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- PDB-3rdr: Structure of the catalytic domain of XlyA -

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Basic information

Entry
Database: PDB / ID: 3rdr
TitleStructure of the catalytic domain of XlyA
ComponentsN-acetylmuramoyl-L-alanine amidase XlyA
KeywordsHYDROLASE / T7 lysozyme fold / amidase
Function / homology
Function and homology information


N-acetylmuramoyl-L-alanine amidase / establishment of competence for transformation / peptidoglycan turnover / N-acetylmuramoyl-L-alanine amidase activity / sporulation resulting in formation of a cellular spore / peptidoglycan catabolic process / cell wall organization / extracellular region
Similarity search - Function
PGBD superfamily / Lysozyme-like / Peptidoglycan recognition protein-like / Ami_2 / N-acetylmuramoyl-L-alanine amidase / N-acetylmuramoyl-L-alanine amidase domain / N-acetylmuramoyl-L-alanine amidase/PGRP domain superfamily / Lysin motif / LysM domain superfamily / LysM domain ...PGBD superfamily / Lysozyme-like / Peptidoglycan recognition protein-like / Ami_2 / N-acetylmuramoyl-L-alanine amidase / N-acetylmuramoyl-L-alanine amidase domain / N-acetylmuramoyl-L-alanine amidase/PGRP domain superfamily / Lysin motif / LysM domain superfamily / LysM domain / LysM domain profile. / LysM domain / Peptidoglycan binding-like / Putative peptidoglycan binding domain / PGBD-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
N-acetylmuramoyl-L-alanine amidase XlyA
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsLow, L.Y. / Liddington, R.C.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Role of net charge on catalytic domain and influence of cell wall binding domain on bactericidal activity, specificity, and host range of phage lysins.
Authors: Low, L.Y. / Yang, C. / Perego, M. / Osterman, A. / Liddington, R.
History
DepositionApr 1, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 10, 2011Provider: repository / Type: Initial release
Revision 1.1Aug 17, 2011Group: Database references
SupersessionSep 7, 2011ID: 3HMA
Revision 1.2Dec 21, 2011Group: Database references
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: N-acetylmuramoyl-L-alanine amidase XlyA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,2093
Polymers17,1081
Non-polymers1012
Water1,17165
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: N-acetylmuramoyl-L-alanine amidase XlyA
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)103,25318
Polymers102,6486
Non-polymers60512
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-y-1,x-y-1,z1
crystal symmetry operation3_545-x+y,-x-1,z1
crystal symmetry operation10_445-y-1,-x-1,-z+1/21
crystal symmetry operation11_555-x+y,y,-z+1/21
crystal symmetry operation12_545x,x-y-1,-z+1/21
Buried area10220 Å2
ΔGint-321 kcal/mol
Surface area33240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.700, 96.700, 114.300
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-207-

HOH

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Components

#1: Protein N-acetylmuramoyl-L-alanine amidase XlyA / Autolysin / Cell wall hydrolase


Mass: 17107.969 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: xlyA, BSU12810 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3
References: UniProt: P39800, N-acetylmuramoyl-L-alanine amidase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 65 / Source method: isolated from a natural source / Formula: H2O

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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: 4.51 Å3/Da / Density % sol: 72.72 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 40% peg400, 0.1M mes, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction
IDCrystal-ID
11
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONALS 12.3.111.28279
SYNCHROTRONALS 12.3.121.21972
Detector
TypeIDDetectorDate
ADSC QUANTUM 315r1CCDDec 16, 2005
ADSC QUANTUM 315r2CCDDec 16, 2005
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.282791
21.219721
ReflectionResolution: 2→100 Å / Num. obs: 30364 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 11.2 % / Biso Wilson estimate: 24.1 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 18.6

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SOLVEphasing
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.2→48.35 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 2135702.15 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.235 1504 5 %RANDOM
Rwork0.219 ---
all0.219 30364 --
obs0.219 30359 99.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 42.9535 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 29 Å2
Baniso -1Baniso -2Baniso -3
1-4.26 Å20 Å20 Å2
2--4.26 Å20 Å2
3----8.52 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.15 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 2.2→48.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1178 0 2 65 1245
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.81
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.227 252 5 %
Rwork0.259 4786 -
obs-4786 99.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top

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