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- PDB-8gfq: Crystal structure of soluble lytic transglycosylase Cj0843 of Cam... -

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Basic information

Entry
Database: PDB / ID: 8gfq
TitleCrystal structure of soluble lytic transglycosylase Cj0843 of Campylobacter jejuni in complex with Fv32r inhibitor
ComponentsLytic transglycosylase domain-containing protein
KeywordsLYASE/LYASE Inhibitor / soluble lytic transglycosylase / inhibitor / LYASE / LYASE-LYASE Inhibitor complex
Function / homology
Function and homology information


peptidoglycan lytic transglycosylase activity / peptidoglycan metabolic process / membrane
Similarity search - Function
Prokaryotic transglycosylase, active site / Prokaryotic transglycosylases signature. / Transglycosylase SLT domain 1 / Transglycosylase SLT domain / Lysozyme-like domain superfamily
Similarity search - Domain/homology
Chem-9AM / CITRIC ACID / TRIETHYLENE GLYCOL / Lytic transglycosylase domain-containing protein
Similarity search - Component
Biological speciesCampylobacter jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
Authorsvan den Akker, F. / Kumar, V.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1R21AI148875 United States
CitationJournal: Protein Sci. / Year: 2023
Title: Exploring the inhibition of the soluble lytic transglycosylase Cj0843c of Campylobacter jejuni via targeting different sites with different scaffolds.
Authors: Kumar, V. / Boorman, J. / Greenlee, W.J. / Zeng, X. / Lin, J. / van den Akker, F.
History
DepositionMar 8, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 24, 2023Provider: repository / Type: Initial release
Revision 1.1May 31, 2023Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jul 12, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation_author.identifier_ORCID
Revision 1.3Oct 25, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lytic transglycosylase domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,4336
Polymers63,6451
Non-polymers7895
Water3,135174
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)176.669, 176.669, 176.669
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number197
Space group name H-MI23

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein Lytic transglycosylase domain-containing protein / Transglycosylase SLT domain-containing protein


Mass: 63644.652 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni (Campylobacter)
Gene: A0X18_03655, A0X31_01845, A9372_04065, APU74_07480, B1933_07625, BBS05_05650, BCB47_05730, BED64_07690, C3I22_05260, C3I27_06990, C3I35_05175, C7N26_08315, CJ274_08505, CV323_05370, CWD74_ ...Gene: A0X18_03655, A0X31_01845, A9372_04065, APU74_07480, B1933_07625, BBS05_05650, BCB47_05730, BED64_07690, C3I22_05260, C3I27_06990, C3I35_05175, C7N26_08315, CJ274_08505, CV323_05370, CWD74_05755, D0W34_08355, D4Q41_06000, D5I02_03510, D6H33_08420, DPG08_07275, DUX97_06720, DUY05_08000, DWS06_05135, DYE84_06365, E7R20_02805, EAX31_05720, EC071_05580, F0166_06250, F6982_06065, F7521_08930, F7J47_05300, F7U05_05765, F8803_06810, F9778_04965, FCR67_06545, FPD29_09025, FPT92_05795, FV831_05555, FV933_07400, FVI24_07230, FVM64_02425, FVM77_01160, FW220_07595, FW611_08035, FW976_03985, FWA25_07655, FY101_03890, FZ445_05005, FZ878_07970, FZW01_06295, G3M94_001083, GAX22_07420, GCI37_01695, GI172_07425, GIT96_06475, GJ442_07755, GK482_04850, GK486_00445, GL007_04270, GL031_07375, GM780_07860, GMG42_07100, GN862_07225, GNO13_05645, GNO32_03000, GPD80_07165, GRH33_07480, GRM82_06860, GRO30_05060, GRS20_08245, GSH24_05325, GTJ31_06080, GTV40_06285, GTV58_05620, GWW45_06140, GY415_000965, GZ489_001419, GZ499_001624, GZ502_000976, GZ518_001219
Production host: Escherichia coli (E. coli) / References: UniProt: A0A3I4HTM2
#2: Sugar ChemComp-9AM / 9-AMINO-2-DEOXY-2,3-DEHYDRO-N-ACETYL-NEURAMINIC ACID


Type: D-saccharide / Mass: 290.270 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H18N2O7 / Feature type: SUBJECT OF INVESTIGATION

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Non-polymers , 4 types, 178 molecules

#3: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#5: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 174 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 3.61 Å3/Da / Density % sol: 65.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.9
Details: 0.1 M sodium citrate pH 5.9 and 26% (v/v) PEG 600. Protein buffer was 10 mM HEPES pH 8.0, 200 mM ammonium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-1 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 23, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 40529 / % possible obs: 100 % / Redundancy: 11.6 % / Biso Wilson estimate: 50.48 Å2 / Rmerge(I) obs: 0.161 / Rpim(I) all: 0.049 / Rrim(I) all: 0.168 / Χ2: 0.765 / Net I/σ(I): 5.7 / Num. measured all: 471964
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2
2.3-2.3812.12.05840170.5880.6162.1490.483
2.38-2.4811.91.39739980.7350.4211.460.507
2.48-2.5911.80.97940460.8330.2971.0240.57
2.59-2.7311.60.69540260.8930.2120.7280.666
2.73-2.911.30.43340300.9480.1340.4530.744
2.9-3.1210.20.28940410.9680.0950.3050.914
3.12-3.4412.30.20640350.9850.0610.2141.006
3.44-3.9312.30.15740590.9890.0460.1630.973
3.93-4.9511.90.12240860.9930.0370.1280.874
4.95-5011.10.07841910.9980.0240.0810.917

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.20_4459refinement
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6CF9

6cf9


Resolution: 2.3→47.22 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 24.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2167 2060 5.08 %
Rwork0.1776 38467 -
obs0.1796 40527 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 112.38 Å2 / Biso mean: 57.4174 Å2 / Biso min: 33.41 Å2
Refinement stepCycle: final / Resolution: 2.3→47.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4268 0 48 174 4490
Biso mean--71.93 56.05 -
Num. residues----515
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.3-2.360.3051510.264125412692
2.36-2.420.2771410.243825472688
2.42-2.480.27291150.243425262641
2.48-2.550.26751530.229125482701
2.56-2.640.25661390.231125692708
2.64-2.730.32231200.238925372657
2.73-2.840.27351410.230325492690
2.84-2.970.25081470.215725352682
2.97-3.130.24211600.216725392699
3.13-3.320.24931340.20425492683
3.32-3.580.26771400.198425662706
3.58-3.940.21131250.166425802705
3.94-4.510.16631300.14425972727
4.51-5.680.17171350.1526012736
5.68-47.220.17531290.133426832812

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