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- PDB-8iqe: Crystal structure of tetrameric K2-2 TSP -

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Basic information

Entry
Database: PDB / ID: 8iqe
TitleCrystal structure of tetrameric K2-2 TSP
ComponentsK2-VCL6 TSP
KeywordsHYDROLASE / bacteriophage / tailspike protein / Klebsiella pneumoniae K2
Biological speciesKlebsiella phage VLC6 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.17 Å
AuthorsYe, T.J. / Huang, K.F. / Tu, I.F. / Lee, I.M. / Chang, Y.P. / Wu, S.H.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
National Science Council (NSC, Taiwan) Taiwan
CitationJournal: Mbio / Year: 2024
Title: Klebsiella pneumoniae K2 capsular polysaccharide degradation by a bacteriophage depolymerase does not require trimer formation.
Authors: Ye, T.J. / Fung, K.M. / Lee, I.M. / Ko, T.P. / Lin, C.Y. / Wong, C.L. / Tu, I.F. / Huang, T.Y. / Yang, F.L. / Chang, Y.P. / Wang, J.T. / Lin, T.L. / Huang, K.F. / Wu, S.H.
History
DepositionMar 16, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 21, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Apr 3, 2024Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: K2-VCL6 TSP
B: K2-VCL6 TSP
C: K2-VCL6 TSP
D: K2-VCL6 TSP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)249,85524
Polymers248,0134
Non-polymers1,84220
Water37,2912070
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)232.876, 232.876, 102.270
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
Space group name HallP6c
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/2
#3: y,-x+y,z+1/2
#4: -y,x-y,z
#5: -x+y,-x,z
#6: -x,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 16 through 87 or resid 89...
d_2ens_1(chain "B" and (resid 16 through 87 or resid 89...
d_3ens_1(chain "C" and (resid 16 through 87 or resid 89...
d_4ens_1(chain "D" and (resid 16 through 87 or resid 89...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11TYRTYRALAALAAA16 - 8716 - 87
d_12METMETLEULEUAA89 - 11889 - 118
d_13ILEILESERSERAA120 - 166120 - 166
d_14LEULEUVALVALAA179 - 206179 - 206
d_15ASNASNARGARGAA213 - 231213 - 231
d_16GLYGLYLEULEUAA233 - 262233 - 262
d_17ILEILELEULEUAA268 - 372268 - 372
d_18LEULEUPROPROAA374 - 578374 - 578
d_19GOLGOLGOLGOLAK607
d_21TYRTYRALAALABB16 - 8716 - 87
d_22METMETLEULEUBB89 - 11889 - 118
d_23ILEILEARGARGBB120 - 231120 - 231
d_24GLYGLYLEULEUBB233 - 372233 - 372
d_25LEULEUPROPROBB374 - 578374 - 578
d_26GOLGOLGOLGOLBM601
d_31TYRTYRALAALACC16 - 8716 - 87
d_32METMETLEULEUCC89 - 11889 - 118
d_33ILEILESERSERCC120 - 166120 - 166
d_34LEULEUVALVALCC179 - 206179 - 206
d_35ASNASNARGARGCC213 - 231213 - 231
d_36GLYGLYLEULEUCC233 - 262233 - 262
d_37ILEILELEULEUCC268 - 372268 - 372
d_38LEULEUPROPROCC374 - 578374 - 578
d_39GOLGOLGOLGOLCR603
d_41TYRTYRALAALADD16 - 8716 - 87
d_42METMETLEULEUDD89 - 11889 - 118
d_43ILEILESERSERDD120 - 166120 - 166
d_44LEULEUARGARGDD179 - 231179 - 231
d_45GLYGLYLEULEUDD233 - 262233 - 262
d_46ILEILELEULEUDD268 - 372268 - 372
d_47LEULEUPROPRODD374 - 578374 - 578
d_48GOLGOLGOLGOLDW604

NCS oper:
IDCodeMatrixVector
1given(-0.0528660250104, -0.000716422165805, -0.998601356968), (0.998092036938, 0.0319045446221, -0.0528619507094), (0.0318977930263, -0.999490663674, -0.000971611195159)-71.3784111728, 5.96243050295, -62.476137994
2given(0.444389106866, 0.581251779567, -0.68166317962), (0.789208043246, -0.614058424519, -0.00910580874153), (-0.423873785665, -0.533927541927, -0.731609454421)-36.9848191764, 9.96856916295, -42.372055886
3given(0.520970275707, 0.707519235695, -0.477500264871), (-0.670368579101, -0.00715194482864, -0.741993812535), (-0.528389950685, 0.706657895171, 0.47057271405)-22.5544687709, -49.9432063095, 30.6310659558

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Components

#1: Protein
K2-VCL6 TSP


Mass: 62003.211 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella phage VLC6 (virus) / Gene: VLC6_58 / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2070 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.23 Å3/Da / Density % sol: 61.89 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Bicine pH 9.0, 10% PEG-4000, 10% polyacrylic acid 2100 sodium salt

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 3, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.17→30 Å / Num. obs: 166451 / % possible obs: 100 % / Redundancy: 5 % / Biso Wilson estimate: 29.91 Å2 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.036 / Rrim(I) all: 0.082 / Rsym value: 0.05 / Χ2: 0.922 / Net I/σ(I): 20.6
Reflection shellResolution: 2.17→2.25 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.825 / Mean I/σ(I) obs: 2 / Num. unique obs: 16573 / CC1/2: 0.702 / Rpim(I) all: 0.417 / Rrim(I) all: 0.925 / Rsym value: 0.728 / Χ2: 0.908 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-2000data scaling
MOLREPphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: in-house model derived from MAD experiment

Resolution: 2.17→29.56 Å / SU ML: 0.2019 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.4662
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1978 7985 5.02 %
Rwork0.1683 150977 -
obs0.1698 158962 95.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.9 Å2
Refinement stepCycle: LAST / Resolution: 2.17→29.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16465 0 120 2070 18655
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002516957
X-RAY DIFFRACTIONf_angle_d0.655723048
X-RAY DIFFRACTIONf_chiral_restr0.04872601
X-RAY DIFFRACTIONf_plane_restr0.0042991
X-RAY DIFFRACTIONf_dihedral_angle_d5.86242426
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS2.08824678148
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS1.46047356038
ens_1d_4AX-RAY DIFFRACTIONTorsion NCS2.25736374987
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.17-2.190.2861070.24272805X-RAY DIFFRACTION52.87
2.19-2.220.24762040.24093386X-RAY DIFFRACTION64.99
2.22-2.250.2632360.23993914X-RAY DIFFRACTION75.15
2.25-2.280.25622280.2374344X-RAY DIFFRACTION82.8
2.28-2.310.26812380.2374797X-RAY DIFFRACTION91.15
2.31-2.340.27492940.22755071X-RAY DIFFRACTION97.07
2.34-2.370.24822470.2245246X-RAY DIFFRACTION99.08
2.37-2.410.24692660.21965240X-RAY DIFFRACTION99.76
2.41-2.440.26232970.21295252X-RAY DIFFRACTION100
2.44-2.480.27422800.21565241X-RAY DIFFRACTION100
2.48-2.530.26662940.215237X-RAY DIFFRACTION100
2.53-2.570.23192800.20595261X-RAY DIFFRACTION100
2.57-2.620.24652930.2015267X-RAY DIFFRACTION100
2.62-2.680.23182880.19825254X-RAY DIFFRACTION100
2.68-2.730.23672800.19815216X-RAY DIFFRACTION100
2.73-2.80.24322600.18985295X-RAY DIFFRACTION100
2.8-2.870.22482680.18265273X-RAY DIFFRACTION100
2.87-2.940.19862700.18085301X-RAY DIFFRACTION100
2.94-3.030.21482690.17485297X-RAY DIFFRACTION100
3.03-3.130.20172620.17375255X-RAY DIFFRACTION100
3.13-3.240.20542990.16545225X-RAY DIFFRACTION100
3.24-3.370.20572960.16115269X-RAY DIFFRACTION100
3.37-3.520.18452410.1535349X-RAY DIFFRACTION100
3.52-3.710.17432410.14345314X-RAY DIFFRACTION99.98
3.71-3.940.15673250.13985241X-RAY DIFFRACTION99.96
3.94-4.240.14662980.13055302X-RAY DIFFRACTION100
4.24-4.670.14642980.11375264X-RAY DIFFRACTION99.96
4.67-5.340.1392750.1265322X-RAY DIFFRACTION99.93
5.34-6.720.16952810.15955358X-RAY DIFFRACTION100
6.72-29.560.20452700.17515381X-RAY DIFFRACTION98.74
Refinement TLS params.Method: refined / Origin x: -64.2404682432 Å / Origin y: -23.7412569257 Å / Origin z: -0.218977772078 Å
111213212223313233
T0.208547430111 Å2-0.0613296619317 Å2-0.0320451692309 Å2-0.23869638992 Å2-0.00548895876946 Å2--0.174826730887 Å2
L0.526410768637 °20.0292296616456 °2-0.147251668915 °2-0.424800304447 °20.0139825980296 °2--0.341817186115 °2
S-0.0390603219831 Å °0.00869259444118 Å °0.00918015584199 Å °-0.110196527116 Å °0.0305204342999 Å °0.12896131013 Å °0.0939268246184 Å °-0.138050300876 Å °0.00281364914348 Å °
Refinement TLS groupSelection details: all

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