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- PDB-6ssc: N-acetylmuramoyl-L-alanine amidase LysC from Clostridium intestin... -

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Basic information

Entry
Database: PDB / ID: 6ssc
TitleN-acetylmuramoyl-L-alanine amidase LysC from Clostridium intestinale URNW
ComponentsN-acetylmuramoyl-L-alanine amidase
KeywordsHYDROLASE / amidase / zinc binding / cell wall degradation / endolysine
Function / homology
Function and homology information


N-acetylmuramoyl-L-alanine amidase / N-acetylmuramoyl-L-alanine amidase activity / peptidoglycan catabolic process / zinc ion binding
Similarity search - Function
Peptidoglycan recognition protein family domain, metazoa/bacteria / Peptidoglycan recognition protein / Animal peptidoglycan recognition proteins homologous to Bacteriophage T3 lysozyme. / Ami_2 / N-acetylmuramoyl-L-alanine amidase / N-acetylmuramoyl-L-alanine amidase domain / N-acetylmuramoyl-L-alanine amidase/PGRP domain superfamily
Similarity search - Domain/homology
PHOSPHATE ION / N-acetylmuramoyl-L-alanine amidase
Similarity search - Component
Biological speciesClostridium intestinale (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.21 Å
AuthorsHakansson, M. / Al-Karadaghi, S. / Kovacic, R. / Plotka, M. / Kaczorowska, A.K. / Kaczorowski, T.
Funding support Sweden, 1items
OrganizationGrant numberCountry
European Research Council685778 Sweden
CitationJournal: Int J Mol Sci / Year: 2020
Title: Molecular Characterization of a Novel Lytic Enzyme LysC from Clostridium intestinale URNW and Its Antibacterial Activity Mediated by Positively Charged N -Terminal Extension.
Authors: Plotka, M. / Szadkowska, M. / Hakansson, M. / Kovacic, R. / Al-Karadaghi, S. / Walse, B. / Werbowy, O. / Kaczorowska, A.K. / Kaczorowski, T.
History
DepositionSep 6, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 30, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 14, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)22,7326
Polymers22,2921
Non-polymers4405
Water4,161231
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1030 Å2
ΔGint-56 kcal/mol
Surface area7370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.400, 53.780, 76.710
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 22292.391 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium intestinale (bacteria) / Gene: CINTURNW_1763 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: U2NM08
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 231 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.24 Å3/Da / Density % sol: 45.15 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 7.4 / Details: NaKHPO4, PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97951 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 26, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97951 Å / Relative weight: 1
ReflectionResolution: 1.21→14.9 Å / Num. obs: 47839 / % possible obs: 99.8 % / Redundancy: 5.3 % / CC1/2: 1 / Rmerge(I) obs: 0.07 / Net I/σ(I): 12.1
Reflection shellResolution: 1.21→1.23 Å / Rmerge(I) obs: 1.11 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 2324 / CC1/2: 0.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
XDSdata reduction
PDB_EXTRACT3.25data extraction
xia2data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6SU5

6su5


Resolution: 1.21→14.9 Å / Cor.coef. Fo:Fc: 0.985 / Cor.coef. Fo:Fc free: 0.976 / SU B: 1.298 / SU ML: 0.025 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.033 / ESU R Free: 0.037
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1607 2353 4.9 %RANDOM
Rwork0.1205 ---
obs0.1225 45430 99.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 74.61 Å2 / Biso mean: 16.156 Å2 / Biso min: 8.58 Å2
Baniso -1Baniso -2Baniso -3
1--0.95 Å20 Å20 Å2
2--0.07 Å20 Å2
3---0.88 Å2
Refinement stepCycle: final / Resolution: 1.21→14.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1213 0 40 232 1485
Biso mean--24.47 33.55 -
Num. residues----149
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0131392
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171246
X-RAY DIFFRACTIONr_angle_refined_deg2.2221.661897
X-RAY DIFFRACTIONr_angle_other_deg1.5511.5792912
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6045172
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.79921.90584
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.88615239
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2621511
X-RAY DIFFRACTIONr_chiral_restr0.130.2173
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.021576
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02305
X-RAY DIFFRACTIONr_rigid_bond_restr4.23332638
LS refinement shellResolution: 1.21→1.241 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 175 -
Rwork0.254 3284 -
all-3459 -
obs--99.77 %

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