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- PDB-24qi: Crystal structure of a tailspike depolymerase (Belisarius_gp86) f... -

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Basic information

Entry
Database: PDB / ID: 24qi
TitleCrystal structure of a tailspike depolymerase (Belisarius_gp86) from Acinetobacter phage Belisarius
ComponentsTailspike depolymerase
KeywordsVIRAL PROTEIN / depolymerase / Acinetobacter phage Solidus / viruses / tailspike
Function / homologyTRIETHYLENE GLYCOL
Function and homology information
Biological speciesAcinetobacter phage Belisarius (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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)66,0435
Polymers65,5581
Non-polymers4854
Water3,117173
1
A: Tailspike depolymerase
hetero molecules

A: Tailspike depolymerase
hetero molecules

A: Tailspike depolymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)198,12915
Polymers196,6753
Non-polymers1,45412
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 area26000 Å2
ΔGint-70 kcal/mol
Surface area55560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.975, 100.975, 784.525
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-750-

HOH

21A-810-

HOH

31A-840-

HOH

41A-852-

HOH

51A-860-

HOH

61A-867-

HOH

71A-873-

HOH

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Components

#1: Protein Tailspike depolymerase


Mass: 65558.398 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter phage Belisarius (virus) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 173 / 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: 5.87 Å3/Da / Density % sol: 79.05 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / Details: Bis-tris pH 5.5, 2.4M NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: LNLS SIRIUS / Beamline: MANACA / Wavelength: 0.97718 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 28, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97718 Å / Relative weight: 1
ReflectionResolution: 2.2→49.67 Å / Num. obs: 79321 / % possible obs: 99.9 % / Redundancy: 14.4 % / CC1/2: 0.957 / Rmerge(I) obs: 0.305 / Rpim(I) all: 0.084 / Rrim(I) all: 0.317 / Χ2: 0.96 / Net I/σ(I): 8.2 / Num. measured all: 1138450
Reflection shellResolution: 2.2→2.24 Å / % possible obs: 100 % / Redundancy: 14.5 % / Rmerge(I) obs: 1.936 / Num. measured all: 65047 / Num. unique obs: 4496 / CC1/2: 0.75 / Rpim(I) all: 0.523 / Rrim(I) all: 2.007 / Χ2: 0.96 / Net I/σ(I) obs: 1.7

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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: 2.2→49.67 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.938 / SU B: 3.791 / SU ML: 0.094 / Cross valid method: THROUGHOUT / ESU R: 0.134 / ESU R Free: 0.126 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2261 3993 5 %RANDOM
Rwork0.2104 ---
obs0.21119 75166 99.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 49.898 Å2
Baniso -1Baniso -2Baniso -3
1--0.37 Å2-0.18 Å2-0 Å2
2---0.37 Å2-0 Å2
3---1.19 Å2
Refinement stepCycle: 1 / Resolution: 2.2→49.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4379 0 32 173 4584
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0134540
X-RAY DIFFRACTIONr_bond_other_d0.0030.0154085
X-RAY DIFFRACTIONr_angle_refined_deg1.9241.6376168
X-RAY DIFFRACTIONr_angle_other_deg1.3611.5789363
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.725582
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.13722.723235
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.48115675
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.381524
X-RAY DIFFRACTIONr_chiral_restr0.0910.2596
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.025320
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021140
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_it6.3385.3742307
X-RAY DIFFRACTIONr_mcbond_other6.3375.3732306
X-RAY DIFFRACTIONr_mcangle_it8.7978.042884
X-RAY DIFFRACTIONr_mcangle_other8.7978.042885
X-RAY DIFFRACTIONr_scbond_it6.4265.5262233
X-RAY DIFFRACTIONr_scbond_other6.4255.5272234
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.7778.193281
X-RAY DIFFRACTIONr_long_range_B_refined9.55117634
X-RAY DIFFRACTIONr_long_range_B_other9.55217616
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 322 -
Rwork0.286 5412 -
obs--99.58 %

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