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- PDB-5jlt: The crystal structure of the bacteriophage T4 MotA C-terminal dom... -

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Basic information

Entry
Database: PDB / ID: 5jlt
TitleThe crystal structure of the bacteriophage T4 MotA C-terminal domain in complex with dsDNA reveals a novel protein-DNA recognition motif
Components
  • DNA (5'-D(*GP*AP*AP*GP*CP*TP*TP*TP*GP*CP*TP*TP*AP*AP*TP*AP*AP*TP*CP*CP*AP*C)-3')
  • DNA (5'-D(*GP*TP*GP*GP*AP*TP*TP*AP*TP*TP*AP*AP*GP*CP*AP*AP*AP*GP*CP*TP*TP*C)-3')
  • Middle transcription regulatory protein motA
KeywordsVIRAL PROTEIN/DNA / MotA / dsDNA / "Double wing" / DNA binding motif / VIRAL PROTEIN-DNA complex
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
DNA / DNA (> 10) / Middle transcription regulatory protein motA
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.955 Å
AuthorsCuypers, M.G. / Robertson, R.M. / Knipling, L. / Hinton, D.M. / White, S.W.
CitationJournal: Nucleic Acids Res. / Year: 2018
Title: The phage T4 MotA transcription factor contains a novel DNA binding motif that specifically recognizes modified DNA.
Authors: Cuypers, M.G. / Robertson, R.M. / Knipling, L. / Waddell, M.B. / Moon, K. / Hinton, D.M. / White, S.W.
History
DepositionApr 27, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 3, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2019Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Middle transcription regulatory protein motA
B: Middle transcription regulatory protein motA
C: Middle transcription regulatory protein motA
D: Middle transcription regulatory protein motA
E: DNA (5'-D(*GP*AP*AP*GP*CP*TP*TP*TP*GP*CP*TP*TP*AP*AP*TP*AP*AP*TP*CP*CP*AP*C)-3')
F: DNA (5'-D(*GP*TP*GP*GP*AP*TP*TP*AP*TP*TP*AP*AP*GP*CP*AP*AP*AP*GP*CP*TP*TP*C)-3')
G: DNA (5'-D(*GP*TP*GP*GP*AP*TP*TP*AP*TP*TP*AP*AP*GP*CP*AP*AP*AP*GP*CP*TP*TP*C)-3')
H: DNA (5'-D(*GP*AP*AP*GP*CP*TP*TP*TP*GP*CP*TP*TP*AP*AP*TP*AP*AP*TP*CP*CP*AP*C)-3')


Theoretical massNumber of molelcules
Total (without water)85,1978
Polymers85,1978
Non-polymers00
Water6,972387
1
A: Middle transcription regulatory protein motA
E: DNA (5'-D(*GP*AP*AP*GP*CP*TP*TP*TP*GP*CP*TP*TP*AP*AP*TP*AP*AP*TP*CP*CP*AP*C)-3')
F: DNA (5'-D(*GP*TP*GP*GP*AP*TP*TP*AP*TP*TP*AP*AP*GP*CP*AP*AP*AP*GP*CP*TP*TP*C)-3')


Theoretical massNumber of molelcules
Total (without water)28,0503
Polymers28,0503
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4050 Å2
ΔGint-19 kcal/mol
Surface area13040 Å2
MethodPISA
2
C: Middle transcription regulatory protein motA
G: DNA (5'-D(*GP*TP*GP*GP*AP*TP*TP*AP*TP*TP*AP*AP*GP*CP*AP*AP*AP*GP*CP*TP*TP*C)-3')
H: DNA (5'-D(*GP*AP*AP*GP*CP*TP*TP*TP*GP*CP*TP*TP*AP*AP*TP*AP*AP*TP*CP*CP*AP*C)-3')


Theoretical massNumber of molelcules
Total (without water)28,0503
Polymers28,0503
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3380 Å2
ΔGint-24 kcal/mol
Surface area13500 Å2
MethodPISA
3
A: Middle transcription regulatory protein motA
D: Middle transcription regulatory protein motA
E: DNA (5'-D(*GP*AP*AP*GP*CP*TP*TP*TP*GP*CP*TP*TP*AP*AP*TP*AP*AP*TP*CP*CP*AP*C)-3')
F: DNA (5'-D(*GP*TP*GP*GP*AP*TP*TP*AP*TP*TP*AP*AP*GP*CP*AP*AP*AP*GP*CP*TP*TP*C)-3')


Theoretical massNumber of molelcules
Total (without water)42,5994
Polymers42,5994
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5030 Å2
ΔGint-29 kcal/mol
Surface area18650 Å2
MethodPISA
4
B: Middle transcription regulatory protein motA
C: Middle transcription regulatory protein motA
G: DNA (5'-D(*GP*TP*GP*GP*AP*TP*TP*AP*TP*TP*AP*AP*GP*CP*AP*AP*AP*GP*CP*TP*TP*C)-3')
H: DNA (5'-D(*GP*AP*AP*GP*CP*TP*TP*TP*GP*CP*TP*TP*AP*AP*TP*AP*AP*TP*CP*CP*AP*C)-3')


Theoretical massNumber of molelcules
Total (without water)42,5994
Polymers42,5994
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4530 Å2
ΔGint-32 kcal/mol
Surface area18790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.270, 72.270, 279.369
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein
Middle transcription regulatory protein motA


Mass: 14548.928 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: non-native amino acids from expression vector= EGDIHM. N-TERM RESIDUES (93-96) = ELLK. LINKER (97-104) = KRATRKAR. HTTP://WWW.UNIPROT.ORG/UNIPROT/P22915
Source: (gene. exp.) Enterobacteria phage T4 (virus) / Gene: motA / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P22915
#2: DNA chain DNA (5'-D(*GP*AP*AP*GP*CP*TP*TP*TP*GP*CP*TP*TP*AP*AP*TP*AP*AP*TP*CP*CP*AP*C)-3')


Mass: 6710.366 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*GP*TP*GP*GP*AP*TP*TP*AP*TP*TP*AP*AP*GP*CP*AP*AP*AP*GP*CP*TP*TP*C)-3')


Mass: 6790.414 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 387 / 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: 2.47 Å3/Da / Density % sol: 53.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 23% PEG 8K, 0.1 M Na Acetate, 0.1 M NaCacodylate, pH 6.5, and 3% glycerol

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: cryostream
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Jun 25, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.955→93.12 Å / Num. obs: 17332 / % possible obs: 100 % / Redundancy: 23.4 % / Biso Wilson estimate: 65.2 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.167 / Net I/σ(I): 15.1
Reflection shellResolution: 2.955→3.11 Å / Redundancy: 23.5 % / Mean I/σ(I) obs: 2 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(dev_2363)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KAF + DNA helix from COOT

1kaf


Resolution: 2.955→62.588 Å / Cross valid method: FREE R-VALUE / σ(F): 1.42 / Phase error: 35.46
Details: The settings of PHENIX.REFINE were tuned to use reference model restraints (PDB: 1KAF), NCS and the twin law K,H,-L.
RfactorNum. reflection% reflectionSelection details
Rfree0.2446 856 4.96 %random
Rwork0.2195 ---
obs0.2208 17252 99.98 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 65.2 Å2
Refinement stepCycle: LAST / Resolution: 2.955→62.588 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3550 1792 0 387 5729
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075603
X-RAY DIFFRACTIONf_angle_d1.5447893
X-RAY DIFFRACTIONf_dihedral_angle_d24.4813107
X-RAY DIFFRACTIONf_chiral_restr0.081884
X-RAY DIFFRACTIONf_plane_restr0.006705
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9554-3.14030.34781440.33662776X-RAY DIFFRACTION95
3.1403-3.38230.25121520.21862674X-RAY DIFFRACTION95
3.3823-3.72190.26551270.23882727X-RAY DIFFRACTION96
3.7219-4.25860.24611520.2312736X-RAY DIFFRACTION95
4.2586-5.35840.26371400.20232701X-RAY DIFFRACTION95
5.3584-26.78780.19551410.19012751X-RAY DIFFRACTION95

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