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- PDB-4lhf: Crystal structure of a DNA binding protein from phage P2 -

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Basic information

Entry
Database: PDB / ID: 4lhf
TitleCrystal structure of a DNA binding protein from phage P2
ComponentsRegulatory protein cox
KeywordsVIRAL PROTEIN / helix-turn-helix / DNA binding
Function / homologyMultidrug-efflux Transporter Regulator; Chain: A; Domain 2 / Regulatory phage protein Cox / Regulatory phage protein Cox / Cox superfamily / Regulatory phage protein cox / Helix non-globular / Special / DNA binding / Regulatory protein cox
Function and homology information
Biological speciesEnterobacteria phage P2 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.401 Å
AuthorsBerntsson, R.P.-A. / Odegrip, R. / Sehlen, W. / Skaar, K. / Svensson, L.M. / Massad, T. / Haggard-Ljungquist, E. / Stenmark, P.
CitationJournal: Nucleic Acids Res. / Year: 2014
Title: Structural insight into DNA binding and oligomerization of the multifunctional Cox protein of bacteriophage P2.
Authors: Berntsson, R.P. / Odegrip, R. / Sehlen, W. / Skaar, K. / Svensson, L.M. / Massad, T. / Hogbom, M. / Haggard-Ljungquist, E. / Stenmark, P.
History
DepositionJul 1, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 5, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 12, 2014Group: Database references
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Regulatory protein cox


Theoretical massNumber of molelcules
Total (without water)10,3141
Polymers10,3141
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)66.254, 66.254, 33.802
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65
DetailsIt is oligomeric, but its exact oligomeric state is dependant on the concentration of the protein, something also reflected in the functionality of the protein

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Components

#1: Protein Regulatory protein cox


Mass: 10313.957 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage P2 (virus) / Gene: cox / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P07695

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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: 2.08 Å3/Da / Density % sol: 40.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 0.2 M Na-citrate pH 5.0, 24% PEG 4000, 20% isopropanol, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONESRF ID23-110.8726
SYNCHROTRONSLS X06SA20.9793
Detector
TypeIDDetectorDate
MARMOSAIC 225 mm CCD1CCDMar 5, 2010
DECTRIS PILATUS 6M2PIXELMar 26, 2012
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.87261
20.97931
ReflectionResolution: 2.401→57.378 Å / Num. all: 3108 / Num. obs: 3108 / % possible obs: 92.9 % / Redundancy: 6 % / Rmerge(I) obs: 0.077 / Rsym value: 0.077 / Net I/σ(I): 17.3
Reflection shell

Diffraction-ID: 1,2

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.4-2.533.60.4791.614474030.47986.1
2.53-2.684.40.2942.617484010.29487.6
2.68-2.874.30.1574.816093770.15788.6
2.87-3.15.30.16419093610.1691.3
3.1-3.397.60.1564.328513760.15699.4
3.39-3.797.60.0927.225673360.09299.4
3.79-4.387.70.0641023193020.06498.5
4.38-5.377.90.0591119622480.05997.9
5.37-7.597.70.0639.914991940.06397
7.59-33.8477.50.04212.78271100.04292.7

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Processing

Software
NameVersionClassificationNB
SCALA3.2.25data scaling
PHENIX1.8_1069refinement
PDB_EXTRACT3.11data extraction
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.401→33.127 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.6817 / SU ML: 0 / σ(F): 1.4 / Phase error: 35.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2528 132 4.26 %random
Rwork0.2089 ---
obs0.211 3097 90.74 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 148.75 Å2 / Biso mean: 90.6137 Å2 / Biso min: 57.7 Å2
Refinement stepCycle: LAST / Resolution: 2.401→33.127 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms631 0 0 0 631
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003647
X-RAY DIFFRACTIONf_angle_d0.733875
X-RAY DIFFRACTIONf_chiral_restr0.05192
X-RAY DIFFRACTIONf_plane_restr0.003108
X-RAY DIFFRACTIONf_dihedral_angle_d13.716240
LS refinement shellResolution: 2.401→2.487 Å / Total num. of bins used: 1
RfactorNum. reflection% reflection
Rfree0.2528 132 -
Rwork0.2089 2965 -
all-3097 -
obs--91 %

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