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- PDB-7w1d: Crystal structure of Klebsiella pneumoniae K1 capsule-specific po... -

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Basic information

Entry
Database: PDB / ID: 7w1d
TitleCrystal structure of Klebsiella pneumoniae K1 capsule-specific polysaccharide lyase in a C2 crystal form
ComponentsK1 LYASE
KeywordsVIRAL PROTEIN / BETA-HELIX / POLYSACCHARIDE LYASE / TAIL SPIKE PROTEIN
Function / homology
Function and homology information


symbiont entry into host cell via disruption of host cell glycocalyx / Lyases / symbiont entry into host cell via disruption of host cell envelope / virus tail / adhesion receptor-mediated virion attachment to host cell / lyase activity
Similarity search - Function
Pectin lyase fold / Pectin lyase fold/virulence factor
Similarity search - Domain/homology
CITRIC ACID / CARBONATE ION / Depolymerase, capsule K1-specific
Similarity search - Component
Biological speciesKlebsiella phage NTUH-K2044-K1-1 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / molecular replacement / Resolution: 2.78 Å
AuthorsTu, I.F. / Ko, T.P. / Huang, K.F. / Wu, S.H.
Funding support Taiwan, 2items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, Taiwan)MOST-108-2113-M-001-008 Taiwan
Academia Sinica (Taiwan)AS-KPQ-110-ITAR-11 Taiwan
CitationJournal: J.Biomed.Sci. / Year: 2022
Title: Structural and biological insights into Klebsiella pneumoniae surface polysaccharide degradation by a bacteriophage K1 lyase: implications for clinical use.
Authors: Tu, I.F. / Lin, T.L. / Yang, F.L. / Lee, I.M. / Tu, W.L. / Liao, J.H. / Ko, T.P. / Wu, W.J. / Jan, J.T. / Ho, M.R. / Chou, C.Y. / Wang, A.H. / Wu, C.Y. / Wang, J.T. / Huang, K.F. / Wu, S.H.
History
DepositionNov 19, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 18, 2022Provider: repository / Type: Initial release
Revision 1.1May 29, 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: K1 LYASE
B: K1 LYASE
C: K1 LYASE
D: K1 LYASE
E: K1 LYASE
F: K1 LYASE
G: K1 LYASE
H: K1 LYASE
I: K1 LYASE
J: K1 LYASE
K: K1 LYASE
L: K1 LYASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)868,82231
Polymers865,56812
Non-polymers3,25419
Water24,6451368
1
A: K1 LYASE
B: K1 LYASE
C: K1 LYASE
hetero molecules


  • defined by author&software
  • Evidence: equilibrium centrifugation
  • 217 kDa, 3 polymers
Theoretical massNumber of molelcules
Total (without water)217,4139
Polymers216,3923
Non-polymers1,0216
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18160 Å2
ΔGint-7 kcal/mol
Surface area58780 Å2
MethodPISA
2
D: K1 LYASE
E: K1 LYASE
F: K1 LYASE
hetero molecules


  • defined by author&software
  • 217 kDa, 3 polymers
Theoretical massNumber of molelcules
Total (without water)217,1607
Polymers216,3923
Non-polymers7684
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18180 Å2
ΔGint-13 kcal/mol
Surface area58340 Å2
MethodPISA
3
G: K1 LYASE
H: K1 LYASE
I: K1 LYASE
hetero molecules


  • defined by author&software
  • 217 kDa, 3 polymers
Theoretical massNumber of molelcules
Total (without water)217,0287
Polymers216,3923
Non-polymers6364
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17580 Å2
ΔGint-6 kcal/mol
Surface area58970 Å2
MethodPISA
4
J: K1 LYASE
K: K1 LYASE
L: K1 LYASE
hetero molecules


  • defined by author&software
  • 217 kDa, 3 polymers
Theoretical massNumber of molelcules
Total (without water)217,2208
Polymers216,3923
Non-polymers8295
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18250 Å2
ΔGint-9 kcal/mol
Surface area57930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)363.945, 239.626, 121.632
Angle α, β, γ (deg.)90.000, 100.130, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11J-857-

HOH

21J-859-

HOH

31J-860-

HOH

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Components

#1: Protein
K1 LYASE


Mass: 72130.633 Da / Num. of mol.: 12 / Mutation: D391A, D392A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella phage NTUH-K2044-K1-1 (virus)
Plasmid: PET28A / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A068Q5Q5
#2: Chemical
ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C6H8O7 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CO3 / CARBONATE ION


Mass: 60.009 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CO3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1368 / 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: 3.02 Å3/Da / Density % sol: 59.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 15% (W/V) PEG 6000, 0.1 M CITRATE (PH 5.5), 0.019 M N-DECYL-N,N-DIMETHYLGLYCINE, VAPOR DIFFUSION

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 1.0, 1.05372, 1.07194
DetectorType: BRUKER SMART 6500 / Detector: CCD / Date: Jul 15, 2013 / Details: HORIZONTAL FOCUSING MIRROR
RadiationMonochromator: DOUBLE-CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
21.053721
31.071941
ReflectionResolution: 2.78→30 Å / Num. obs: 257393 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 3.2 % / Rmerge(I) obs: 0.139 / Net I/σ(I): 11.24
Reflection shellResolution: 2.78→2.88 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.625 / Mean I/σ(I) obs: 2.47 / Num. unique obs: 25697 / % possible all: 99.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PHENIXPhenix1.17.1-3660refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MAD / Resolution: 2.78→29.95 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.913 / SU B: 10.688 / SU ML: 0.206 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 3.611 / ESU R Free: 0.31 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.219 12744 5 %RANDOM
Rwork0.182 ---
obs0.184 241124 97.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 138.44 Å2 / Biso mean: 32.86 Å2 / Biso min: 3.31 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å20 Å2-0.65 Å2
2---1.36 Å20 Å2
3---1.28 Å2
Refinement stepCycle: final / Resolution: 2.78→29.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms58385 0 220 1368 59973
Biso mean--56.93 27.28 -
Num. residues----7718
LS refinement shellResolution: 2.78→2.84 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.342 946 -
Rwork0.31 17123 -
obs--94.46 %

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