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- PDB-2fio: Phage phi29 transcription regulator p4-DNA complex -

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Basic information

Entry
Database: PDB / ID: 2fio
TitlePhage phi29 transcription regulator p4-DNA complex
Components
  • (DNA (41-MER)) x 2
  • Late genes activator
KeywordsTRANSCRIPTION/DNA / PROTEIN-DNA COMPLEX / N-HOOK DNA-BINDING MOTIF / TRANSCRIPTION REGULATION / TRANSCRIPTION-DNA COMPLEX
Function / homology
Function and homology information


sigma factor activity / DNA-directed RNA polymerase activity / regulation of DNA-templated transcription / DNA binding
Similarity search - Function
Phi-29-like late genes activator, P4 / Phi-29-like late genes activator / Phi-29-like late genes activator superfamily / Phi-29-like late genes activator (early protein GP4) / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Late genes activator p4
Similarity search - Component
Biological speciesBacillus phage phi29 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsBadia, D. / Camacho, A. / Perez-Lago, L. / Escandon, C. / Salas, M. / Coll, M.
CitationJournal: Mol.Cell / Year: 2006
Title: The structure of phage phi29 transcription regulator p4-DNA complex reveals an N-hook motif for DNA
Authors: Badia, D. / Camacho, A. / Perez-Lago, L. / Escandon, C. / Salas, M. / Coll, M.
History
DepositionDec 30, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 26, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.4Feb 14, 2024Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms
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
C: DNA (41-MER)
D: DNA (41-MER)
A: Late genes activator
B: Late genes activator


Theoretical massNumber of molelcules
Total (without water)55,0914
Polymers55,0914
Non-polymers00
Water1,54986
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.400, 27.800, 192.800
Angle α, β, γ (deg.)90.00, 97.40, 90.00
Int Tables number3
Space group name H-MP121

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Components

#1: DNA chain DNA (41-MER)


Mass: 12641.237 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain DNA (41-MER)


Mass: 12591.121 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein Late genes activator / Early protein GP4


Mass: 14929.089 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus phage phi29 (virus) / Genus: Phi29-like viruses / Gene: 4 / Production host: Escherichia coli (E. coli) / References: UniProt: P03682
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / 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: 2.51 Å3/Da / Density % sol: 50.93 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% PEG 6000, 80mM magnesium chloride, 50mM CHES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 600011
2MgCl211
3CHES11
4PEG 600012
5MgCl212
6CHES12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID13 / Wavelength: 0.978 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 27, 2004
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. all: 15917 / Num. obs: 13386 / % possible obs: 0.84 % / Observed criterion σ(I): 2
Reflection shellResolution: 2.7→3 Å / % possible all: 0.59

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Processing

Software
NameClassification
MAR345data collection
XDSdata reduction
AMoREphasing
CNSrefinement
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.279 1091 6.9 %RANDOM
Rwork0.229 ---
all0.234 15751 --
obs0.232 15751 99.1 %-
Solvent computationBsol: 37.635 Å2
Displacement parametersBiso mean: 60.854 Å2
Baniso -1Baniso -2Baniso -3
1--17.42 Å20 Å20.271 Å2
2---2.371 Å20 Å2
3---19.791 Å2
Refinement stepCycle: LAST / Resolution: 2.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2016 1675 0 86 3777
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.26
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:dna-rna_rep.param
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.param

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