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- PDB-2gn5: REFINED STRUCTURE OF THE GENE 5 DNA BINDING PROTEIN FROM BACTERIO... -

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Basic information

Entry
Database: PDB / ID: 2gn5
TitleREFINED STRUCTURE OF THE GENE 5 DNA BINDING PROTEIN FROM BACTERIOPHAGE FD
ComponentsGENE V PROTEIN
KeywordsDNA BINDING (VIRAL)
Function / homology
Function and homology information


rolling circle single-stranded viral DNA replication / single-stranded DNA binding / DNA replication
Similarity search - Function
Bacteriophage M13, G5P, DNA-binding / Helix-destabilising protein / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
DNA-Binding protein G5P
Similarity search - Component
Biological speciesEnterobacteria phage M13 (virus)
MethodX-RAY DIFFRACTION / Resolution: 2.3 Å
AuthorsBrayer, G.D. / McPherson, A.
Citation
Journal: J.Mol.Biol. / Year: 1983
Title: Refined structure of the gene 5 DNA binding protein from bacteriophage fd.
Authors: Brayer, G.D. / McPherson, A.
#1: Journal: Eur.J.Biochem. / Year: 1985
Title: A Model for Intracellular Complexation between Gene-5 Protein and Bacteriophage Fd DNA
Authors: Brayer, G.D. / McPherson, A.
#2: Journal: J.Biomol.Struct.Dyn. / Year: 1985
Title: Topological Comparison of Two Helix Destabilizing Proteins. Ribonucleasea and the Gene-5 DNA Binding Protein
Authors: Brayer, G.D. / McPherson, A.
#3: Journal: J.Biomol.Struct.Dyn. / Year: 1984
Title: Cooperative Interactions of the Gene-5 Protein
Authors: Brayer, G.D. / McPherson, A.
#4: Journal: Biological Macromolecules and Assemblies / Year: 1984
Title: The Gene-5 Protein and its Molecular Complexes
Authors: McPherson, A. / Brayer, G.D.
#5: Journal: Biochemistry / Year: 1984
Title: Mechanism of DNA Binding to the Gene 5 Protein of Bacteriophage Fd
Authors: Brayer, G.D. / McPherson, A.
History
DepositionJan 13, 1986Processing site: BNL
SupersessionJan 21, 1986ID: 1GN5
Revision 1.0Jan 21, 1986Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GENE V PROTEIN


Theoretical massNumber of molelcules
Total (without water)9,6991
Polymers9,6991
Non-polymers00
Water21612
1
A: GENE V PROTEIN

A: GENE V PROTEIN


Theoretical massNumber of molelcules
Total (without water)19,3982
Polymers19,3982
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Unit cell
Length a, b, c (Å)76.080, 27.780, 42.000
Angle α, β, γ (deg.)90.00, 102.70, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein GENE V PROTEIN


Mass: 9699.214 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage M13 (virus) / Genus: Inovirus / References: UniProt: P69542
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.23 Å3/Da / Density % sol: 44.86 %
Crystal grow
*PLUS
pH: 7.6 / Method: vapor diffusion / Details: referred to J.Mol.Biol. 106.1077-1081
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115 mg/mlprotein1drop
20.05 MTris-HCl1drop
320 %PEG40001drop
410 %PEG40001reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.3 Å / Num. obs: 3905 / Observed criterion σ(I): 3 / Num. measured all: 8747 / Rmerge F obs: 0.043 / Biso Wilson estimate: 24.8 Å2

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementRfactor Rwork: 0.217 / Highest resolution: 2.3 Å
Refinement stepCycle: LAST / Highest resolution: 2.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms682 0 0 12 694
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.04
X-RAY DIFFRACTIONo_bond_d_na
X-RAY DIFFRACTIONo_bond_d_prot
X-RAY DIFFRACTIONo_angle_d0.176
X-RAY DIFFRACTIONo_angle_d_na
X-RAY DIFFRACTIONo_angle_d_prot
X-RAY DIFFRACTIONo_angle_deg
X-RAY DIFFRACTIONo_angle_deg_na
X-RAY DIFFRACTIONo_angle_deg_prot
X-RAY DIFFRACTIONo_dihedral_angle_d
X-RAY DIFFRACTIONo_dihedral_angle_d_na
X-RAY DIFFRACTIONo_dihedral_angle_d_prot
X-RAY DIFFRACTIONo_improper_angle_d
X-RAY DIFFRACTIONo_improper_angle_d_na
X-RAY DIFFRACTIONo_improper_angle_d_prot
X-RAY DIFFRACTIONo_mcbond_it
X-RAY DIFFRACTIONo_mcangle_it
X-RAY DIFFRACTIONo_scbond_it
X-RAY DIFFRACTIONo_scangle_it
Refinement
*PLUS
Highest resolution: 2.3 Å / Rfactor obs: 0.217
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 24.8 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal targetDev ideal
X-RAY DIFFRACTIONo_bond_d0.013
X-RAY DIFFRACTIONo_angle_d0.039
X-RAY DIFFRACTIONo_planar_d0.0390.161
X-RAY DIFFRACTIONo_plane_restr0.0170.043
X-RAY DIFFRACTIONo_chiral_restr0.120.523

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