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- PDB-9hu2: Crystal structure of GH19 domain of D29-LysA in complex with prod... -

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Basic information

Entry
Database: PDB / ID: 9hu2
TitleCrystal structure of GH19 domain of D29-LysA in complex with products (GlcNAc y GlcNAc2)
ComponentsEndolysin A
KeywordsHYDROLASE / Peptidoglycan hydrolase / GH19 / D29-LysA / GlcNAc / (GlcNAc)2
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: 3.1 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 20, 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
C: Endolysin A
D: Endolysin A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,31516
Polymers86,5734
Non-polymers2,74312
Water1448
1
A: Endolysin A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3294
Polymers21,6431
Non-polymers6863
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Endolysin A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3294
Polymers21,6431
Non-polymers6863
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Endolysin A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3294
Polymers21,6431
Non-polymers6863
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Endolysin A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3294
Polymers21,6431
Non-polymers6863
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.707, 84.205, 135.319
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221
Space group name HallP22ab(y,z,x)
Symmetry operation#1: x,y,z
#2: x+1/2,-y,-z+1/2
#3: -x,y,-z
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
d_1ens_1(chain "A" and resid 180 through 369)
d_2ens_1chain "B"
d_3ens_1chain "C"
d_4ens_1chain "D"

NCS domain segments:

Component-ID: 1 / Ens-ID: ens_1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: GLY / End label comp-ID: GLY / Auth seq-ID: 180 - 369 / Label seq-ID: 4 - 193

Dom-IDAuth asym-IDLabel asym-ID
d_1AA
d_2BB
d_3CC
d_4DD

NCS oper:
IDCodeMatrixVector
1given(0.730569793711, -0.00817592190776, -0.682789082234), (0.00429965200814, -0.999853412232, 0.0165730817798), (-0.68282449393, -0.0150435483856, -0.730427547497)0.361274465666, -17.1559240299, 0.349847086427
2given(0.0441766271445, 0.0157686138134, 0.998899282427), (-0.013757804175, 0.999790210704, -0.0151742348886), (-0.998929000699, -0.0130723142013, 0.0443843008619)-0.840318631536, 0.313459786981, -0.260117546887
3given(-0.681308786845, -0.0109907914543, -0.73191361476), (-0.00698648095444, 0.999939364172, -0.00851217142233), (0.731962790074, -0.000685916655341, -0.681344262078)39.7218822795, 17.2390822572, -67.1062387475

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Components

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


Mass: 21643.150 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: GP N-terminal residues of a PreScission protease cleavage site (not modeled). GH19 domain (179 to 370)
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


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#3: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Chemical
ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 8 / 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: 2.59 Å3/Da / Density % sol: 52.51 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 9% MPD, 9% PEG 1K, 9% PEG 3350, 0.1 M Tris/BICINE pH 8.5, 30mM MgCl2, 30mM CaCl2

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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: 3.1→43.81 Å / Num. obs: 16002 / % possible obs: 95.2 % / Redundancy: 4.6 % / Biso Wilson estimate: 68.14 Å2 / CC1/2: 0.985 / Rpim(I) all: 0.136 / Net I/σ(I): 5.2
Reflection shellResolution: 3.1→3.31 Å / Redundancy: 4.8 % / Num. unique obs: 2889 / CC1/2: 0.523 / Rpim(I) all: 0.71 / % possible all: 96.4

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
autoPROCdata processing
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.1→43.81 Å / SU ML: 0.4691 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.6963
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2842 749 4.69 %
Rwork0.2451 15213 -
obs0.247 15962 94.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 62.02 Å2
Refinement stepCycle: LAST / Resolution: 3.1→43.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6007 0 180 8 6195
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00256311
X-RAY DIFFRACTIONf_angle_d0.44628594
X-RAY DIFFRACTIONf_chiral_restr0.0379966
X-RAY DIFFRACTIONf_plane_restr0.01021113
X-RAY DIFFRACTIONf_dihedral_angle_d10.16932502
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS0.508311737561
ens_1d_3AAX-RAY DIFFRACTIONTorsion NCS0.626527483246
ens_1d_4AAX-RAY DIFFRACTIONTorsion NCS0.552589518246
LS refinement shellResolution: 3.1→3.34 Å
RfactorNum. reflection% reflection
Rfree0.355 141 -
Rwork0.3224 3040 -
obs--95.96 %

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