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

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Basic information

Entry
Database: PDB / ID: 8gfg
TitleCrystal structure of soluble lytic transglycosylase Cj0843 of Campylobacter jejuni in complex with Z7912 inhibitor
ComponentsLytic transglycosylase domain-containing protein
KeywordsLYASE/LYASE INHIBITOR / soluble lytic transglycosylase / inhibitor / LYASE / LYASE-LYASE INHIBITOR complex
Function / homology
Function and homology information


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
CITRIC ACID / Chem-ZHL / Lytic transglycosylase domain-containing protein
Similarity search - Component
Biological speciesCampylobacter jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.48 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: Data collection / Database references / Category: citation / citation_author / pdbx_validate_planes
Item: _citation.journal_volume / _citation_author.identifier_ORCID / _pdbx_validate_planes.type
Revision 1.3Aug 16, 2023Group: Data collection
Category: chem_comp_atom / chem_comp_bond / pdbx_validate_planes
Item: _pdbx_validate_planes.type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)64,4296
Polymers63,6451
Non-polymers7845
Water1,58588
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)176.299, 176.299, 176.299
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number197
Space group name H-MI23

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Components

#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: Chemical ChemComp-ZHL / (3S,3aR,5S,6S,6aS)-2-oxohexahydro-2H-3,5-methanocyclopenta[b]furan-6-yl 2-acetamido-2-deoxy-beta-D-glucopyranoside


Mass: 357.356 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H23NO8 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / 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: 3.59 Å3/Da / Density % sol: 65.71 %
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 buffer

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.9201 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 22, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9201 Å / Relative weight: 1
ReflectionResolution: 2.48→29.38 Å / Num. obs: 32190 / % possible obs: 99.7 % / Redundancy: 20.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.127 / Rpim(I) all: 0.029 / Rrim(I) all: 0.13 / Net I/σ(I): 17.8 / Num. measured all: 663176
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.48-2.5517.21.9693996023170.5360.4682.0271.396.5
11.1-29.3819.60.041742437810.0090.04365.694.9

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.4data scaling
REFMAC5.8.0349refinement
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6CF9

6cf9


Resolution: 2.48→29.38 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.956 / SU B: 8.617 / SU ML: 0.179 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.253 / ESU R Free: 0.207 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2159 1652 5.1 %RANDOM
Rwork0.1718 ---
obs0.174 30520 99.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 173.03 Å2 / Biso mean: 68.786 Å2 / Biso min: 26.03 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 2.48→29.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4259 0 50 88 4397
Biso mean--82.6 61.6 -
Num. residues----514
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0124410
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164041
X-RAY DIFFRACTIONr_angle_refined_deg1.4661.6455954
X-RAY DIFFRACTIONr_angle_other_deg0.4811.5599456
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3785513
X-RAY DIFFRACTIONr_dihedral_angle_2_deg15.7441018
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.35310810
X-RAY DIFFRACTIONr_chiral_restr0.0670.2644
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024854
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02878
LS refinement shellResolution: 2.483→2.547 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 120 -
Rwork0.304 2185 -
all-2305 -
obs--97.71 %

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