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- PDB-5o2n: Lytic transglycosylase in action -

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Basic information

Entry
Database: PDB / ID: 5o2n
TitleLytic transglycosylase in action
ComponentsTransglycosylase
KeywordsHYDROLASE / lytic transglycosylases / acid/base catalysis / peptidoglycan / bacteria
Function / homology
Function and homology information


catalytic activity / hydrolase activity, hydrolyzing O-glycosyl compounds / periplasmic space / metal ion binding
Similarity search - Function
Lytic transglycosylase, superhelical linker domain superfamily / Lytic transglycosylase, superhelical U-shaped / Transglycosylase SLT domain 1 / Transglycosylase SLT domain / Prokaryotic membrane lipoprotein lipid attachment site profile. / Lysozyme-like domain superfamily
Similarity search - Domain/homology
CITRATE ANION / : / Soluble lytic murein transglycosylase
Similarity search - Component
Biological speciesNeisseria meningitidis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.513 Å
AuthorsWilliams, A.H. / Hoauz, A. / Boneca, I.G.
CitationJournal: J. Biol. Chem. / Year: 2018
Title: A step-by-stepin crystalloguide to bond cleavage and 1,6-anhydro-sugar product synthesis by a peptidoglycan-degrading lytic transglycosylase.
Authors: Williams, A.H. / Wheeler, R. / Rateau, L. / Malosse, C. / Chamot-Rooke, J. / Haouz, A. / Taha, M.K. / Boneca, I.G.
History
DepositionMay 22, 2017Deposition site: PDBE / Processing site: PDBE
SupersessionMar 14, 2018ID: 4YP4
Revision 1.0Mar 14, 2018Provider: repository / Type: Initial release
Revision 1.1May 2, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Nov 28, 2018Group: Data collection / Structure summary / Category: audit_author
Revision 1.3Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transglycosylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,7694
Polymers68,5281
Non-polymers1,2413
Water18,8801048
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2470 Å2
ΔGint26 kcal/mol
Surface area24730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.100, 72.600, 125.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Transglycosylase


Mass: 68527.797 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis (bacteria) / Gene: slt, ERS514729_01258 / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): GOLD
References: UniProt: A0A0Y5YPU4, UniProt: Q9JXP1*PLUS, Lyases; Carbon-oxygen lyases; Acting on polysaccharides
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 830.786 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAca1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,4,3/[a2122h-1a_1-5_2*NCC/3=O][a2122h-1b_1-5_2*NCC/3=O]/1-2-2-2/a4-b1_b4-c1_c4-d1WURCSPDB2Glycan 1.1.0
[][a-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}}LINUCSPDB-CARE
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1048 / Source method: isolated from a natural source / Formula: H2O

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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: 2.24 Å3/Da / Density % sol: 45.2 % / Description: Rod Shape
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.01 M tri sodium citrate, 33% (w/v) PEG 6000, Hepes pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 26, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.51→45.75 Å / Num. obs: 93982 / % possible obs: 97.98 % / Redundancy: 9 % / Rmerge(I) obs: 0.106 / Net I/σ(I): 15.95

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.513→45.734 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 2.03 / Phase error: 17.38
RfactorNum. reflection% reflection
Rfree0.1917 4699 5 %
Rwork0.1616 --
obs0.1631 93983 97.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.513→45.734 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4490 0 85 1048 5623
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064694
X-RAY DIFFRACTIONf_angle_d0.866368
X-RAY DIFFRACTIONf_dihedral_angle_d12.2892836
X-RAY DIFFRACTIONf_chiral_restr0.047688
X-RAY DIFFRACTIONf_plane_restr0.005841
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5126-1.52980.33931350.31982555X-RAY DIFFRACTION85
1.5298-1.54780.25521530.26382913X-RAY DIFFRACTION97
1.5478-1.56670.2591520.23922891X-RAY DIFFRACTION97
1.5667-1.58650.23881540.21132923X-RAY DIFFRACTION98
1.5865-1.60740.25091540.19972929X-RAY DIFFRACTION97
1.6074-1.62940.21891540.18992920X-RAY DIFFRACTION97
1.6294-1.65270.1971540.16932928X-RAY DIFFRACTION97
1.6527-1.67730.20411550.16982952X-RAY DIFFRACTION97
1.6773-1.70350.20121530.17032907X-RAY DIFFRACTION98
1.7035-1.73150.21851570.1692982X-RAY DIFFRACTION98
1.7315-1.76130.21041540.16662920X-RAY DIFFRACTION97
1.7613-1.79340.22471560.16292955X-RAY DIFFRACTION98
1.7934-1.82780.20661560.16612977X-RAY DIFFRACTION98
1.8278-1.86520.20941560.16942952X-RAY DIFFRACTION97
1.8652-1.90570.21721550.17482949X-RAY DIFFRACTION99
1.9057-1.950.19221570.16242981X-RAY DIFFRACTION99
1.95-1.99880.19431560.15032973X-RAY DIFFRACTION98
1.9988-2.05290.19621560.14842965X-RAY DIFFRACTION98
2.0529-2.11330.17711570.14842983X-RAY DIFFRACTION98
2.1133-2.18150.1671590.1453010X-RAY DIFFRACTION99
2.1815-2.25940.15981580.14223006X-RAY DIFFRACTION99
2.2594-2.34990.1571590.15233014X-RAY DIFFRACTION99
2.3499-2.45680.15841580.15013009X-RAY DIFFRACTION99
2.4568-2.58640.20291590.16093026X-RAY DIFFRACTION99
2.5864-2.74840.17811600.16863040X-RAY DIFFRACTION100
2.7484-2.96060.20531610.16833049X-RAY DIFFRACTION99
2.9606-3.25840.20571610.16043064X-RAY DIFFRACTION100
3.2584-3.72970.15991630.14723098X-RAY DIFFRACTION100
3.7297-4.69830.17321650.1313138X-RAY DIFFRACTION100
4.6983-45.75490.19951720.17253275X-RAY DIFFRACTION100

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