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

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Basic information

Entry
Database: PDB / ID: 8gfe
TitleCrystal structure of soluble lytic transglycosylase Cj0843 of Campylobacter jejuni in complex with Z3261 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
CITRIC ACID / Chem-ZH8 / Lytic transglycosylase domain-containing protein
Similarity search - Component
Biological speciesCampylobacter jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.42 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
Revision 1.4Oct 16, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)64,4526
Polymers63,6451
Non-polymers8075
Water1,38777
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)175.474, 175.474, 175.474
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-ZH8 / ~{N}-[(2~{R},3~{R},4~{R},5~{S},6~{R})-6-(hydroxymethyl)-4,5-bis(oxidanyl)-2-[(4-oxidanylidene-3~{H}-pyrido[1,2-a]pyrimidin-2-yl)methoxy]oxan-3-yl]ethanamide


Mass: 380.372 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H22N3O7 / 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.: 77 / Source method: isolated from a natural source / Formula: H2O
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: 3.54 Å3/Da / Density % sol: 65.23 %
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: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 2, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.42→39.24 Å / Num. obs: 34115 / % possible obs: 99.8 % / Redundancy: 17.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.13 / Rpim(I) all: 0.032 / Rrim(I) all: 0.134 / Net I/σ(I): 13.5 / Num. measured all: 607758 / Scaling rejects: 291
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
2.42-2.5217.14.066036935240.5280.9934.1820.698.3
9.07-39.2418.10.043127637040.9990.010.04446.798.8

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.7data scaling
REFMAC5.8.0349refinement
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6CF9

6cf9


Resolution: 2.42→39.24 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.95 / SU B: 9.819 / SU ML: 0.207 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.25 / ESU R Free: 0.222 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2452 1648 4.8 %RANDOM
Rwork0.1868 ---
obs0.1896 32437 99.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 193.62 Å2 / Biso mean: 72.556 Å2 / Biso min: 30.25 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 2.42→39.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4251 0 52 77 4380
Biso mean--84.61 64.77 -
Num. residues----513
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0124403
X-RAY DIFFRACTIONr_bond_other_d0.0020.0164035
X-RAY DIFFRACTIONr_angle_refined_deg1.3071.6445941
X-RAY DIFFRACTIONr_angle_other_deg0.4331.5599436
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4675512
X-RAY DIFFRACTIONr_dihedral_angle_2_deg11.4891017
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.44410809
X-RAY DIFFRACTIONr_chiral_restr0.0630.2638
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024851
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02882
LS refinement shellResolution: 2.424→2.486 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.378 127 -
Rwork0.328 2350 -
all-2477 -
obs--98.49 %

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