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- PDB-7laq: Crystal structure of Campylobacter jejuni Cj0843c lytic transglyc... -

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Basic information

Entry
Database: PDB / ID: 7laq
TitleCrystal structure of Campylobacter jejuni Cj0843c lytic transglycosylase in complex with N,N'-diacetylchitobiose
ComponentsLytic transglycosylase domain-containing protein
KeywordsLYASE/LYASE INHIBITOR / inhibitor / complex / substrate analog / 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
ACETATE ION / CITRIC ACID / Lytic transglycosylase domain-containing protein
Similarity search - Component
Biological speciesCampylobacter jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.58 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)1 R21 AI148875-01 United States
CitationJournal: Biochemistry / Year: 2021
Title: Turnover Chemistry and Structural Characterization of the Cj0843c Lytic Transglycosylase of Campylobacter jejuni .
Authors: Kumar, V. / Mathure, S.A. / Lee, M. / Boorman, J. / Zeng, X. / Lin, J. / Hesek, D. / Lastochkin, E. / Mobashery, S. / van den Akker, F.
History
DepositionJan 6, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 21, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2021Group: 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
Revision 1.2Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)64,7455
Polymers63,6451
Non-polymers1,1004
Water3,477193
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)176.989, 176.989, 176.989
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number197
Space group name H-MI23
Components on special symmetry positions
IDModelComponents
11A-832-

HOH

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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: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2 / Source method: obtained synthetically
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 193 / 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: 3.63 Å3/Da / Density % sol: 66.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 100 sodium citrate buffer pH 5.1-6.0, and 25-33% PEG 600. The protein was concentrated to 10 mg/ml in 10 mM HEPES pH 8.0 and 200 mM ammonium sulfate
PH range: 5.1-6.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X17B1 / Wavelength: 0.97935 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 29, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97935 Å / Relative weight: 1
ReflectionResolution: 2.58→29.52 Å / Num. obs: 28913 / % possible obs: 99.5 % / Redundancy: 13.9 % / CC1/2: 0.997 / Rmerge(I) obs: 0.17 / Net I/σ(I): 13
Reflection shellResolution: 2.58→2.65 Å / Rmerge(I) obs: 1.018 / Num. unique obs: 2029 / CC1/2: 0.782

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6CF9

6cf9


Resolution: 2.58→29.5 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.929 / SU B: 8.497 / SU ML: 0.178 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.326 / ESU R Free: 0.246 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2287 1574 5.4 %RANDOM
Rwork0.1757 ---
obs0.1786 27339 99.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 147.66 Å2 / Biso mean: 42.196 Å2 / Biso min: 5.97 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 2.58→29.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4276 0 75 193 4544
Biso mean--50.41 38.35 -
Num. residues----516
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0134453
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174097
X-RAY DIFFRACTIONr_angle_refined_deg1.5231.6526013
X-RAY DIFFRACTIONr_angle_other_deg1.2921.5779569
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1595515
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.18623.697238
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.92315815
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8791516
X-RAY DIFFRACTIONr_chiral_restr0.0760.2587
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024845
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02915
LS refinement shellResolution: 2.583→2.65 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.323 130 -
Rwork0.259 1899 -
all-2029 -
obs--94.77 %

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