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- PDB-8opz: Crystal structure of a tailspike depolymerase (APK16_gp47) from A... -

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Basic information

Entry
Database: PDB / ID: 8opz
TitleCrystal structure of a tailspike depolymerase (APK16_gp47) from Acinetobacter phage APK16
ComponentsTailspike depolymerase (APK16_gp47) from Acinetobacter phage APK16
KeywordsVIRAL PROTEIN / bacteriophage / Acinetobacter baumannii / tailspike depolymerase / VIRUS
Biological speciesAcinetobacter phage APK16 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 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 1.0May 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 depolymerase (APK16_gp47) from Acinetobacter phage APK16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,4602
Polymers68,3681
Non-polymers921
Water1,40578
1
A: Tailspike depolymerase (APK16_gp47) from Acinetobacter phage APK16
hetero molecules

A: Tailspike depolymerase (APK16_gp47) from Acinetobacter phage APK16
hetero molecules

A: Tailspike depolymerase (APK16_gp47) from Acinetobacter phage APK16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)205,3806
Polymers205,1043
Non-polymers2763
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area31020 Å2
ΔGint-123 kcal/mol
Surface area63410 Å2
Unit cell
Length a, b, c (Å)88.045, 88.045, 254.969
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-960-

HOH

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Components

#1: Protein Tailspike depolymerase (APK16_gp47) from Acinetobacter phage APK16


Mass: 68368.008 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter phage APK16 (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.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / 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: 2.78 Å3/Da / Density % sol: 55.78 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 100 mM Tris pH 8.5, 2.0M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.97 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: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.5→84.99 Å / Num. obs: 117005 / % possible obs: 99.8 % / Redundancy: 20.9 % / CC1/2: 0.996 / Rmerge(I) obs: 0.25 / Rpim(I) all: 0.057 / Rrim(I) all: 0.256 / Χ2: 0.31 / Net I/σ(I): 4.7 / Num. measured all: 2443418
Reflection shellResolution: 1.5→1.53 Å / % possible obs: 98.5 % / Redundancy: 20.9 % / Rmerge(I) obs: 5.952 / Num. measured all: 120018 / Num. unique obs: 5743 / CC1/2: 0.482 / Rpim(I) all: 1.321 / Rrim(I) all: 6.098 / Χ2: 0.02 / 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: 1.5→84.99 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.96 / SU B: 0.534 / SU ML: 0.021 / Cross valid method: THROUGHOUT / ESU R: 0.013 / ESU R Free: 0.014 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.21471 5830 5 %RANDOM
Rwork0.17473 ---
obs0.17667 111172 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.03 Å2
Baniso -1Baniso -2Baniso -3
1-7.25 Å20 Å20 Å2
2--7.25 Å20 Å2
3----14.5 Å2
Refinement stepCycle: 1 / Resolution: 1.5→84.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4714 0 6 78 4798
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0124825
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg3.0781.6276563
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.935631
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.14423.886229
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.41615751
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.4651519
X-RAY DIFFRACTIONr_chiral_restr0.2550.2662
X-RAY DIFFRACTIONr_gen_planes_refined0.0180.023689
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_it4.1942.7362527
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.7964.1363157
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.8843.0132296
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined6.58238.2916772
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: 1.504→1.543 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.35 408 -
Rwork0.308 8264 -
obs--98.75 %

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