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- PDB-6tku: Crystal structure of a capsule-specific depolymerase produced by ... -

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Basic information

Entry
Database: PDB / ID: 6tku
TitleCrystal structure of a capsule-specific depolymerase produced by Klebsiella phage
Componentsdepolymerase KP32gp38
KeywordsHYDROLASE / Klebsiella pneumoniae capsule / phage depolymerase / tail fiber branching system
Function / homologysymbiont entry into host cell via disruption of host cell glycocalyx / symbiont entry into host cell via disruption of host cell envelope / virus tail / adhesion receptor-mediated virion attachment to host cell / Pectin lyase fold / Pectin lyase fold/virulence factor / Depolymerase 2, capsule K21-specific
Function and homology information
Biological speciesKlebsiella phage KP32 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsBerisio, R. / Squeglia, F.
Funding support Italy, 1items
OrganizationGrant numberCountry
Italian Ministry of Education2017SFBFER Italy
CitationJournal: Structure / Year: 2020
Title: Structural and Functional Studies of a Klebsiella Phage Capsule Depolymerase Tailspike: Mechanistic Insights into Capsular Degradation.
Authors: Squeglia, F. / Maciejewska, B. / Latka, A. / Ruggiero, A. / Briers, Y. / Drulis-Kawa, Z. / Berisio, R.
History
DepositionNov 29, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 22, 2020Provider: repository / Type: Initial release
Revision 1.1May 20, 2020Group: Database references / Category: citation
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jun 10, 2020Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.3Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: depolymerase KP32gp38


Theoretical massNumber of molelcules
Total (without water)63,3171
Polymers63,3171
Non-polymers00
Water7,999444
1
A: depolymerase KP32gp38

A: depolymerase KP32gp38

A: depolymerase KP32gp38


Theoretical massNumber of molelcules
Total (without water)189,9523
Polymers189,9523
Non-polymers00
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 area18210 Å2
ΔGint-42 kcal/mol
Surface area51290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.726, 71.726, 208.197
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number150
Space group name H-MP321
Components on special symmetry positions
IDModelComponents
11A-914-

HOH

21A-937-

HOH

31A-943-

HOH

41A-959-

HOH

51A-1029-

HOH

61A-1043-

HOH

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Components

#1: Protein depolymerase KP32gp38


Mass: 63317.254 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella phage KP32 (virus) / Gene: 38 / Production host: Escherichia coli (E. coli) / References: UniProt: D1L2X1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 444 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.46 Å3/Da / Density % sol: 50.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Ammonium citrate tribasic pH 7.0 and 20% w/v polyethylene glycol 3,350.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 0.9759 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 7, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9759 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. obs: 59968 / % possible obs: 99.9 % / Redundancy: 13.6 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 19.7
Reflection shellResolution: 1.8→1.84 Å / Rmerge(I) obs: 0.232 / Num. unique obs: 4226

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.8→14.91 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.933 / SU B: 3.575 / SU ML: 0.107 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.132 / ESU R Free: 0.132
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES
RfactorNum. reflection% reflectionSelection details
Rfree0.251 2939 5 %RANDOM
Rwork0.2045 ---
obs0.2069 55417 99.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 102.26 Å2 / Biso mean: 40.1911 Å2 / Biso min: 12.16 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å2-0 Å2
3----0.01 Å2
Refinement stepCycle: final / Resolution: 1.8→14.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4063 0 0 444 4507
Biso mean---40.27 -
Num. residues----545
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0134211
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173864
X-RAY DIFFRACTIONr_angle_refined_deg1.6861.6425734
X-RAY DIFFRACTIONr_angle_other_deg1.2571.5728954
X-RAY DIFFRACTIONTORSION ANGLES. PERIOD 1 (DEGREES)8.3175563
X-RAY DIFFRACTIONTORSION ANGLES. PERIOD 2 (DEGREES)36.58922.892204
X-RAY DIFFRACTIONTORSION ANGLES. PERIOD 3 (DEGREES)12.7115633
X-RAY DIFFRACTIONTORSION ANGLES. PERIOD 4 (DEGREES)16.4361524
X-RAY DIFFRACTIONr_chiral_restr0.0670.2567
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024852
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02888
LS refinement shellResolution: 1.8→1.846 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 204 -
Rwork0.305 3958 -
all-4162 -
obs--98.81 %

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