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- PDB-2fip: Phage phi29 transcription regulator p4 -

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Basic information

Entry
Database: PDB / ID: 2fip
TitlePhage phi29 transcription regulator p4
ComponentsLate genes activator
KeywordsTRANSCRIPTION / PROTEIN-DNA COMPLEX / N-HOOK DNA-BINDING MOTIF / TRANSCRIPTION REGULATION
Function / homology
Function and homology information


sigma factor activity / DNA-directed 5'-3' 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
Late genes activator p4
Similarity search - Component
Biological speciesBacillus phage phi29 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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

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Assembly

Deposited unit
A: Late genes activator
B: Late genes activator
C: Late genes activator
D: Late genes activator
E: Late genes activator
F: Late genes activator


Theoretical massNumber of molelcules
Total (without water)83,2076
Polymers83,2076
Non-polymers00
Water10,124562
1
A: Late genes activator
B: Late genes activator


Theoretical massNumber of molelcules
Total (without water)27,7362
Polymers27,7362
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1640 Å2
ΔGint-17 kcal/mol
Surface area12740 Å2
MethodPISA
2
C: Late genes activator
D: Late genes activator


Theoretical massNumber of molelcules
Total (without water)27,7362
Polymers27,7362
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1800 Å2
ΔGint-17 kcal/mol
Surface area12590 Å2
MethodPISA
3
E: Late genes activator
F: Late genes activator


Theoretical massNumber of molelcules
Total (without water)27,7362
Polymers27,7362
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1680 Å2
ΔGint-17 kcal/mol
Surface area12170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.349, 136.232, 140.409
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Late genes activator / Early protein GP4


Mass: 13867.782 Da / Num. of mol.: 6
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
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 562 / 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: 3.81 Å3/Da / Density % sol: 67.73 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 2M NaCl, 10% PEG 6000, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 8, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2→55 Å / Num. all: 86815 / Num. obs: 81606 / % possible obs: 0.94 % / Observed criterion σ(I): 2
Reflection shellResolution: 2→2.11 Å / % possible all: 0.94

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Processing

Software
NameVersionClassification
MAR345data collection
SCALAdata scaling
AMoREphasing
CNSrefinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→40 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.256 8164 9.4 %RANDOM
Rwork0.227 ---
all0.235 86679 --
obs0.232 81377 93.9 %-
Solvent computationBsol: 51.606 Å2
Displacement parametersBiso mean: 33.506 Å2
Baniso -1Baniso -2Baniso -3
1-4.241 Å20 Å20 Å2
2---6.65 Å20 Å2
3---2.409 Å2
Refinement stepCycle: LAST / Resolution: 2→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5837 0 0 562 6399
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.24
X-RAY DIFFRACTIONc_bond_d0.007
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:water_rep.param

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