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- PDB-8oq1: Crystal structure of tailspike depolymerase (APK14_gp49) from Aci... -

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Basic information

Entry
Database: PDB / ID: 8oq1
TitleCrystal structure of tailspike depolymerase (APK14_gp49) from Acinetobacter phage vB_AbaP_APK14
ComponentsTail spike protein, structural depolymerase
KeywordsVIRAL PROTEIN / bacteriophage / Acinetobacter baumannii / tailspike depolymerase / Acinetobacter phage
Function / homologyPectin lyase fold / Pectin lyase fold/virulence factor / DI(HYDROXYETHYL)ETHER / Tail spike protein, structural depolymerase
Function and homology information
Biological speciesAcinetobacter phage vB_AbaP_APK14 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.55 Å
AuthorsMatyuta, I.O. / Boyko, K.M. / Nikolaeva, A.Y. / Shneider, M.M. / Timoshina, O.Y. / Miroshnikov, K.A. / Popov, V.O.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
Ministry of Science and Higher Education of the Russian Federation075-15-2021-1354 Russian Federation
CitationJournal: Int J Mol Sci / Year: 2023
Title: Friunavirus Phage-Encoded Depolymerases Specific to Different Capsular Types of Acinetobacter baumannii.
Authors: Timoshina, O.Y. / Kasimova, A.A. / Shneider, M.M. / Matyuta, I.O. / Nikolaeva, A.Y. / Evseev, P.V. / Arbatsky, N.P. / Shashkov, A.S. / Chizhov, A.O. / Shelenkov, A.A. / Mikhaylova, Y.V. / ...Authors: Timoshina, O.Y. / Kasimova, A.A. / Shneider, M.M. / Matyuta, I.O. / Nikolaeva, A.Y. / Evseev, P.V. / Arbatsky, N.P. / Shashkov, A.S. / Chizhov, A.O. / Shelenkov, A.A. / Mikhaylova, Y.V. / Slukin, P.V. / Volozhantsev, N.V. / Boyko, K.M. / Knirel, Y.A. / Miroshnikov, K.A. / Popova, A.V.
History
DepositionApr 10, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 7, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tail spike protein, structural depolymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,8534
Polymers79,6191
Non-polymers2343
Water6,305350
1
A: Tail spike protein, structural depolymerase
hetero molecules

A: Tail spike protein, structural depolymerase
hetero molecules

A: Tail spike protein, structural depolymerase
hetero molecules


  • defined by author&software
  • Evidence: gel filtration
  • 240 kDa, 3 polymers
Theoretical massNumber of molelcules
Total (without water)239,55812
Polymers238,8573
Non-polymers7019
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area19940 Å2
ΔGint-61 kcal/mol
Surface area64560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.394, 77.394, 228.536
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11A-903-

CL

21A-1005-

HOH

31A-1024-

HOH

41A-1328-

HOH

51A-1336-

HOH

61A-1340-

HOH

71A-1341-

HOH

81A-1343-

HOH

91A-1350-

HOH

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Components

#1: Protein Tail spike protein, structural depolymerase


Mass: 79618.969 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter phage vB_AbaP_APK14 (virus)
Gene: ABPK482_gp49 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A4P1LUD8
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 350 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.48 Å3/Da / Density % sol: 50.44 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 50mM CaCl2, 100mM Bis-tris pH 6.5, 30%PEG 550 MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 12, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.55→228.54 Å / Num. obs: 111761 / % possible obs: 100 % / Redundancy: 15.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.145 / Rpim(I) all: 0.039 / Rrim(I) all: 0.15 / Χ2: 0.25 / Net I/σ(I): 7.7 / Num. measured all: 1713096
Reflection shellResolution: 1.55→1.58 Å / % possible obs: 100 % / Redundancy: 11.9 % / Rmerge(I) obs: 2.706 / Num. measured all: 65962 / Num. unique obs: 5547 / CC1/2: 0.431 / Rpim(I) all: 0.819 / Rrim(I) all: 2.83 / Χ2: 0.03 / Net I/σ(I) obs: 0.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimlessdata scaling
DIALSdata reduction
CRANK2phasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: SAD / Resolution: 1.55→114.27 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.948 / SU B: 2.551 / SU ML: 0.086 / Cross valid method: THROUGHOUT / ESU R: 0.084 / ESU R Free: 0.088 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23574 5588 5 %RANDOM
Rwork0.19951 ---
obs0.20141 106071 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.268 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å2-0.04 Å20 Å2
2---0.09 Å20 Å2
3---0.28 Å2
Refinement stepCycle: 1 / Resolution: 1.55→114.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5494 0 14 350 5858
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0135652
X-RAY DIFFRACTIONr_bond_other_d0.0030.0155180
X-RAY DIFFRACTIONr_angle_refined_deg2.1031.647677
X-RAY DIFFRACTIONr_angle_other_deg1.5411.58111880
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.6445698
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.65923.102303
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.74915907
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0241528
X-RAY DIFFRACTIONr_chiral_restr0.1250.2747
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.026531
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021390
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_it2.7962.6472795
X-RAY DIFFRACTIONr_mcbond_other2.7952.6462794
X-RAY DIFFRACTIONr_mcangle_it3.4623.9683492
X-RAY DIFFRACTIONr_mcangle_other3.4613.9683493
X-RAY DIFFRACTIONr_scbond_it3.6932.8872856
X-RAY DIFFRACTIONr_scbond_other3.6932.8882857
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.0314.2274185
X-RAY DIFFRACTIONr_long_range_B_refined5.71930.8136071
X-RAY DIFFRACTIONr_long_range_B_other5.70330.6876028
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.352 366 -
Rwork0.345 7854 -
obs--100 %

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