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- PDB-9qrm: X-ray structure of Kp32gp38 in complex with K21 pyr5 -

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Basic information

Entry
Database: PDB / ID: 9qrm
TitleX-ray structure of Kp32gp38 in complex with K21 pyr5
ComponentsDepolymerase 2, capsule K21-specific
KeywordsVIRAL PROTEIN / Klebsiella pneumoniae / phage depolymerase / protein structure / CPS degradation / immune response induction
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 / DI(HYDROXYETHYL)ETHER / Depolymerase 2, capsule K21-specific
Function and homology information
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsNapolitano, V. / Squeglia, F. / Privitera, M. / Berisio, R.
Funding support Italy, 1items
OrganizationGrant numberCountry
NextGenerationEU-MUR PNRR Extended Partnership initiative on Emerging Infectious Diseases (INF-ACT)0001554 Italy
CitationJournal: Int J Antimicrob Agents / Year: 2025
Title: Structural and functional features of Klebsiella pneumoniae capsular degradation by the phage depolymerase KP32gp38: Implications for vaccination against K. pneumoniae.
Authors: Napolitano, V. / Privitera, M. / Drulis-Kawa, Z. / Marasco, D. / Fallarini, S. / Berisio, R. / Squeglia, F.
History
DepositionApr 3, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 3, 2025Provider: repository / Type: Initial release
Revision 1.1Oct 1, 2025Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Depolymerase 2, capsule K21-specific
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,9445
Polymers62,7551
Non-polymers1,1894
Water9,170509
1
B: Depolymerase 2, capsule K21-specific
hetero molecules

B: Depolymerase 2, capsule K21-specific
hetero molecules

B: Depolymerase 2, capsule K21-specific
hetero molecules


Theoretical massNumber of molelcules
Total (without water)191,83115
Polymers188,2643
Non-polymers3,56712
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation2_445-y-1,x-y-1,z1
point symmetry operation3_545-x+y,-x-1,z1
Buried area25540 Å2
ΔGint11 kcal/mol
Surface area51730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.492, 70.492, 205.594
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321
Components on special symmetry positions
IDModelComponents
11B-1009-

HOH

21B-1037-

HOH

31B-1110-

HOH

41B-1173-

HOH

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Components

#1: Protein Depolymerase 2, capsule K21-specific / Gene product 38 / gp38 / KP32gp38 / Probable tail spike protein


Mass: 62754.504 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: 38 / Production host: Escherichia coli (E. coli) / References: UniProt: D1L2X1
#2: Polysaccharide (2~{S},4~{a}~{S},6~{R},7~{S},8~{R},8~{a}~{R})-2-methyl-6,7,8-tris(oxidanyl)-4,4~{a},6,7,8,8~{a}- ...(2~{S},4~{a}~{S},6~{R},7~{S},8~{R},8~{a}~{R})-2-methyl-6,7,8-tris(oxidanyl)-4,4~{a},6,7,8,8~{a}-hexahydropyrano[3,2-d][1,3]dioxine-2-carboxylic acid-(4-4)-beta-D-glucopyranose-(1-3)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-galactopyranose


Type: oligosaccharide / Mass: 898.766 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
[][b-D-Galp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{[(3+1)][b-D-Glcp]{[(4+1)]{}}}}}LINUCSPDB-CARE
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 509 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.35 Å3/Da / Density % sol: 47.65 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.03 M citric acid, 0.045 M BIS-TRIS propane (pH 6.4), 15% (wt/vol) polyethylene glycol 3350, and 25% (vol/vol) glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.965 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 14, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.965 Å / Relative weight: 1
ReflectionResolution: 1.8→60 Å / Num. obs: 53382 / % possible obs: 99.6 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.82 / Net I/σ(I): 9
Reflection shellResolution: 1.8→1.83 Å / Rmerge(I) obs: 0.44 / Num. unique obs: 2693 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→14.94 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.934 / SU B: 6.115 / SU ML: 0.103 / Cross valid method: THROUGHOUT / ESU R: 0.14 / ESU R Free: 0.137 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2354 2751 5.2 %RANDOM
Rwork0.18824 ---
obs0.19074 50657 95.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.89 Å2
Baniso -1Baniso -2Baniso -3
1--0.34 Å2-0.17 Å20 Å2
2---0.34 Å20 Å2
3---1.09 Å2
Refinement stepCycle: 1 / Resolution: 1.8→14.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4178 0 80 509 4767
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0124512
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7831.7926152
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.2655595
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.711528
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.24210706
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1250.2720
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023427
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_it1.3971.6342341
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.1162.9222949
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.6451.7622171
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined621.387401
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: 1.8→1.846 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 221 -
Rwork0.254 3784 -
obs--99.65 %
Refinement TLS params.Method: refined / Origin x: -2.0502 Å / Origin y: -26.5292 Å / Origin z: 48.3671 Å
111213212223313233
T0.2815 Å2-0 Å20.0224 Å2-0.2582 Å2-0.0975 Å2--0.0386 Å2
L0.6046 °2-0.0054 °2-0.1895 °2-0.4763 °2-0.0056 °2--1.2263 °2
S0.0157 Å °-0.3796 Å °0.1457 Å °0.3532 Å °-0.0093 Å °0.0306 Å °-0.1589 Å °-0.0319 Å °-0.0065 Å °

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