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- PDB-9hty: Crystal structure of Ami2B domain of DS6A-LysA in complex with L-... -

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Basic information

Entry
Database: PDB / ID: 9hty
TitleCrystal structure of Ami2B domain of DS6A-LysA in complex with L-Ala-D-iso-Gln-L-Lys- D-Ala-D-Ala
Components
  • L-Ala-D-iso-Gln-L-Lys- D-Ala-D-Ala
  • N-acetylmuramoyl-L-alanine amidase
KeywordsHYDROLASE / Peptidoglycan hydrolase / Amidase / DS6A-LysA / crystal complex
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)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.74 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 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: N-acetylmuramoyl-L-alanine amidase
B: N-acetylmuramoyl-L-alanine amidase
C: N-acetylmuramoyl-L-alanine amidase
F: L-Ala-D-iso-Gln-L-Lys- D-Ala-D-Ala
H: L-Ala-D-iso-Gln-L-Lys- D-Ala-D-Ala
I: L-Ala-D-iso-Gln-L-Lys- D-Ala-D-Ala
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,68512
Polymers65,2046
Non-polymers4816
Water1,24369
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.683, 121.237, 80.052
Angle α, β, γ (deg.)90.000, 106.250, 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 228 or (resid 229...
d_2ens_1(chain "B" and (resid 208 through 235 or (resid 236...
d_3ens_1(chain "C" and (resid 208 through 225 or (resid 226...

NCS domain segments:

Component-ID: 1 / Ens-ID: ens_1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: ARG / End label comp-ID: ARG / Auth seq-ID: 208 - 394 / Label seq-ID: 5 - 191

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

NCS oper:
IDCodeMatrixVector
1given(-0.411518353359, -0.842774632334, -0.346963346686), (0.857820141202, -0.486766537141, 0.164933149087), (-0.307891620863, -0.22975912912, 0.923262417945)56.8617357179, -18.0018310895, 12.7672593927
2given(-0.44808616436, 0.8385836157, -0.309832710974), (-0.836114737845, -0.515776653327, -0.186779519867), (-0.316434723866, 0.175362377273, 0.932264502257)44.3926328039, 41.5626115968, 9.6461306625

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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 of PreScission protease cleavage site (not modeled). Ami2B domain from 206 to 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: Protein/peptide L-Ala-D-iso-Gln-L-Lys- D-Ala-D-Ala


Mass: 488.557 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.49 Å3/Da / Density % sol: 50.73 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.1M HEPES pH 7.5, NaH2PO4 0.8M, KH2PO4 0.4M

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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 PILATUS3 X 6M / Detector: PIXEL / Date: Jun 1, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.74→60.62 Å / Num. obs: 16754 / % possible obs: 98 % / Redundancy: 3.4 % / Biso Wilson estimate: 36.43 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.112 / Net I/σ(I): 5.6
Reflection shellResolution: 2.74→2.79 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.415 / Num. unique obs: 845 / CC1/2: 0.864 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.20_4459refinement
autoPROCdata processing
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.74→60.62 Å / SU ML: 0.2406 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 19.9932
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.197 797 4.76 %
Rwork0.1622 15952 -
obs0.1639 16749 97.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.65 Å2
Refinement stepCycle: LAST / Resolution: 2.74→60.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4326 0 120 69 4515
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054578
X-RAY DIFFRACTIONf_angle_d0.74056255
X-RAY DIFFRACTIONf_chiral_restr0.0513644
X-RAY DIFFRACTIONf_plane_restr0.0072823
X-RAY DIFFRACTIONf_dihedral_angle_d4.4417672
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS0.484075903577
ens_1d_3AAX-RAY DIFFRACTIONTorsion NCS0.421716003918
LS refinement shellResolution: 2.74→2.91 Å
RfactorNum. reflection% reflection
Rfree0.2851 133 -
Rwork0.2054 2711 -
obs--99.68 %

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