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- PDB-8oq0: Crystal structure of tailspike depolymerase (APK09_gp48) from Aci... -

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Basic information

Entry
Database: PDB / ID: 8oq0
TitleCrystal structure of tailspike depolymerase (APK09_gp48) from Acinetobacter phage APK09
ComponentsTailspike protein
KeywordsVIRAL PROTEIN / bacteriophage / Acinetobacter baumannii / tailspike depolymerase
Function / homologyDI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciesAcinetobacter phage APK09 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.59 Å
AuthorsMatyuta, I.O. / Boyko, K.M. / Nikolaeva, A.Y. / Shneider, M.M. / Timoshina, O.Y. / Popova, A.V. / 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 1.0May 31, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 7, 2023Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jun 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: Tailspike protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,7043
Polymers66,4921
Non-polymers2122
Water1629
1
A: Tailspike protein
hetero molecules

A: Tailspike protein
hetero molecules

A: Tailspike protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)200,1139
Polymers199,4773
Non-polymers6376
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-y-1,x-y,z1
crystal symmetry operation3_445-x+y-1,-x-1,z1
Buried area30800 Å2
ΔGint-116 kcal/mol
Surface area51450 Å2
Unit cell
Length a, b, c (Å)88.688, 88.688, 421.040
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 protein


Mass: 66492.203 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter phage APK09 (virus) / Gene: B1_45 / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 2.4 Å3/Da / Density % sol: 48.67 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 2% PEG200, 100mM HEPES pH 7.5, 20% tacsimate pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.7749 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 12, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7749 Å / Relative weight: 1
ReflectionResolution: 2.59→72.15 Å / Num. obs: 20409 / % possible obs: 99.1 % / Redundancy: 18.5 % / CC1/2: 0.993 / Rmerge(I) obs: 0.339 / Rpim(I) all: 0.081 / Rrim(I) all: 0.349 / Χ2: 0.99 / Net I/σ(I): 10.9 / Num. measured all: 377770
Reflection shellResolution: 2.59→2.7 Å / % possible obs: 94 % / Redundancy: 13.6 % / Rmerge(I) obs: 2.467 / Num. measured all: 31386 / Num. unique obs: 2302 / CC1/2: 0.303 / Rpim(I) all: 0.674 / Rrim(I) all: 2.566 / Χ2: 0.93 / Net I/σ(I) obs: 1.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimlessdata scaling
DIALSdata reduction
MOLREPphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.59→72.15 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.915 / SU B: 13.472 / SU ML: 0.282 / Cross valid method: THROUGHOUT / ESU R: 1.155 / ESU R Free: 0.351 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.27157 1052 5.2 %RANDOM
Rwork0.18867 ---
obs0.19312 19304 99.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 58.755 Å2
Baniso -1Baniso -2Baniso -3
1-0.68 Å20.34 Å2-0 Å2
2--0.68 Å2-0 Å2
3----2.22 Å2
Refinement stepCycle: 1 / Resolution: 2.59→72.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4588 0 14 9 4611
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0124693
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.3791.6336393
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.175605
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.9323.394218
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.90115718
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6041519
X-RAY DIFFRACTIONr_chiral_restr0.1730.2658
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.023571
X-RAY DIFFRACTIONr_gen_planes_other
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_it7.5085.7752423
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it9.9618.673027
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it9.1715.9182268
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined1379.1386763
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.59→2.657 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.344 75 -
Rwork0.302 1310 -
obs--93.33 %

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