[English] 日本語
Yorodumi
- PDB-28mg: crystal structure of Dpo31, of a tail-spike protein with depolyme... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 28mg
Titlecrystal structure of Dpo31, of a tail-spike protein with depolymerase activity identified in a marine podovirus
ComponentsDpo31-deltaD1, viral depolymerase depleted of domain 1
KeywordsVIRAL PROTEIN / tailspike protein / marine virus / podovirus
Function / homologyDI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciesCobetia phage Carin1 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsCzjzek, M. / Sirigu, S. / Roret, T. / Baudoux, A.C.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-15-CE01-0009 France
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2026
Title: Biochemical and structural characterization of a tail-spike protein with depolymerase activity identified in a marine podovirus.
Authors: Sirigu, S. / Roret, T. / Mocaer, P.Y. / Larocque, R. / Jouanneau, D. / Legrand, P. / Baudoux, A.C. / Czjzek, M.
History
DepositionFeb 6, 2026Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 1, 2026Provider: repository / Type: Initial release
Revision 1.1Jul 8, 2026Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Dpo31-deltaD1, viral depolymerase depleted of domain 1
B: Dpo31-deltaD1, viral depolymerase depleted of domain 1
C: Dpo31-deltaD1, viral depolymerase depleted of domain 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)261,12211
Polymers260,5743
Non-polymers5478
Water7,404411
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area41580 Å2
ΔGint-247 kcal/mol
Surface area54180 Å2
Unit cell
Length a, b, c (Å)93.727, 75.607, 124.937
Angle α, β, γ (deg.)90.00, 103.30, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Dpo31-deltaD1, viral depolymerase depleted of domain 1


Mass: 86858.156 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: The crystal structure contains a truncated version missing domain 1 of the polypetidic chain : Dpo31-DeltaD1. The crystal structure also covers the mature protein only, and does not contain ...Details: The crystal structure contains a truncated version missing domain 1 of the polypetidic chain : Dpo31-DeltaD1. The crystal structure also covers the mature protein only, and does not contain the C-terminal domain D4.
Source: (gene. exp.) Cobetia phage Carin1 (virus) / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 411 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.51 Å3/Da / Density % sol: 50.99 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 20% PEG 3350 and 200 mM Potassium nitrate. drop ratio 2:1 (protein to reservoir)

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 5, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.15→47.4 Å / Num. obs: 59091 / % possible obs: 63.4 % / Redundancy: 6.2 % / Biso Wilson estimate: 26.77 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.115 / Rpim(I) all: 0.05 / Net I/σ(I): 9.5
Reflection shellResolution: 2.15→2.21 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.543 / Num. unique obs: 1200 / CC1/2: 0.613 / Rpim(I) all: 0.351 / % possible all: 6.7

-
Processing

Software
NameVersionClassification
BUSTER2.10.4 (21-NOV-2022)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→47.38 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.916 / SU R Cruickshank DPI: 0.628 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.609 / SU Rfree Blow DPI: 0.274 / SU Rfree Cruickshank DPI: 0.279
RfactorNum. reflection% reflectionSelection details
Rfree0.2431 2978 5.04 %RANDOM
Rwork0.2123 ---
obs0.2138 59091 63.8 %-
Displacement parametersBiso mean: 66.75 Å2
Baniso -1Baniso -2Baniso -3
1-6.9311 Å20 Å2-5.2998 Å2
2---7.872 Å20 Å2
3---0.9409 Å2
Refine analyzeLuzzati coordinate error obs: 0.31 Å
Refinement stepCycle: LAST / Resolution: 2.15→47.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12050 0 34 411 12495
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00612319HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.8716742HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4126SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes2245HARMONIC5
X-RAY DIFFRACTIONt_it12319HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.1
X-RAY DIFFRACTIONt_other_torsion15.59
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1692SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact10779SEMIHARMONIC4
LS refinement shellResolution: 2.15→2.27 Å / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.3343 -4.99 %
Rwork0.2356 1123 -
all0.2404 1182 -
obs--8.74 %
Refinement TLS params.Method: refined / Origin x: 30.544 Å / Origin y: 0.0754 Å / Origin z: 27.8786 Å
111213212223313233
T-0.0363 Å20.0296 Å2-0.0651 Å2-0.304 Å20.11 Å2---0.0887 Å2
L2.9855 °2-0.3447 °2-1.5766 °2-0.4885 °20.1304 °2--1.9835 °2
S0.1127 Å °0.4044 Å °0.1853 Å °-0.1018 Å °-0.0987 Å °-0.1596 Å °0.0179 Å °0.6549 Å °-0.014 Å °
Refinement TLS groupSelection details: { *|* }

+
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