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- PDB-9hnv: Crystal structure of a N-terminal GH19 domain of DS6A-LysA -

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Basic information

Entry
Database: PDB / ID: 9hnv
TitleCrystal structure of a N-terminal GH19 domain of DS6A-LysA
ComponentsN-acetylmuramoyl-L-alanine amidase
KeywordsHYDROLASE / GH19 / DS6A-LysA / glycosil hydrolase / Peptidoglycan hydrolisis
Function / homology
Function and homology information


symbiont-mediated cytolysis of host cell / N-acetylmuramoyl-L-alanine amidase / N-acetylmuramoyl-L-alanine amidase activity / peptidoglycan turnover / peptidoglycan catabolic process / cell wall organization / defense response to bacterium
Similarity search - Function
: / Rv3766 C-terminal domain / : / N-acetylmuramoyl-L-alanine amidase / Ami_2 / N-acetylmuramoyl-L-alanine amidase domain / N-acetylmuramoyl-L-alanine amidase/PGRP domain superfamily / Lysozyme-like domain superfamily
Similarity search - Domain/homology
N-acetylmuramoyl-L-alanine amidase
Similarity search - Component
Biological speciesMycobacterium phage DS6A (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 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 11, 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: N-acetylmuramoyl-L-alanine amidase
B: N-acetylmuramoyl-L-alanine amidase
C: N-acetylmuramoyl-L-alanine amidase


Theoretical massNumber of molelcules
Total (without water)65,0653
Polymers65,0653
Non-polymers00
Water1,71195
1
A: N-acetylmuramoyl-L-alanine amidase


Theoretical massNumber of molelcules
Total (without water)21,6881
Polymers21,6881
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: N-acetylmuramoyl-L-alanine amidase


Theoretical massNumber of molelcules
Total (without water)21,6881
Polymers21,6881
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: N-acetylmuramoyl-L-alanine amidase


Theoretical massNumber of molelcules
Total (without water)21,6881
Polymers21,6881
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.175, 145.941, 147.703
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11B-236-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
d_1ens_1(chain "A" and resid 1 through 196)
d_2ens_1(chain "B" and (resid 1 through 18 or (resid 19...
d_3ens_1(chain "C" and (resid 1 through 18 or (resid 19...

NCS domain segments:

Component-ID: 1 / Ens-ID: ens_1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: ALA / End label comp-ID: ALA / Auth seq-ID: 1 - 196 / Label seq-ID: 3 - 198

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

NCS oper:
IDCodeMatrixVector
1given(-0.159919346419, 0.255552703242, -0.953477120075), (0.471318073437, -0.828929835928, -0.30122184642), (-0.867343689833, -0.497562200107, 0.0121153098351)-16.0876250856, -55.0425442465, -82.3108281769
2given(-0.467367784298, -0.847044620293, -0.25314573951), (0.811291405079, -0.297170515622, -0.503483803801), (0.351245797477, -0.44068707251, 0.826087945607)-65.7059177599, -71.0726916392, -42.1445371075

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Components

#1: Protein N-acetylmuramoyl-L-alanine amidase


Mass: 21688.297 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: GH19 domain of DS6A-LysA (residues from 1 to 196) N-terminal GP residues from PreSccision protease cleavage site.
Source: (gene. exp.) Mycobacterium phage DS6A (virus) / Gene: 30, DS6A_30 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: G8I4E0, N-acetylmuramoyl-L-alanine amidase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 95 / 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: 3.64 Å3/Da / Density meas: 66.24 Mg/m3 / Density % sol: 66.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 2.2M de NaCl, 50 mM Tris-HCl pH 8

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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: Jul 9, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.75→76.34 Å / Num. obs: 25458 / % possible obs: 100 % / Redundancy: 8.3 % / Biso Wilson estimate: 42.32 Å2 / CC1/2: 0.984 / Rpim(I) all: 0.128 / Net I/σ(I): 6.7
Reflection shellResolution: 2.75→2.88 Å / Num. unique obs: 3356 / CC1/2: 0.512 / Rpim(I) all: 0.799

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Processing

Software
NameVersionClassification
BUSTERrefinement
PHENIX1.20-4459refinement
Cootmodel building
PHASERphasing
autoPROCdata processing
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.75→76.34 Å / SU ML: 0.4444 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.2719
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2828 1266 4.98 %
Rwork0.239 24172 -
obs0.241 25438 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.85 Å2
Refinement stepCycle: LAST / Resolution: 2.75→76.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4535 0 0 95 4630
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00284659
X-RAY DIFFRACTIONf_angle_d0.6146335
X-RAY DIFFRACTIONf_chiral_restr0.0434639
X-RAY DIFFRACTIONf_plane_restr0.0055844
X-RAY DIFFRACTIONf_dihedral_angle_d17.61291652
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS0.974440586587
ens_1d_3AAX-RAY DIFFRACTIONTorsion NCS0.824517038937
LS refinement shellResolution: 2.75→2.86 Å
RfactorNum. reflection% reflection
Rfree0.3901 150 -
Rwork0.377 2639 -
obs--99.89 %

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