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- PDB-9hyr: Crystal structure of a peptidase N4 domain of D29-LysA -

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Basic information

Entry
Database: PDB / ID: 9hyr
TitleCrystal structure of a peptidase N4 domain of D29-LysA
ComponentsEndolysin A
KeywordsHYDROLASE / Peptidoglycan hydrolase / peptidase domain / D29-LysA / Mycobacteriophage
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: 3.2 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
DepositionJan 10, 2025Deposition 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


Theoretical massNumber of molelcules
Total (without water)42,7162
Polymers42,7162
Non-polymers00
Water00
1
A: Endolysin A


Theoretical massNumber of molelcules
Total (without water)21,3581
Polymers21,3581
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Endolysin A


Theoretical massNumber of molelcules
Total (without water)21,3581
Polymers21,3581
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.170, 66.976, 82.967
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 2 through 108 or (resid 109...
d_2ens_1chain "B"

NCS domain segments:

Component-ID: 1 / Ens-ID: ens_1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: ASP / End label comp-ID: ASP / Auth seq-ID: 2 - 173 / Label seq-ID: 20 - 191

Dom-IDAuth asym-IDLabel asym-ID
d_1AA
d_2BB

NCS oper: (Code: givenMatrix: (-0.992144602088, -0.0588865365274, 0.110369671395), (0.0284905208481, -0.965457122628, -0.258999680672), (0.121808779527, -0.253820645697, 0.95955078086)Vector: -30. ...NCS oper: (Code: given
Matrix: (-0.992144602088, -0.0588865365274, 0.110369671395), (0.0284905208481, -0.965457122628, -0.258999680672), (0.121808779527, -0.253820645697, 0.95955078086)
Vector: -30.0812637202, -17.4097022355, 0.189452576269)

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Components

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


Mass: 21358.041 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: From 1 to 15 residues (included) and C-terminal Gly are not observed in the electron density map
Source: (gene. exp.) Mycobacterium phage D29 (virus) / Gene: 10 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O64203, Hydrolases
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: 2.12 Å3/Da / Density % sol: 41.97 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.1M HEPES pH 7.5, 1.8M NaCl

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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 PILATUS3 6M / Detector: PIXEL / Date: Jul 21, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 3.2→82.97 Å / Num. obs: 6267 / % possible obs: 99.1 % / Redundancy: 4.4 % / Biso Wilson estimate: 33.81 Å2 / CC1/2: 0.934 / Rpim(I) all: 0.173 / Net I/σ(I): 4.7
Reflection shellResolution: 3.2→3.42 Å / Redundancy: 4.5 % / Num. unique obs: 1110 / CC1/2: 0.728 / Rpim(I) all: 0.376 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
PHASERphasing
Cootmodel building
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→51.25 Å / SU ML: 0.333 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.0012
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3144 315 5.05 %
Rwork0.2457 5918 -
obs0.2491 6233 98.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.35 Å2
Refinement stepCycle: LAST / Resolution: 3.2→51.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2714 0 0 0 2714
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00242793
X-RAY DIFFRACTIONf_angle_d0.54313792
X-RAY DIFFRACTIONf_chiral_restr0.0406383
X-RAY DIFFRACTIONf_plane_restr0.0078497
X-RAY DIFFRACTIONf_dihedral_angle_d11.5891978
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.793654951271 Å
LS refinement shellResolution: 3.2→4.03 Å
RfactorNum. reflection% reflection
Rfree0.3135 144 -
Rwork0.2713 2921 -
obs--98.97 %

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