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- PDB-9hna: Crystal structure of apo Ami2B domain of DS6A-LysA -

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Basic information

Entry
Database: PDB / ID: 9hna
TitleCrystal structure of apo Ami2B domain of DS6A-LysA
ComponentsN-acetylmuramoyl-L-alanine amidase
KeywordsVIRUS / DS6A-LysA / Amidase / Pepdidoglycan 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
PHOSPHATE ION / N-acetylmuramoyl-L-alanine amidase
Similarity search - Component
Biological speciesMycobacterium phage DS6A (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.04 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 10, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,40911
Polymers63,7383
Non-polymers6718
Water4,810267
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.998, 121.085, 80.731
Angle α, β, γ (deg.)90.000, 107.160, 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
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
d_1ens_1(chain "A" and (resid 208 through 235 or (resid 236...
d_2ens_1(chain "B" and (resid 208 through 256 or (resid 257...
d_3ens_1(chain "C" and (resid 208 through 235 or (resid 236...

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_11ALAALAILEILEAA208 - 3235 - 120
d_12PROPROARGARGAA325 - 394122 - 191
d_21ALAALAILEILEBB208 - 3235 - 120
d_22PROPROARGARGBB325 - 394122 - 191
d_31ALAALAILEILECC208 - 3235 - 120
d_32PROPROARGARGCC325 - 394122 - 191

NCS oper:
IDCodeMatrixVector
1given(-0.424281630444, 0.852304419146, -0.305879510873), (-0.852301776539, -0.489974064739, -0.183049440296), (-0.305886874149, 0.183037135543, 0.934307565652)43.4521432096, 44.4692543936, 9.29769624807
2given(-0.431014333414, -0.845523652584, -0.315145041708), (0.848608685718, -0.498545102285, 0.176963497682), (-0.306740839987, -0.191161015662, 0.932398800501)59.339564956, -16.5985879698, 12.675421658

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Components

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


Mass: 21246.096 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: GP N-terminal residues from PreScission protease site. Ami2B central domain of DS6A-LysA (206-395)
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: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 267 / 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: 2.55 Å3/Da / Density % sol: 51.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1M HEPES pH 7.5, 0.8M sodium phosphate y 0.4M de potassium phosphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 11, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.036→77.14 Å / Num. obs: 41716 / % possible obs: 98.7 % / Redundancy: 6.8 % / Biso Wilson estimate: 32.73 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.134 / Rpim(I) all: 0.055 / Net I/σ(I): 10.2
Reflection shellResolution: 2.036→2.071 Å / Redundancy: 7.1 % / Rmerge(I) obs: 1.24 / Num. unique obs: 2098 / CC1/2: 0.666 / Rpim(I) all: 0.497

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Processing

Software
NameVersionClassification
BUSTER2.20.4refinement
PHENIX1.20_4459refinement
Cootmodel building
autoPROCdata processing
PHASERphasing
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.04→77.14 Å / SU ML: 0.2157 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.2427
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.209 2041 4.89 %
Rwork0.1858 39660 -
obs0.1869 41701 98.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 37.3 Å2
Refinement stepCycle: LAST / Resolution: 2.04→77.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4361 0 28 267 4656
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_angle_d0.7886188
X-RAY DIFFRACTIONf_chiral_restr0.0531629
X-RAY DIFFRACTIONf_plane_restr0.0069801
X-RAY DIFFRACTIONf_dihedral_angle_d4.4078614
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS0.233947750522
ens_1d_3AAX-RAY DIFFRACTIONTorsion NCS0.278825005516
LS refinement shellResolution: 2.04→2.08 Å
RfactorNum. reflection% reflection
Rfree0.2709 154 -
Rwork0.2675 2608 -
obs--97.7 %

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