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- PDB-7w1c: Crystal structure of Klebsiella pneumoniae K1 capsule-specific po... -

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Basic information

Entry
Database: PDB / ID: 7w1c
TitleCrystal structure of Klebsiella pneumoniae K1 capsule-specific polysaccharide lyase in a P1 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
IMIDAZOLE / (2S)-2-hydroxybutanedioic acid / Depolymerase, capsule K1-specific
Similarity search - Component
Biological speciesKlebsiella phage NTUH-K2044-K1-1 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.48 Å
AuthorsTu, I.F. / 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

Downloads & links

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)436,96954
Polymers432,7846
Non-polymers4,18548
Water72,7994041
1
A: K1 LYASE
B: K1 LYASE
C: K1 LYASE
hetero molecules


  • defined by author&software
  • Evidence: equilibrium centrifugation
  • 218 kDa, 3 polymers
Theoretical massNumber of molelcules
Total (without water)218,45227
Polymers216,3923
Non-polymers2,06024
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21750 Å2
ΔGint22 kcal/mol
Surface area57960 Å2
MethodPISA
2
D: K1 LYASE
E: K1 LYASE
F: K1 LYASE
hetero molecules


  • defined by author&software
  • 219 kDa, 3 polymers
Theoretical massNumber of molelcules
Total (without water)218,51727
Polymers216,3923
Non-polymers2,12524
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21310 Å2
ΔGint16 kcal/mol
Surface area57630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.281, 100.574, 125.033
Angle α, β, γ (deg.)80.500, 70.320, 83.430
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
K1 LYASE


Mass: 72130.633 Da / Num. of mol.: 6 / 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-LMR / (2S)-2-hydroxybutanedioic acid / L-Malate


Mass: 134.087 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C4H6O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical...
ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: C3H5N2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4041 / 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: 2.45 Å3/Da / Density % sol: 49.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 15% (W/V) PEG 4000, 0.2 M IMIDAZOLE MALATE, PH 6.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Oct 27, 2014
RadiationMonochromator: LN2-COOLED, FIXED-EXIT DOUBLE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.48→30 Å / Num. obs: 656693 / % possible obs: 97 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 25.44
Reflection shellResolution: 1.48→1.53 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.741 / Mean I/σ(I) obs: 2.28 / Num. unique obs: 64500 / % possible all: 95.4

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
SHELXphasing
SOLOMONphasing
REFMAC5.7.0032refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MAD / Resolution: 1.48→30 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.961 / SU B: 2.479 / SU ML: 0.042 / Cross valid method: THROUGHOUT / ESU R: 0.067 / ESU R Free: 0.065 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.184 32922 5 %RANDOM
Rwork0.137 ---
obs0.139 623420 96.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 125.19 Å2 / Biso mean: 21.99 Å2 / Biso min: 5.08 Å2
Baniso -1Baniso -2Baniso -3
1--0.72 Å20.24 Å2-0.51 Å2
2--0.77 Å2-1.4 Å2
3----0.28 Å2
Refinement stepCycle: final / Resolution: 1.48→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms28913 0 286 4041 33240
Biso mean--35 36.83 -
Num. residues----3824
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.01929830
X-RAY DIFFRACTIONr_bond_other_d0.0020.0227533
X-RAY DIFFRACTIONr_angle_refined_deg1.6971.93940550
X-RAY DIFFRACTIONr_angle_other_deg1.0163.00363000
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.14953826
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.78823.6151300
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.007154422
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.26515189
X-RAY DIFFRACTIONr_chiral_restr0.1170.24591
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0234728
X-RAY DIFFRACTIONr_gen_planes_other0.0020.027264
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_rigid_bond_restr5.577357363
X-RAY DIFFRACTIONr_sphericity_free35.20551484
X-RAY DIFFRACTIONr_sphericity_bonded11.541559323
LS refinement shellResolution: 1.48→1.52 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 2355 -
Rwork0.206 44494 -
all-46849 -
obs--93.66 %

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