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- PDB-5o2o: Lytic transglycosylase in action -

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Basic information

Entry
Database: PDB / ID: 5o2o
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
: / Soluble lytic murein transglycosylase
Similarity search - Component
Biological speciesNeisseria meningitidis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.43 Å
AuthorsWilliams, A.H. / Hoauz, A. / Boneca, I.G.
CitationJournal: To Be Published
Title: Lytic transglycosylase in action
Authors: Williams, A.H. / Wheeler, R. / Rateau, L. / Malosse, C. / Rooke, J.C. / Hoauz, A. / Taha, M.-K. / Boneca, I.G.
History
DepositionMay 22, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 13, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 28, 2018Group: Data collection / Structure summary / Category: audit_author
Revision 1.2Oct 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 / pdbx_struct_mod_residue / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _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 / _pdbx_struct_mod_residue.auth_asym_id / _pdbx_struct_mod_residue.auth_seq_id / _pdbx_struct_mod_residue.label_asym_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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: Transglycosylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,8715
Polymers67,8241
Non-polymers1,0464
Water15,259847
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1910 Å2
ΔGint24 kcal/mol
Surface area24850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.714, 72.681, 124.924
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: 67824.352 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis (bacteria) / Gene: slt, ERS514729_01258 / Plasmid: PGEX4T1 / Details (production host): GST TAG / Production host: Escherichia coli BL21 / 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


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
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-NHE / 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID / N-CYCLOHEXYLTAURINE / CHES


Mass: 207.290 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H17NO3S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 847 / 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: 2.23 Å3/Da / Density % sol: 44.91 % / Description: Rod Shape
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 9.5
Details: 100 mM CHES pH 9.5, 100 mM tri sodium citrate, 30% PEG 3000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 1.1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.43→49.15 Å / Num. obs: 110458 / % possible obs: 97.6 % / Redundancy: 9.3 % / Net I/av σ(I): 14.41 / Net I/σ(I): 0.185

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YIM

4yim
PDB Unreleased entry


Resolution: 1.43→49.15 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.951 / SU B: 1.912 / SU ML: 0.07 / Cross valid method: THROUGHOUT / ESU R: 0.07 / ESU R Free: 0.073
RfactorNum. reflection% reflectionSelection details
Rfree0.22578 2002 1.8 %RANDOM
Rwork0.19138 ---
obs0.19199 108023 97.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 24.892 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.43→49.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4479 0 68 847 5394
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0194670
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5911.9616330
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0185585
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.81923.026228
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.14115762
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3331552
X-RAY DIFFRACTIONr_chiral_restr0.1990.2678
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0213607
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.0792.0532316
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.7033.0752897
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.6492.4322354
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined6.20720.0348431
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.429→1.466 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.382 142 -
Rwork0.36 7074 -
obs--87.9 %

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