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- PDB-1yhb: CRYSTAL STRUCTURES OF Y41H AND Y41F MUTANTS OF GENE V PROTEIN FRO... -

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Basic information

Entry
Database: PDB / ID: 1yhb
TitleCRYSTAL STRUCTURES OF Y41H AND Y41F MUTANTS OF GENE V PROTEIN FROM FF PHAGE SUGGEST POSSIBLE PROTEIN-PROTEIN INTERACTIONS IN GVP-SSDNA COMPLEX
ComponentsGENE V PROTEIN
KeywordsDNA BINDING PROTEIN / DNA-BINDING PROTEIN
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 f1 (virus)
MethodX-RAY DIFFRACTION / Resolution: 2.2 Å
AuthorsGuan, Y. / Zhang, H. / Konings, R.N.H. / Hilbers, C.W. / Terwilliger, T.C. / Wang, A.H.-J.
Citation
Journal: Biochemistry / Year: 1994
Title: Crystal structures of Y41H and Y41F mutants of gene V protein from Ff phage suggest possible protein-protein interactions in the GVP-ssDNA complex.
Authors: Guan, Y. / Zhang, H. / Konings, R.N. / Hilbers, C.W. / Terwilliger, T.C. / Wang, A.H.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1994
Title: Structure of the Gene V Protein of Bacteriophage F1 Determined by Multiwavelength X-Ray Diffraction on the Selenomethionyl Protein
Authors: Skinner, M.M. / Zhang, H. / Leschnitzer, D.H. / Guan, Y. / Bellamy, H. / Sweet, R.M. / Gray, C.W. / Konings, R.N.H. / Wang, A.H.-J. / Terwilliger, T.C.
History
DepositionApr 14, 1994Processing site: BNL
Revision 1.0Jun 22, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other / Structure summary
Category: pdbx_database_status / struct_conf ...pdbx_database_status / struct_conf / struct_conf_type / struct_keywords
Item: _pdbx_database_status.process_site / _struct_keywords.text
Revision 1.4Feb 14, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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)9,6831
Polymers9,6831
Non-polymers00
Water39622
1
A: GENE V PROTEIN

A: GENE V PROTEIN


Theoretical massNumber of molelcules
Total (without water)19,3662
Polymers19,3662
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Unit cell
Length a, b, c (Å)74.970, 27.900, 42.550
Angle α, β, γ (deg.)90.00, 103.09, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein GENE V PROTEIN


Mass: 9683.214 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage f1 (virus) / Genus: Inovirus / Species: Enterobacteria phage M13 / References: UniProt: P69543
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / 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: 2.24 Å3/Da / Density % sol: 45.01 %
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.5 mMGene V protein1drop
24 mMTris1drop
315 %PEG40001drop
415 %PEG40001reservoir

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Processing

RefinementResolution: 2.2→8 Å / σ(F): 3
RfactorNum. reflection% reflection
Rwork0.18 --
obs-3210 74 %
Refinement stepCycle: LAST / Resolution: 2.2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms686 0 0 22 708
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.017
X-RAY DIFFRACTIONo_bond_d_na
X-RAY DIFFRACTIONo_bond_d_prot
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_d_na
X-RAY DIFFRACTIONo_angle_d_prot
X-RAY DIFFRACTIONo_angle_deg3.5
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
Rfactor Rfree: 0.172 / Rfactor Rwork: 0.18
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_angle_d3.5
X-RAY DIFFRACTIONo_dihedral_angle_d28
X-RAY DIFFRACTIONo_dihedral_angle_deg1.7

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