[English] 日本語
Yorodumi
- PDB-8s9i: Crystal structure of the gp32 C-terminal peptide/Dda/dT8 -

+
Open data


ID or keywords:

Loading...

-
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 / ATP hydrolysis activity / 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 / Nucleic acid-binding, OB-fold / ATPases associated with a variety of cellular activities ...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 / Nucleic acid-binding, OB-fold / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / 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: Nucleic Acids Res. / Year: 2024
Title: Structural and functional insights into the interaction between the bacteriophage T4 DNA processing proteins gp32 and Dda.
Authors: He, X. / Yun, M.K. / Li, Z. / Waddell, M.B. / Nourse, A. / Churion, K.A. / Kreuzer, K.N. / Byrd, A.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
Revision 1.2Jan 22, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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
Water00
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

-
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)
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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.

-
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

-
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)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more