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- PDB-1c1k: BACTERIOPHAGE T4 GENE 59 HELICASE ASSEMBLY PROTEIN -

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Basic information

Entry
Database: PDB / ID: 1c1k
TitleBACTERIOPHAGE T4 GENE 59 HELICASE ASSEMBLY PROTEIN
ComponentsBPT4 GENE 59 HELICASE ASSEMBLY PROTEIN
KeywordsDNA BINDING PROTEIN / HELICASE ASSEMBLY / DNA REPLICATION / DNA RECOMBINATION / FORKED DNA
Function / homology
Function and homology information


bidirectional double-stranded viral DNA replication / DNA replication / DNA binding
Similarity search - Function
Bacteriophage T4, Gp59, helicase assembly protein, C-terminal domain / Bacteriophage T4, Gp59, helicase assembly protein / Bacteriophage T4, Gp59, helicase assembly protein, N-terminal / Bacteriophage T4, Gp59, helicase assembly protein, C-terminal / Bacteriophage T4, Gp59, helicase assembly protein domain superfamily / Bacteriophage T4, Gp59, helicase assembly protein, C-terminal domain superfamily / T4 gene Gp59 loader of gp41 DNA helicase / T4 gene Gp59 loader of gp41 DNA helicase C-term / Annexin V; domain 1 / Helicase, Ruva Protein; domain 3 - #60 ...Bacteriophage T4, Gp59, helicase assembly protein, C-terminal domain / Bacteriophage T4, Gp59, helicase assembly protein / Bacteriophage T4, Gp59, helicase assembly protein, N-terminal / Bacteriophage T4, Gp59, helicase assembly protein, C-terminal / Bacteriophage T4, Gp59, helicase assembly protein domain superfamily / Bacteriophage T4, Gp59, helicase assembly protein, C-terminal domain superfamily / T4 gene Gp59 loader of gp41 DNA helicase / T4 gene Gp59 loader of gp41 DNA helicase C-term / Annexin V; domain 1 / Helicase, Ruva Protein; domain 3 - #60 / Helicase, Ruva Protein; domain 3 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.45 Å
AuthorsMueser, T.C. / Jones, C.E. / Nossal, N.G. / Hyde, C.C.
CitationJournal: J.Mol.Biol. / Year: 2000
Title: Bacteriophage T4 gene 59 helicase assembly protein binds replication fork DNA. The 1.45 A resolution crystal structure reveals a novel alpha-helical two-domain fold.
Authors: Mueser, T.C. / Jones, C.E. / Nossal, N.G. / Hyde, C.C.
History
DepositionJul 22, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 16, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BPT4 GENE 59 HELICASE ASSEMBLY PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,84615
Polymers26,0361
Non-polymers81014
Water5,368298
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)31.865, 65.882, 108.166
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121

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Components

#1: Protein BPT4 GENE 59 HELICASE ASSEMBLY PROTEIN


Mass: 26036.279 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T4 (virus) / Genus: T4-like viruses / Species: Enterobacteria phage T4 sensu lato / Plasmid: PVEX11 (T7 PROMOTER) / Production host: Escherichia coli (E. coli) / References: UniProt: P13342
#2: Chemical ChemComp-IR / IRIDIUM ION


Mass: 192.217 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ir
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 298 / 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: 2.18 Å3/Da / Density % sol: 43.58 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 100 MM NA CACODYLATE, PH 6.5 200 MM NH4 ACETATE, 50 MM (NH4)2SO4, 10 - 14% PEG 3350 GRADIENT, 20% ETHYLENE GLYCOL, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
115 mg/mlprotein1drop
250 mMbis-Tris-HCl1drop
350 mM1dropNH4Cl
410 mM1dropMgCl2
51 mMdithiothreitol1drop
6100 mMNa cacodylate1reservoir
7200 mMammonium acetate1reservoir
850 mMammonium sulfate1reservoir
914 %(w/v)PEG33501reservoir
1020 %(w/v)ethylene glycol1reservoir

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.9795
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 27, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.45→50 Å / Num. obs: 37155 / % possible obs: 89.8 % / Observed criterion σ(I): 1 / Redundancy: 3.95 % / Biso Wilson estimate: 12.1 Å2 / Rmerge(I) obs: 0.043 / Net I/σ(I): 26.9
Reflection shellResolution: 1.45→1.5 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.073 / % possible all: 71.8
Reflection
*PLUS
Num. measured all: 150823 / Rmerge(I) obs: 0.038

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Processing

Software
NameVersionClassification
PHASESphasing
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 1.45→5 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.253 1961 5.8 %RANDOM
Rwork0.2 ---
all0.205 35937 --
obs0.205 33976 96.7 %-
Refinement stepCycle: LAST / Resolution: 1.45→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1838 0 14 298 2150
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.05
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it

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