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- PDB-9h68: Crystal Structure of the spore gernation lytic transglycosylase S... -

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Basic information

Entry
Database: PDB / ID: 9h68
TitleCrystal Structure of the spore gernation lytic transglycosylase SleC from Clostridioides difficile in its zymogenic form (prepro-SleC)
ComponentsSpore cortex-lytic enzyme pre-pro-form
KeywordsHYDROLASE / Spore germination lytic transglycosylase
Function / homologyPGBD superfamily / peptidoglycan lytic transglycosylase activity / Peptidoglycan binding-like / Putative peptidoglycan binding domain / PGBD-like superfamily / Spore cortex-lytic enzyme pre-pro-form
Function and homology information
Biological speciesClostridioides difficile 630 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsMolina, R. / Garay-Alvarez, A. / Hermoso, J.A.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and UniversitiesPID2020-115331GB-I00 Spain
CitationJournal: J.Am.Chem.Soc. / Year: 2025
Title: Reactions of SleC, Its Structure and Inhibition in Mitigation of Spore Germination in Clostridioides difficile.
Authors: Kim, C. / Molina, R. / Lee, M. / Garay-Alvarez, A. / Yang, J. / Qian, Y. / Birhanu, B.T. / Hesek, D. / Hermoso, J.A. / Chang, M. / Mobashery, S.
History
DepositionOct 23, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 12, 2025Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2025Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Spore cortex-lytic enzyme pre-pro-form
D: Spore cortex-lytic enzyme pre-pro-form
B: Spore cortex-lytic enzyme pre-pro-form
C: Spore cortex-lytic enzyme pre-pro-form


Theoretical massNumber of molelcules
Total (without water)213,6734
Polymers213,6734
Non-polymers00
Water10,611589
1
A: Spore cortex-lytic enzyme pre-pro-form


Theoretical massNumber of molelcules
Total (without water)53,4181
Polymers53,4181
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Spore cortex-lytic enzyme pre-pro-form


Theoretical massNumber of molelcules
Total (without water)53,4181
Polymers53,4181
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: Spore cortex-lytic enzyme pre-pro-form


Theoretical massNumber of molelcules
Total (without water)53,4181
Polymers53,4181
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
C: Spore cortex-lytic enzyme pre-pro-form


Theoretical massNumber of molelcules
Total (without water)53,4181
Polymers53,4181
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.431, 89.781, 99.621
Angle α, β, γ (deg.)76.899, 75.874, 89.123
Int Tables number1
Space group name H-MP1
Space group name HallP1

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Components

#1: Protein
Spore cortex-lytic enzyme pre-pro-form


Mass: 53418.168 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridioides difficile 630 (bacteria)
Gene: sleC, CD630_05510 / Production host: Escherichia coli (E. coli) / References: UniProt: Q188Z5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 589 / Source method: isolated from a natural source / Formula: H2O
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: 2.62 Å3/Da / Density % sol: 53.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M sodium citrate (pH 5.6) and 10% Jeffamine M-2000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97926 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Oct 15, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 2.1→96.03 Å / Num. obs: 72598 / % possible obs: 98.4 % / Redundancy: 5.3 % / CC1/2: 0.99 / Net I/σ(I): 8.7
Reflection shellResolution: 2.1→2.36 Å / Num. unique obs: 3454 / CC1/2: 0.53

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
autoPROCdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→72.9 Å / SU ML: 0.3191 / Cross valid method: FREE R-VALUE / σ(F): 1.92 / Phase error: 38.1525
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2611 3686 5.08 %
Rwork0.2112 68892 -
obs0.2137 72578 57.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 54.36 Å2
Refinement stepCycle: LAST / Resolution: 2.1→72.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12949 0 0 589 13538
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008713293
X-RAY DIFFRACTIONf_angle_d1.022918177
X-RAY DIFFRACTIONf_chiral_restr0.06032023
X-RAY DIFFRACTIONf_plane_restr0.01062375
X-RAY DIFFRACTIONf_dihedral_angle_d19.46974831
LS refinement shellResolution: 4.94→6.22 Å
RfactorNum. reflection% reflection
Rfree0.2508 220 -
Rwork0.1839 4540 -
obs--97.4 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.50187906892-0.0951251116855-0.300984567681.00742530940.4070190005721.370586263870.03244415712680.03067477493110.4102434063160.05140293622470.0494863534222-0.117163134978-0.1350292114330.00620160731766-0.0076927492010.227496676050.04823831280890.02561019619090.1218867914260.08097361096770.389416330927.931264813234.6953170618-4.49960078189
21.0327549937-0.1468830418160.7089595987411.43874173496-0.4606809654123.01746495005-0.1741360967-0.09196240579690.171523846914-0.0994809584662-0.0409710577990.0557938210432-0.578236249186-0.9604879728110.05850594784890.2026881990340.111765554342-0.0254627044890.461777194905-0.1293512686730.149343588688.4111949913934.418712553644.2755940206
31.89848596553-0.04836328849020.5705021505261.35537017816-0.4187480054311.723682600330.0588799155902-0.0445530172237-0.3070186776520.1548596434090.01659522937870.06329318504920.1614766162480.01371415002450.0009959218890180.165458487690.0386802645902-0.0005817242709480.0356837552304-0.03084719284080.22306573338.79110485362-2.84108515116-4.19012615083
41.34439400793-0.0885463406319-0.008929591469871.676523197490.6064715664122.079330297350.08335587942160.0618182589825-0.2416984703340.073861767206-0.0208446123825-0.1517543669250.884204604480.300772282911-0.02755622148020.506906586112-0.0387070339706-0.04595872429550.346348904473-0.07686906651880.26447506821726.8848849411-2.3509949064244.3590300472
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11(chain A and resseq -7:417)AA-7 - 4171 - 412
22(chain D and resseq -1:415)DB-1 - 4151 - 404
33(chain B and resseq -5:415)BC-5 - 4151 - 410
44(chain C and resseq -1:415)CD-1 - 4151 - 406

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