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- PDB-24qj: Crystal structure of a tailspike depolymerase (Solidus_gp83) from... -

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Basic information

Entry
Database: PDB / ID: 24qj
TitleCrystal structure of a tailspike depolymerase (Solidus_gp83) from Acinetobacter phage Solidus
ComponentsTailspike depolymerase
KeywordsVIRAL PROTEIN / depolymerase / Acinetobacter phage Solidus / viruses / tailspike
Biological speciesAcinetobacter phage Solidus (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.49 Å
AuthorsMatyuta, I.O. / Shneider, M.M. / Timoshina, O.Y. / Boyko, K.M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Novel Genus of Phages Infecting Acinetobacter baumannii
Authors: Shneider, M.M. / Timoshina, O.Y. / Matyuta, I.O. / Lukianova, A.A. / Tokmakova, A.D. / Shelenkov, A.A. / Mikhailova, O.Y. / Kasimova, A.A. / Boyko, K.M. / Prokhorov, N.S. / Popov, V.O. / ...Authors: Shneider, M.M. / Timoshina, O.Y. / Matyuta, I.O. / Lukianova, A.A. / Tokmakova, A.D. / Shelenkov, A.A. / Mikhailova, O.Y. / Kasimova, A.A. / Boyko, K.M. / Prokhorov, N.S. / Popov, V.O. / Knirel, Y.A. / Miroshnikov, K.A.
History
DepositionMar 16, 2026Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 25, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tailspike depolymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,6663
Polymers52,2331
Non-polymers4332
Water37821
1
A: Tailspike depolymerase
hetero molecules

A: Tailspike depolymerase
hetero molecules

A: Tailspike depolymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,9989
Polymers156,7003
Non-polymers1,2986
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area55730 Å2
ΔGint-203 kcal/mol
Surface area46610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.224, 84.224, 529.394
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein Tailspike depolymerase


Mass: 52233.465 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter phage Solidus (virus) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / 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: 3.46 Å3/Da / Density % sol: 64.44 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / Details: 0.8M K-Na-tartrate, 0.1M Tris pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.87313 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 11, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87313 Å / Relative weight: 1
ReflectionResolution: 2.49→44.12 Å / Num. obs: 25822 / % possible obs: 99.1 % / Redundancy: 6.9 % / CC1/2: 0.992 / Rmerge(I) obs: 0.215 / Rpim(I) all: 0.088 / Rrim(I) all: 0.233 / Χ2: 1.02 / Net I/σ(I): 7.6 / Num. measured all: 177979
Reflection shellResolution: 2.49→2.6 Å / % possible obs: 94.5 % / Redundancy: 6.8 % / Rmerge(I) obs: 1.54 / Num. measured all: 18667 / Num. unique obs: 2734 / CC1/2: 0.495 / Rpim(I) all: 0.626 / Rrim(I) all: 1.667 / Χ2: 0.94 / Net I/σ(I) obs: 1.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.49→40.17 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.896 / SU B: 5.284 / SU ML: 0.126 / Cross valid method: THROUGHOUT / ESU R: 0.068 / ESU R Free: 0.058 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27673 1325 5.1 %RANDOM
Rwork0.2073 ---
obs0.21093 24496 99.09 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.186 Å2
Baniso -1Baniso -2Baniso -3
1-17.84 Å20 Å20 Å2
2--17.84 Å20 Å2
3----35.68 Å2
Refinement stepCycle: 1 / Resolution: 2.49→40.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3592 0 29 21 3642
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0133702
X-RAY DIFFRACTIONr_bond_other_d0.0040.0153363
X-RAY DIFFRACTIONr_angle_refined_deg2.2071.6465044
X-RAY DIFFRACTIONr_angle_other_deg1.4191.5797737
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.3955474
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.07823.523176
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.94915543
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6711515
X-RAY DIFFRACTIONr_chiral_restr0.10.2499
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.024303
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02859
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.2394.2611899
X-RAY DIFFRACTIONr_mcbond_other5.2344.261898
X-RAY DIFFRACTIONr_mcangle_it6.7916.3972372
X-RAY DIFFRACTIONr_mcangle_other6.7916.3972373
X-RAY DIFFRACTIONr_scbond_it6.2514.6011803
X-RAY DIFFRACTIONr_scbond_other6.254.6031804
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other86.7652673
X-RAY DIFFRACTIONr_long_range_B_refined9.38649.7413885
X-RAY DIFFRACTIONr_long_range_B_other9.38649.753886
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.494→2.558 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.373 69 -
Rwork0.247 1680 -
obs--91.71 %

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