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- PDB-9hp7: Crystal structure of GH19 E228Q domain of D29-LysA in complex wit... -

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Basic information

Entry
Database: PDB / ID: 9hp7
TitleCrystal structure of GH19 E228Q domain of D29-LysA in complex with (GlcNAc)4
ComponentsEndolysin A
KeywordsHYDROLASE / Peptidoglycan hydrolase / D29-LysA / GH19 / (GlcNAc)4
Function / homology: / Hydrolases / viral release from host cell by cytolysis / Lysozyme-like domain superfamily / defense response to bacterium / hydrolase activity / Endolysin A
Function and homology information
Biological speciesMycobacterium phage D29 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 Å
AuthorsCeballos-Zuniga, F. / Perez-Dorado, I.
Funding support Spain, 2items
OrganizationGrant numberCountry
Comunidad de Madrid2019-T1/BMD-14774 Spain
Spanish National Research Council202380E208 Spain
CitationJournal: Int.J.Biol.Macromol. / Year: 2025
Title: Dissecting the molecular basis underlying mycobacterial cell-wall hydrolysis by the catalytic domains of D29LysA and DS6ALysA phage endolysins.
Authors: Ceballos-Zuniga, F. / Galvez-Larrosa, L. / Munoz, I.G. / Infantes, L. / Fernandez-Carrillo, J. / Perez-Dorado, I.
History
DepositionDec 12, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 22, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Endolysin A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5133
Polymers21,6421
Non-polymers8712
Water2,000111
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1640 Å2
ΔGint22 kcal/mol
Surface area8380 Å2
Unit cell
Length a, b, c (Å)91.062, 44.845, 69.530
Angle α, β, γ (deg.)90.000, 126.419, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein Endolysin A / Gene 10 protein / Gp10 / Lysis protein / Lysozyme


Mass: 21642.166 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: N-terminal GP residues correspond to PreScission cleavege site. Residues from 179 to 370 correspond to GH19 domain of D29-LysA with the mutation E228Q
Source: (gene. exp.) Mycobacterium phage D29 (virus) / Gene: 10 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O64203, Hydrolases
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 830.786 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,4,3/[a2122h-1b_1-5_2*NCC/3=O]/1-1-1-1/a4-b1_b4-c1_c4-d1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}}LINUCSPDB-CARE
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / 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: 2.6 Å3/Da / Density % sol: 52.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Condition E1 from Morpheus crystal screening: - 0.12M Ethylene glycols - 0.1M Buffer System 1 pH 6.5 - 30% Precipitant mix 1

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 1, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.826→38.25 Å / Num. obs: 19241 / % possible obs: 95.1 % / Redundancy: 6.6 % / Biso Wilson estimate: 23.55 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.073 / Net I/σ(I): 15.1
Reflection shellResolution: 1.826→1.858 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.758 / Num. unique obs: 991 / CC1/2: 0.872 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
PHENIX1.20-4459refinement
Aimlessdata scaling
PHASERphasing
autoPROCdata processing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.83→38.25 Å / SU ML: 0.1772 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.9023
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2007 977 5.08 %
Rwork0.18 18248 -
obs0.1811 19225 94.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.69 Å2
Refinement stepCycle: LAST / Resolution: 1.83→38.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1516 0 58 111 1685
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00431609
X-RAY DIFFRACTIONf_angle_d0.65952193
X-RAY DIFFRACTIONf_chiral_restr0.0419250
X-RAY DIFFRACTIONf_plane_restr0.0062284
X-RAY DIFFRACTIONf_dihedral_angle_d13.9616652
LS refinement shellResolution: 1.83→1.92 Å
RfactorNum. reflection% reflection
Rfree0.3311 136 -
Rwork0.2774 2706 -
obs--99.65 %

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