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- PDB-8gme: Crystal structure of the gp32-Dda-dT17 complex -

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Basic information

Entry
Database: PDB / ID: 8gme
TitleCrystal structure of the gp32-Dda-dT17 complex
Components
  • Dda helicase
  • dT17
  • gp32
KeywordsDNA BINDING PROTEIN/DNA / T4 / gp32 / Dda / complex / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


bidirectional double-stranded viral DNA replication / helicase activity / single-stranded DNA binding / DNA recombination / DNA replication / DNA repair / metal ion binding
Similarity search - Function
Dda helicase SH3 domain / Dda helicase SH3 domain / Bacteriophage T4, Gp32, single-stranded DNA-binding domain / Bacteriophage T4, Gp32, single-stranded DNA-binding superfamily / Bacteriophage T4, Gp32, single-stranded DNA-binding / gp32 DNA binding protein like / AAA domain / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Nucleic acid-binding, OB-fold / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA helicase / Single-stranded DNA-binding protein
Similarity search - Component
Biological speciesTequatrovirus T4
Tequatrovirus
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.98 Å
AuthorsHe, X. / Yun, M.K. / White, S.W.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P20GM121293 United States
Other privateCA021765
CitationJournal: To Be Published
Title: Crystal structure of the gp32-Dda-dT17 complex
Authors: He, X. / Yun, M.K. / White, S.W.
History
DepositionMar 24, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 28, 2023Provider: repository / Type: Initial release
Revision 2.0Nov 1, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / entity_src_gen / pdbx_contact_author / pdbx_poly_seq_scheme / pdbx_unobs_or_zero_occ_residues / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / software / struct_conf
Item: _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_gene_src_scientific_name ..._entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_gene_src_scientific_name / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.pdb_mon_id / _refine.B_iso_mean / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.pdbx_diffrn_id / _refine.pdbx_ls_sigma_F / _refine.pdbx_overall_phase_error / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_protein / _refine_ls_restr.dev_ideal / _refine_ls_restr.number / _software.classification / _software.name
Description: Model completeness / Provider: author / Type: Coordinate replacement
Revision 3.0Dec 20, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Database references / Derived calculations / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / entity ...atom_site / entity / entity_name_com / entity_poly / entity_poly_seq / entity_src_gen / pdbx_poly_seq_scheme / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_residues / struct_conf / struct_conn / struct_ref_seq / struct_ref_seq_dif / struct_sheet_range
Item: _atom_site.label_seq_id / _entity.formula_weight ..._atom_site.label_seq_id / _entity.formula_weight / _entity.pdbx_description / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _struct_conf.beg_label_seq_id / _struct_conf.end_label_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_ref_seq.seq_align_beg / _struct_ref_seq.seq_align_end / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_label_seq_id
Revision 3.1Dec 27, 2023Group: Database references / Structure summary / Category: entity / pdbx_database_related / Item: _entity.pdbx_description

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: gp32
C: Dda helicase
B: gp32
D: Dda helicase
P: dT17
Q: dT17
hetero molecules


Theoretical massNumber of molelcules
Total (without water)181,7158
Polymers181,5856
Non-polymers1312
Water00
1
A: gp32
C: Dda helicase
P: dT17
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,8584
Polymers90,7923
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: gp32
D: Dda helicase
Q: dT17
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,8584
Polymers90,7923
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)109.862, 114.353, 147.379
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein gp32


Mass: 33545.375 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tequatrovirus T4 / Gene: 32 / Production host: Escherichia coli (E. coli) / References: UniProt: P03695
#2: Protein Dda helicase


Mass: 52120.566 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tequatrovirus / Gene: teqhal_52 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A6B9WEE3
#3: DNA chain dT17


Mass: 5126.320 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
Has ligand of interestN

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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: 2.48 Å3/Da / Density % sol: 50.44 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop
Details: 10% (w/v) PEG4000, 0.1 M Hepes pH 7.5, 0.1 M MgCl2. *** *** 25% (w/v) PEG1000; 0.1M Na/K phosphate pH 6.5; 0.2M NaCl.

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Data collection

Diffraction
IDMean temperature (K)Crystal-IDSerial crystal experiment
11001N
21001N
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 22-BM11.27046
SYNCHROTRONAPS 22-ID21
Detector
TypeIDDetectorDate
RAYONIX MX300-HS1CCDNov 26, 2013
RAYONIX MX300-HS2CCDMar 30, 2014
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
11.270461
211
ReflectionResolution: 4.98→29.56 Å / Num. obs: 8255 / % possible obs: 96.83 % / Redundancy: 10.56 % / CC1/2: 1 / Rsym value: 0.0714 / Net I/σ(I): 12.5
Reflection shellResolution: 4.98→5.08 Å / Redundancy: 8.34 % / Mean I/σ(I) obs: 4.24 / Num. unique obs: 419 / CC1/2: 0.77 / Rsym value: 0.3891 / % possible all: 96.83

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-20001.14_3260data scaling
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 4.98→29.56 Å / Cross valid method: FREE R-VALUE / σ(F): 24.36 / Phase error: 36.3875 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3133 436 5.3 %
Rwork0.2862 7796 -
obs0.2969 8232 96.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 200.61 Å2
Refinement stepCycle: LAST / Resolution: 4.98→29.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10565 400 2 0 10967
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003811237
X-RAY DIFFRACTIONf_angle_d0.789615265
X-RAY DIFFRACTIONf_chiral_restr0.04991683
X-RAY DIFFRACTIONf_plane_restr0.00441880
X-RAY DIFFRACTIONf_dihedral_angle_d14.59636650

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