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- PDB-28lx: crystal structure of Dpo31, of a tail-spike protein with depolyme... -

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Basic information

Entry
Database: PDB / ID: 28lx
Titlecrystal structure of Dpo31, of a tail-spike protein with depolymerase activity identified in a marine podovirus
ComponentsDpo31, tailspike protein
KeywordsVIRAL PROTEIN / tailspike protein / marine virus / podovirus
Biological speciesCobetia phage Carin1 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsCzjzek, M. / Sirigu, S. / Roret, T. / Legrand, P. / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dpo31, tailspike protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,61710
Polymers86,8581
Non-polymers7599
Water77543
1
A: Dpo31, tailspike protein
hetero molecules

A: Dpo31, tailspike protein
hetero molecules

A: Dpo31, tailspike protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)262,85130
Polymers260,5743
Non-polymers2,27627
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-y-1,x-y-1,z1
crystal symmetry operation3_545-x+y,-x-1,z1
Buried area48120 Å2
ΔGint-534 kcal/mol
Surface area67530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.200, 88.200, 643.330
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-1000-

HOH

21A-1014-

HOH

31A-1021-

HOH

41A-1032-

HOH

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Components

#1: Protein Dpo31, tailspike protein


Mass: 86858.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The missing residues 98 to 103 could not be modelled, since no electron density was visible; the C-terminal residues from 666 to 830 are simply not present in the crystal structure that ...Details: The missing residues 98 to 103 could not be modelled, since no electron density was visible; the C-terminal residues from 666 to 830 are simply not present in the crystal structure that contains the mature form of Dpo31 without these residues.
Source: (gene. exp.) Cobetia phage Carin1 (virus) / Gene: gp31 / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 3.53 Å3/Da / Density % sol: 65.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: Hanging drops, 2 microL of protein (12 mg/ml) with 1 microL of reservoir solution 1.2 M Ammonium sulfate and 100 mM Citric acid at pH 5.0

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Cryostream / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97911 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 25, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97911 Å / Relative weight: 1
ReflectionResolution: 2.2→49.2 Å / Num. obs: 22469 / % possible obs: 43.7 % / Redundancy: 21.2 % / Biso Wilson estimate: 46.19 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.115 / Rpim(I) all: 0.026 / Net I/σ(I): 18.4
Reflection shellResolution: 2.2→2.26 Å / Redundancy: 8.9 % / Rmerge(I) obs: 0.875 / Num. unique obs: 300 / CC1/2: 0.787 / Rpim(I) all: 0.295 / % possible all: 5.7

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Processing

Software
NameVersionClassification
BUSTER2.10.4 (21-NOV-2022)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: SAD / Resolution: 2.2→49.2 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.885 / SU R Cruickshank DPI: 0.943 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.937 / SU Rfree Blow DPI: 0.359 / SU Rfree Cruickshank DPI: 0.365
Details: HYDROGENS WERE FULLY REFINED WITH ZERO OCCUPANCY AT NUCLEAR POSITION.
RfactorNum. reflection% reflectionSelection details
Rfree0.273 1092 4.86 %RANDOM
Rwork0.252 ---
obs0.253 22468 43.2 %-
Displacement parametersBiso mean: 57.35 Å2
Baniso -1Baniso -2Baniso -3
1--0.3265 Å20 Å20 Å2
2---0.3265 Å20 Å2
3---0.6531 Å2
Refine analyzeLuzzati coordinate error obs: 0.44 Å
Refinement stepCycle: LAST / Resolution: 2.2→49.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4789 0 40 43 4872
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0054926HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.836707HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1641SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes892HARMONIC5
X-RAY DIFFRACTIONt_it4920HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.7
X-RAY DIFFRACTIONt_other_torsion15.99
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion670SEMIHARMONIC5
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_contact4021SEMIHARMONIC4
LS refinement shellResolution: 2.2→2.33 Å
RfactorNum. reflection% reflection
Rfree0.2808 -4.67 %
Rwork0.3003 429 -
obs--58.5 %
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)
14.06990.18523.60056.6727-0.41553.84120.3332-0.3315-0.10720.469-0.0787-0.07250.7435-0.1992-0.25450.13-0.0287-0.0756-0.00450.1318-0.2845-3.559-75.566189.263
20.0125-0.02140.13320.0364-0.16861.31050.0190.01660.0201-0.03520.0534-0.0079-0.1057-0.1461-0.07230.00990.0120.0391-0.010.0203-0.05-2.6376-46.093567.1935
32.0117-1.16530.05825.42490.677200.0876-0.13230.2737-0.5991-0.0907-0.2429-0.1057-0.06950.00310.0003-0.03560.0514-0.20080.03390.0687-5.8888-22.325839.0679
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|7 - A|106 }A7 - 106
2X-RAY DIFFRACTION2{ A|110 - A|442 A|526 - A|663 }A110 - 442
3X-RAY DIFFRACTION2{ A|110 - A|442 A|526 - A|663 }A526 - 663
4X-RAY DIFFRACTION3{ A|443 - A|525 }A443 - 525

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