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- PDB-9hu0: Crystal structure of GH19 domain of D29-LysA in complex with prod... -

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Basic information

Entry
Database: PDB / ID: 9hu0
TitleCrystal structure of GH19 domain of D29-LysA in complex with product (GlcNAc)
ComponentsEndolysin A
KeywordsHYDROLASE / Peptidoglycan hydrolase / GH19 / D29-LysA / NAG
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: 2.43 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,5083
Polymers43,2862
Non-polymers2211
Water77543
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1470 Å2
ΔGint7 kcal/mol
Surface area14740 Å2
Unit cell
Length a, b, c (Å)37.165, 56.577, 152.623
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
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
d_1ens_1(chain "A" and (resid 179 through 261 or (resid 262...
d_2ens_1(chain "B" and (resid 179 through 237 or resid 261 through 369))

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11VALVALGLYGLYAA179 - 3693 - 193
d_21VALVALGLUGLUBB179 - 2373 - 61
d_22ARGARGGLYGLYBB261 - 36985 - 193

NCS oper: (Code: givenMatrix: (-0.590956418922, -0.659608137991, -0.464421807445), (-0.6503653581, 0.0489471162972, 0.758042928065), (-0.477279176079, 0.750014189267, -0.457911895434)Vector: -10. ...NCS oper: (Code: given
Matrix: (-0.590956418922, -0.659608137991, -0.464421807445), (-0.6503653581, 0.0489471162972, 0.758042928065), (-0.477279176079, 0.750014189267, -0.457911895434)
Vector: -10.444984848, 18.663497749, -37.9490838562)

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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 of D29-LysA (179-370). Residues from 238 to 260 not modeled
Source: (gene. exp.) Mycobacterium phage D29 (virus) / Gene: 10 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O64203, Hydrolases
#2: 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.: 1 / 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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / 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

Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 13% (v/v) MPD, 9% (v/v) PEG 1K, 9% PEG (w/v) 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: 2.43→76.31 Å / Num. obs: 12304 / % possible obs: 96.6 % / Redundancy: 3.9 % / Biso Wilson estimate: 33.78 Å2 / CC1/2: 0.983 / Rmerge(I) obs: 0.174 / Net I/σ(I): 6.1
Reflection shellResolution: 2.43→2.52 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.891 / Num. unique obs: 1286 / CC1/2: 0.516 / % possible all: 97.9

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
autoPROCdata processing
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.43→76.31 Å / SU ML: 0.3383 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.7992
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2562 651 5.31 %
Rwork0.2022 11613 -
obs0.205 12264 95.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.02 Å2
Refinement stepCycle: LAST / Resolution: 2.43→76.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2684 0 15 43 2742
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00452757
X-RAY DIFFRACTIONf_angle_d0.7733750
X-RAY DIFFRACTIONf_chiral_restr0.0476414
X-RAY DIFFRACTIONf_plane_restr0.013484
X-RAY DIFFRACTIONf_dihedral_angle_d13.97881016
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 2.32182694677 Å
LS refinement shellResolution: 2.43→2.62 Å
RfactorNum. reflection% reflection
Rfree0.3445 107 -
Rwork0.2699 2325 -
obs--97.44 %

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