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- PDB-8i2d: Crystal structure of Bacillus subtilis LytE -

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Basic information

Entry
Database: PDB / ID: 8i2d
TitleCrystal structure of Bacillus subtilis LytE
ComponentsProbable peptidoglycan endopeptidase LytE
KeywordsANTIMICROBIAL PROTEIN / DL-endopeptidase
Function / homology
Function and homology information


lytic endotransglycosylase activity / Hydrolases; Acting on peptide bonds (peptidases) / cysteine-type peptidase activity / cell wall organization / proteolysis / extracellular region
Similarity search - Function
: / NlpC/P60 family / NlpC/P60 domain profile. / Endopeptidase, NLPC/P60 domain / Lysin motif / LysM domain superfamily / LysM domain / LysM domain profile. / LysM domain / Papain-like cysteine peptidase superfamily
Similarity search - Domain/homology
Probable peptidoglycan endopeptidase LytE
Similarity search - Component
Biological speciesBacillus subtilis subsp. subtilis str. 168 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.31 Å
AuthorsTandukar, S. / Kwon, E. / Kim, D.Y.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Structure / Year: 2023
Title: Structural insights into the regulation of peptidoglycan DL-endopeptidases by inhibitory protein IseA.
Authors: Tandukar, S. / Kwon, E. / Kim, D.Y.
History
DepositionJan 14, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 19, 2023Provider: repository / Type: Initial release
Revision 1.1May 17, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 9, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable peptidoglycan endopeptidase LytE


Theoretical massNumber of molelcules
Total (without water)12,8191
Polymers12,8191
Non-polymers00
Water3,153175
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5870 Å2
Unit cell
Length a, b, c (Å)55.250, 55.250, 68.070
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-406-

HOH

21A-430-

HOH

31A-559-

HOH

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Components

#1: Protein Probable peptidoglycan endopeptidase LytE / Gamma-D-glutamate-meso-diaminopimelate muropeptidase LytE / Minor autolysin LytE / Vegetative cell ...Gamma-D-glutamate-meso-diaminopimelate muropeptidase LytE / Minor autolysin LytE / Vegetative cell wall hydrolase LytE


Mass: 12819.079 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Strain: 168 / Gene: lytE / Production host: Escherichia coli B (bacteria)
References: UniProt: P54421, Hydrolases; Acting on peptide bonds (peptidases)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 175 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.03 Å3/Da / Density % sol: 39.29 %
Crystal growTemperature: 293 K / Method: microbatch / Details: 20% (w/v) PEG3350, 200 mM Sodium thiocyanate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 25, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.31→68.07 Å / Num. obs: 26096 / % possible obs: 100 % / Redundancy: 11.5 % / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.025 / Net I/σ(I): 20.9
Reflection shellResolution: 1.31→1.33 Å / Redundancy: 11.8 % / Rmerge(I) obs: 0.446 / Num. unique obs: 1260 / Rpim(I) all: 0.136 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.19refinement
MOSFLMdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.31→42.9 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1837 1268 4.87 %
Rwork0.174 --
obs0.1745 26032 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.31→42.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms900 0 0 175 1075
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005927
X-RAY DIFFRACTIONf_angle_d0.7541257
X-RAY DIFFRACTIONf_dihedral_angle_d6.177127
X-RAY DIFFRACTIONf_chiral_restr0.077132
X-RAY DIFFRACTIONf_plane_restr0.008156
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.31-1.360.2261460.20482672X-RAY DIFFRACTION100
1.36-1.420.21871450.18872701X-RAY DIFFRACTION100
1.42-1.50.21621270.17652712X-RAY DIFFRACTION100
1.5-1.590.20751290.17392723X-RAY DIFFRACTION100
1.59-1.720.20151730.16982687X-RAY DIFFRACTION100
1.72-1.890.18981230.16372750X-RAY DIFFRACTION100
1.89-2.160.18771270.15972774X-RAY DIFFRACTION100
2.16-2.720.17551470.17422793X-RAY DIFFRACTION100
2.72-42.90.16211510.17772952X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 16.3055 Å / Origin y: 42.0716 Å / Origin z: 33.2787 Å
111213212223313233
T0.0548 Å2-0.0067 Å20.0047 Å2-0.0659 Å2-0.0056 Å2--0.068 Å2
L0.6974 °2-0.3526 °20.0193 °2-0.9586 °20.2536 °2--0.9589 °2
S-0.0191 Å °-0.0626 Å °0.0048 Å °0.0649 Å °0.0016 Å °0.0125 Å °0.0352 Å °-0.0411 Å °0.011 Å °
Refinement TLS groupSelection details: all

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