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- PDB-8wt3: Crystal structure of peptidoglycan DL-endopeptidase CwlO -

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Basic information

Entry
Database: PDB / ID: 8wt3
TitleCrystal structure of peptidoglycan DL-endopeptidase CwlO
ComponentsPeptidoglycan DL-endopeptidase CwlO
KeywordsHYDROLASE / Peptidoglycan DL-endopeptidase / Autolysin
Function / homology
Function and homology information


peptidoglycan metabolic process / Hydrolases; Acting on peptide bonds (peptidases) / cysteine-type peptidase activity / cell wall organization / endopeptidase activity / proteolysis / extracellular region
Similarity search - Function
Peptidoglycan hydrolase PcsB, coiled-coil domain / : / NlpC/P60 family / NlpC/P60 domain profile. / Endopeptidase, NLPC/P60 domain / Papain-like cysteine peptidase superfamily
Similarity search - Domain/homology
Peptidoglycan DL-endopeptidase CwlO
Similarity search - Component
Biological speciesBacillus subtilis subsp. subtilis str. 168 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsTandukar, S. / Kwon, E. / Kim, D.Y.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Febs J. / Year: 2024
Title: Structural analysis of the peptidoglycan DL-endopeptidase CwlO complexed with its inhibitory protein IseA.
Authors: Tandukar, S. / Kwon, E. / Kim, D.Y.
History
DepositionOct 17, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 3, 2024Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peptidoglycan DL-endopeptidase CwlO
B: Peptidoglycan DL-endopeptidase CwlO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4244
Polymers28,3532
Non-polymers712
Water9,350519
1
A: Peptidoglycan DL-endopeptidase CwlO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2122
Polymers14,1771
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Peptidoglycan DL-endopeptidase CwlO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2122
Polymers14,1771
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.320, 58.130, 74.560
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Peptidoglycan DL-endopeptidase CwlO / D-gamma-glutamyl-meso-diaminopimelyl DL-endopeptidase / PSPA2


Mass: 14176.695 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Gene: cwlO, yvcE, yzkA, BSU34800 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P40767, Hydrolases; Acting on peptide bonds (peptidases)
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 519 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.08 Å3/Da / Density % sol: 40.75 %
Crystal growTemperature: 293.15 K / Method: microbatch / pH: 8.5 / Details: 0.1 M Tris HCl pH 8.5 and 2.0 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 6, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.13→45.84 Å / Num. obs: 82799 / % possible obs: 93.9 % / Redundancy: 5.91 % / Rmerge(I) obs: 0.045 / Rpim(I) all: 0.02 / Rrim(I) all: 0.05 / Net I/σ(I): 17.3
Reflection shellResolution: 1.13→1.15 Å / Redundancy: 5.71 % / Rmerge(I) obs: 0.359 / Mean I/σ(I) obs: 4.3 / Num. unique obs: 4029 / Rpim(I) all: 0.162 / Rrim(I) all: 0.396 / % possible all: 92.8

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Processing

Software
NameVersionClassification
PHENIX1.2refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.2→45.84 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 14.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1552 3422 4.91 %
Rwork0.1489 --
obs0.1492 69720 93.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 8.4 Å2
Refinement stepCycle: LAST / Resolution: 1.2→45.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1990 0 2 519 2511
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008
X-RAY DIFFRACTIONf_angle_d1.034
X-RAY DIFFRACTIONf_dihedral_angle_d5.482296
X-RAY DIFFRACTIONf_chiral_restr0.083298
X-RAY DIFFRACTIONf_plane_restr0.015364
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2-1.220.20911330.19472689X-RAY DIFFRACTION93
1.22-1.240.19711490.18372408X-RAY DIFFRACTION83
1.24-1.250.18011420.17652717X-RAY DIFFRACTION94
1.25-1.280.19551500.17472711X-RAY DIFFRACTION94
1.28-1.30.21371360.17132791X-RAY DIFFRACTION94
1.3-1.320.20781320.16612753X-RAY DIFFRACTION94
1.32-1.350.15981250.17072781X-RAY DIFFRACTION94
1.35-1.370.17631600.16492768X-RAY DIFFRACTION95
1.37-1.40.20571230.16542594X-RAY DIFFRACTION89
1.4-1.440.1671450.15382602X-RAY DIFFRACTION89
1.44-1.470.18211360.15372815X-RAY DIFFRACTION96
1.47-1.510.1711640.1522769X-RAY DIFFRACTION96
1.51-1.560.15091440.15492770X-RAY DIFFRACTION95
1.56-1.610.18021500.14792830X-RAY DIFFRACTION97
1.61-1.660.14031480.13942843X-RAY DIFFRACTION97
1.66-1.730.12981240.1342623X-RAY DIFFRACTION89
1.73-1.810.14661390.14192725X-RAY DIFFRACTION92
1.81-1.90.15141570.14162858X-RAY DIFFRACTION98
1.9-2.020.15331650.13512877X-RAY DIFFRACTION97
2.02-2.180.14121460.12792927X-RAY DIFFRACTION98
2.18-2.40.13031050.12492759X-RAY DIFFRACTION91
2.4-2.750.16141260.14632816X-RAY DIFFRACTION93
2.75-3.460.13971710.14822961X-RAY DIFFRACTION98
3.46-45.840.1351520.15852911X-RAY DIFFRACTION92

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