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- PDB-9hrm: Crystal Structure of GH19 domain of D29-LysA (Form III) -

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Basic information

Entry
Database: PDB / ID: 9hrm
TitleCrystal Structure of GH19 domain of D29-LysA (Form III)
ComponentsEndolysin A
KeywordsHYDROLASE / Peptidoglycan hydrolase / GH19 / D29-LysA
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: 2.04 Å
AuthorsGalvez-Larrosa, L. / Ceballos-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 18, 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
A: Endolysin A
B: Endolysin A


Theoretical massNumber of molelcules
Total (without water)43,2862
Polymers43,2862
Non-polymers00
Water4,342241
1
A: Endolysin A


Theoretical massNumber of molelcules
Total (without water)21,6431
Polymers21,6431
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Endolysin A


Theoretical massNumber of molelcules
Total (without water)21,6431
Polymers21,6431
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.048, 57.040, 151.305
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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


Mass: 21643.150 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: GP N-terminal residues of a PreScission protease cleavage site. GH19 domain (179 to 370). Residues 240-260 not modeled.
Source: (gene. exp.) Mycobacterium phage D29 (virus) / Gene: 10 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O64203, Hydrolases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 241 / Source method: isolated from a natural source / Formula: H2O
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: 1.85 Å3/Da / Density % sol: 33.39 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 9% MPD, 9% PEG 1K, 9% PEG 3350, 0.1 M buffer pH 6.1, and DL-amino-acids (glutamic acid, alanine, glycine; lysine, serine) at 20 mM

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jun 13, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2.04→57.04 Å / Num. obs: 20836 / % possible obs: 98.5 % / Redundancy: 3.9 % / Biso Wilson estimate: 22.74 Å2 / CC1/2: 0.979 / Rpim(I) all: 0.121 / Net I/σ(I): 5.5
Reflection shellResolution: 2.04→2.1 Å / Num. unique obs: 1595 / CC1/2: 0.514 / Rpim(I) all: 0.558 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
autoPROCdata processing
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.04→53.37 Å / SU ML: 0.2553 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.0642
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2349 1040 5 %
Rwork0.1778 19749 -
obs0.1807 20789 97.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.11 Å2
Refinement stepCycle: LAST / Resolution: 2.04→53.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2681 0 0 241 2922
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00672739
X-RAY DIFFRACTIONf_angle_d0.77363727
X-RAY DIFFRACTIONf_chiral_restr0.0469411
X-RAY DIFFRACTIONf_plane_restr0.0093482
X-RAY DIFFRACTIONf_dihedral_angle_d12.4976986
LS refinement shellResolution: 2.04→2.15 Å
RfactorNum. reflection% reflection
Rfree0.3195 147 -
Rwork0.2442 2781 -
obs--99.15 %

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