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- PDB-8s9i: Crystal structure of the gp32 C-terminal peptide/Dda/dT8 -

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Basic information

Entry
Database: PDB / ID: 8s9i
TitleCrystal structure of the gp32 C-terminal peptide/Dda/dT8
Components
  • Dda helicase
  • dT8
  • gp32 C-terminal peptide
KeywordsDNA BINDING PROTEIN / T4 / gp32 / Dda
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 helicase / Single-stranded DNA-binding protein
Similarity search - Component
Biological speciesTequatrovirus
Tequatrovirus T4
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.53 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 C-terminal peptide/Dda/dT8
Authors: He, X. / Yun, M.K. / White, S.W.
History
DepositionMar 28, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 28, 2023Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dda helicase
G: gp32 C-terminal peptide
B: dT8


Theoretical massNumber of molelcules
Total (without water)56,9243
Polymers56,9243
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)121.789, 121.789, 88.501
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Dda helicase


Mass: 52120.566 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tequatrovirus / Gene: teqhal_52 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A6B9WEE3
#2: Protein/peptide gp32 C-terminal peptide / SSB protein / Gp32 / Helix-destabilizing protein


Mass: 2414.600 Da / Num. of mol.: 1 / Fragment: chemically synthesized C-terminal peptide / Source method: obtained synthetically / Source: (synth.) Tequatrovirus T4 / References: UniProt: P03695
#3: DNA chain dT8


Mass: 2388.585 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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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: 3.33 Å3/Da / Density % sol: 63.05 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / Details: 20% (w/v) PEG3350, 0.2 M tri-lithium citrate.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Apr 11, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.53→36.35 Å / Num. obs: 9276 / % possible obs: 96.22 % / Redundancy: 4.84 % / CC1/2: 0.92 / Rsym value: 0.1362 / Net I/σ(I): 4.59
Reflection shellResolution: 3.53→3.59 Å / Redundancy: 3.62 % / Mean I/σ(I) obs: 2.62 / Num. unique obs: 490 / CC1/2: 0.29 / Rsym value: 0.356 / % possible all: 98.99

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Processing

Software
NameVersionClassification
KYLIN(1.11.1_2575: ???)data scaling
KYLINdata reduction
PHENIX1.14_3260refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.53→36.348 Å / Cross valid method: FREE R-VALUE / σ(F): 161.43 / Phase error: 30.11 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2779 465 5.03 %
Rwork0.2528 --
obs0.2562 9237 96.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.53→36.348 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3619 65 0 0 3684
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033768
X-RAY DIFFRACTIONf_angle_d0.625114
X-RAY DIFFRACTIONf_dihedral_angle_d4.5652239
X-RAY DIFFRACTIONf_chiral_restr0.047575
X-RAY DIFFRACTIONf_plane_restr0.004639
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5334-4.0440.26781500.24462933X-RAY DIFFRACTION94
4.044-5.09220.24311550.2262901X-RAY DIFFRACTION92
5.0922-33.89950.31981470.28722917X-RAY DIFFRACTION89
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
1-0.00140.0029-0.00750.0547-0.00590.0268-0.06230.002-0.06240.0133-0.0161-0.0671-0.0340.0464-0.18220.04690.059-0.0609-0.1259-0.06920.3749-6.964748.48024.4195
20.27520.35190.06340.50120.04380.14380.0053-0.02580.0177-0.0115-0.016-0.0038-0.0460.0217-0.03120.04790.0068-0.06290.0401-0.01290.2412-24.74952.9221-17.8364
35.84410.2619-3.99574.70562.29634.0372-0.17841.08890.5907-0.96920.1776-0.001-0.4901-0.23360.00030.7926-0.063-0.06291.33220.06730.9283-5.038656.2143-5.7516
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 4 through 439)
2X-RAY DIFFRACTION2(chain 'G' and resid 249 through 269)
3X-RAY DIFFRACTION3(chain 'B' and resid 601 through 604)

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