INTACT MOTA PROTEIN BINDS TO ITS TARGET DNA SITE.

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Components

#1: Protein TRANSCRIPTION REGULATORY PROTEIN MOTA


Mass: 10114.576 Da / Num. of mol.: 2 / Fragment: N-TERMINAL ACTIVATION DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T4 (virus) / Genus: T4-like viruses / Species: Enterobacteria phage T4 sensu lato / Gene: MOTA / Plasmid: PET3C / Species (production host): Escherichia coli / Gene (production host): MOTNF / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 / Variant (production host): DE3 / References: UniProt: P22915
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.12 Å3/Da / Density % sol: 43.37 %
Crystal growpH: 8.5
Details: PROTEIN WAS CRYSTALLIZED FROM 60% SATURATED AMMONIUM SULPHATE, 100 MM BIS-TRIS PROPANE, PH 8.0 - 9.0, pH 8.5
PH range: 8.0-9.0
Crystal grow
*PLUS
Temperature: 22 ℃ / Method: vapor diffusion, hanging drop / Details: Finnin, M.S., (1993) J. Mol. Biol., 232, 301. / PH range low: 9 / PH range high: 8
Components of the solutions
*PLUS
Conc.: 60 %sat / Common name: ammonium sulfate

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Jun 1, 1994 / Details: COLLIMATOR
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.19→10 Å / Num. obs: 9394 / % possible obs: 98.5 % / Observed criterion σ(I): 0 / Redundancy: 7 % / Biso Wilson estimate: 31 Å2 / Rmerge(I) obs: 0.048 / Rsym value: 0.053 / Net I/σ(I): 11
Reflection shellResolution: 2.19→2.3 Å / Redundancy: 5 % / Rmerge(I) obs: 0.081 / Mean I/σ(I) obs: 2.5 / Rsym value: 0.101 / % possible all: 80
Reflection
*PLUS
Num. measured all: 66237 / Rmerge(I) obs: 0.0536

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Processing

Software
NameVersionClassification
X-PLOR3.8model building
X-PLOR3.8refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.8phasing
RefinementMethod to determine structure: MIR / Resolution: 2.19→6 Å / Rfactor Rfree error: 0.017 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: 0 / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.291 333 10 %RANDOM
Rwork0.208 ---
obs0.208 8781 98.5 %-
Displacement parametersBiso mean: 30 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.4 Å
Luzzati d res low-6 Å
Luzzati sigma a0.4 Å0.4 Å
Refinement stepCycle: LAST / Resolution: 2.19→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1422 0 4 61 1487
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.71
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.6
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.6
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refine LS restraints NCSNCS model details: 0
LS refinement shellResolution: 2.19→2.29 Å / Rfactor Rfree error: 0.04 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.32 55 12 %
Rwork0.25 500 -
obs--97.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM19X.PROTOPH19X.PRO
X-RAY DIFFRACTION2
X-RAY DIFFRACTION3
X-RAY DIFFRACTION4
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.6
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.6

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