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- PDB-1kaf: DNA Binding Domain Of The Phage T4 Transcription Factor MotA (AA1... -

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Basic information

Entry
Database: PDB / ID: 1kaf
TitleDNA Binding Domain Of The Phage T4 Transcription Factor MotA (AA105-211)
ComponentsTranscription regulatory protein MOTA
KeywordsTRANSCRIPTION / Escherichia coli / X-ray crystallography / protein-DNA interactions / structural genomics / eubacterial promoters.
Function / homology
Function and homology information


Transcription regulator MotA, C-terminal domain / 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 / Aspartate Aminotransferase, domain 1 / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Middle transcription regulatory protein motA
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.6 Å
AuthorsLi, N. / Sickmier, E.A. / Zhang, R. / Joachimiak, A. / White, S.W.
CitationJournal: Mol.Microbiol. / Year: 2002
Title: The MotA transcription factor from bacteriophage T4 contains a novel DNA-binding domain: the 'double wing' motif.
Authors: Li, N. / Sickmier, E.A. / Zhang, R. / Joachimiak, A. / White, S.W.
History
DepositionNov 1, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 21, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 21, 2022Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4May 22, 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: Transcription regulatory protein MOTA
B: Transcription regulatory protein MOTA
C: Transcription regulatory protein MOTA
D: Transcription regulatory protein MOTA
E: Transcription regulatory protein MOTA
F: Transcription regulatory protein MOTA


Theoretical massNumber of molelcules
Total (without water)75,2316
Polymers75,2316
Non-polymers00
Water11,584643
1
A: Transcription regulatory protein MOTA


Theoretical massNumber of molelcules
Total (without water)12,5391
Polymers12,5391
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Transcription regulatory protein MOTA


Theoretical massNumber of molelcules
Total (without water)12,5391
Polymers12,5391
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Transcription regulatory protein MOTA


Theoretical massNumber of molelcules
Total (without water)12,5391
Polymers12,5391
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Transcription regulatory protein MOTA


Theoretical massNumber of molelcules
Total (without water)12,5391
Polymers12,5391
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Transcription regulatory protein MOTA


Theoretical massNumber of molelcules
Total (without water)12,5391
Polymers12,5391
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Transcription regulatory protein MOTA


Theoretical massNumber of molelcules
Total (without water)12,5391
Polymers12,5391
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)31.284, 54.733, 91.445
Angle α, β, γ (deg.)94.77, 91.10, 95.61
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Transcription regulatory protein MOTA


Mass: 12538.558 Da / Num. of mol.: 6 / Fragment: DNA binding domain residues 105-211
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: pet13a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 DE3 / References: UniProt: P22915
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 643 / 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: 2.06 Å3/Da / Density % sol: 40.39 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: from 19% PEG 8000, 35 mM potassium phosphate pH 5.0, 3% glycerol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
pH: 5 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
119 %PEG80001reservoir
235 mMpotassium phosphate1reservoir
33 %glycerol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9795, 0.9789, 0.9636
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 19, 1999
RadiationMonochromator: GRAPHITE / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97951
20.97891
30.96361
ReflectionResolution: 1.6→30 Å / Num. obs: 60440 / % possible obs: 92 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7 %
Reflection shellResolution: 1.6→1.63 Å / % possible all: 92
Reflection
*PLUS
Lowest resolution: 30 Å / Num. obs: 87713 / % possible obs: 92 % / Num. measured all: 638591 / Rmerge(I) obs: 0.1
Reflection shell
*PLUS
% possible obs: 83 % / Mean I/σ(I) obs: 6.2

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 1.6→30 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.258 3253 random
Rwork0.226 --
all-60440 -
obs-60440 -
Displacement parametersBiso mean: 11.46 Å2
Baniso -1Baniso -2Baniso -3
1-11.19 Å211.06 Å29.45 Å2
2--11.99 Å212.09 Å2
3---13.05 Å2
Refinement stepCycle: LAST / Resolution: 1.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5142 0 0 643 5785
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONbond lengths0.0067
X-RAY DIFFRACTIONbond angles1.31
X-RAY DIFFRACTIONdihedrals23.34
X-RAY DIFFRACTIONimpropers0.62
X-RAY DIFFRACTIONmean B factor11.46
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.6 Å / Lowest resolution: 30 Å / σ(F): 0 / Rfactor obs: 0.226
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0067
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg1.31
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.344
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.62

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