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- PDB-6fbt: The X-ray Structure of Lytic Transglycosylase Slt from Pseudomona... -

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Basic information

Entry
Database: PDB / ID: 6fbt
TitleThe X-ray Structure of Lytic Transglycosylase Slt from Pseudomonas aeruginosa in complex with the reaction product NAG-anhNAMpentapeptide
Components
  • NAG-anhNAMpentapeptide
  • Probable soluble lytic transglycosylase
KeywordsLYASE / Lytic Transglycosylase
Function / homology
Function and homology information


hydrolase activity, hydrolyzing O-glycosyl compounds / periplasmic space
Similarity search - Function
Lytic transglycosylase, superhelical linker domain / Lytic transglycosylase, superhelical linker / Soluble lytic murein transglycosylase L domain / Lytic transglycosylase, superhelical U-shaped / Lytic transglycosylase, superhelical linker domain superfamily / Methyltransferase, Methionine Synthase (B12-binding Domains); Chain A, domain 1 / Transglycosylase SLT domain 1 / Transglycosylase SLT domain / Lysozyme - #10 / Lysozyme ...Lytic transglycosylase, superhelical linker domain / Lytic transglycosylase, superhelical linker / Soluble lytic murein transglycosylase L domain / Lytic transglycosylase, superhelical U-shaped / Lytic transglycosylase, superhelical linker domain superfamily / Methyltransferase, Methionine Synthase (B12-binding Domains); Chain A, domain 1 / Transglycosylase SLT domain 1 / Transglycosylase SLT domain / Lysozyme - #10 / Lysozyme / Lysozyme-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-AH0 / PHOSPHATE ION / polypeptide(D) / Probable soluble lytic transglycosylase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsBatuecas, M.T. / Dominguez-Gil, T. / Hermoso, J.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)AI104987 United States
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Exolytic and endolytic turnover of peptidoglycan by lytic transglycosylase Slt ofPseudomonas aeruginosa.
Authors: Lee, M. / Batuecas, M.T. / Tomoshige, S. / Dominguez-Gil, T. / Mahasenan, K.V. / Dik, D.A. / Hesek, D. / Millan, C. / Uson, I. / Lastochkin, E. / Hermoso, J.A. / Mobashery, S.
History
DepositionDec 19, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 18, 2018Provider: repository / Type: Initial release
Revision 1.1May 2, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / pdbx_chem_comp_identifier ...chem_comp / pdbx_chem_comp_identifier / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type / Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Mar 30, 2022Group: Author supporting evidence / Database references / Structure summary
Category: chem_comp / database_2 / pdbx_audit_support
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization
Revision 2.0Dec 21, 2022Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / entity ...atom_site / entity / entity_name_com / entity_poly / entity_poly_seq / entity_src_gen / pdbx_entity_nonpoly / pdbx_entity_src_syn / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / pdbx_validate_close_contact / pdbx_validate_polymer_linkage / pdbx_validate_torsion / struct_asym / struct_conn / struct_ref / struct_ref_seq
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.group_PDB / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.pdbx_formal_charge / _atom_site.type_symbol / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.pdbx_gene_src_gene / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _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.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref.db_code / _struct_ref.pdbx_db_accession / _struct_ref_seq.db_align_beg / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.seq_align_end
Revision 3.0Nov 15, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / pdbx_validate_close_contact / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _pdbx_validate_close_contact.auth_atom_id_1 / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id
Revision 3.1Jan 31, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 3.2Oct 1, 2025Group: Advisory / Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_modification_feature ...pdbx_entry_details / pdbx_modification_feature / pdbx_validate_close_contact / struct_conn

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Probable soluble lytic transglycosylase
E: NAG-anhNAMpentapeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,4789
Polymers70,5072
Non-polymers9717
Water1,71195
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2860 Å2
ΔGint-13 kcal/mol
Surface area28450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)165.526, 165.526, 54.733
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

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Protein / Polypeptide(D) / Sugars , 3 types, 3 molecules AE

#1: Protein Probable soluble lytic transglycosylase


Mass: 69974.328 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: PA3020 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9HZI6
#2: Polypeptide(D) NAG-anhNAMpentapeptide


Mass: 532.544 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Pseudomonas aeruginosa (bacteria)
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H15NO6 / Source: (synth.) Pseudomonas aeruginosa (bacteria)
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

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Non-polymers , 3 types, 101 molecules

#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-AH0 / 2-(2-ACETYLAMINO-4-HYDROXY-6,8-DIOXA-BICYCLO[3.2.1]OCT-3-YLOXY)-PROPIONIC ACID / 1,6-anhydro-N-acetylmuramic acid


Mass: 275.255 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H17NO7 / Source: (synth.) Pseudomonas aeruginosa (bacteria)
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 95 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.05 Å3/Da / Density % sol: 59.67 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 1.4M sodium potassium phosphate pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97919 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97919 Å / Relative weight: 1
ReflectionResolution: 2.5→143.35 Å / Num. obs: 30002 / % possible obs: 99.93 % / Redundancy: 15.2 % / Rpim(I) all: 0.024 / Net I/σ(I): 15.2
Reflection shellResolution: 2.5→2.59 Å / Rpim(I) all: 0.36

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5OHU

5ohu


Resolution: 2.5→143.35 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.933 / SU B: 11.323 / SU ML: 0.234 / Cross valid method: THROUGHOUT / ESU R: 0.371 / ESU R Free: 0.259 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23944 1457 4.9 %RANDOM
Rwork0.18002 ---
obs0.18298 28541 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 67.247 Å2
Baniso -1Baniso -2Baniso -3
1--1.79 Å2-0.9 Å20 Å2
2---1.79 Å20 Å2
3---5.81 Å2
Refinement stepCycle: 1 / Resolution: 2.5→143.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5013 0 25 96 5134
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0195200
X-RAY DIFFRACTIONr_bond_other_d0.0020.024763
X-RAY DIFFRACTIONr_angle_refined_deg1.6731.9657064
X-RAY DIFFRACTIONr_angle_other_deg1.072310975
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4215619
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.61622.377265
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.68215853
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2451561
X-RAY DIFFRACTIONr_chiral_restr0.0970.2743
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215801
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021186
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_it5.1246.4522449
X-RAY DIFFRACTIONr_mcbond_other5.1236.4522448
X-RAY DIFFRACTIONr_mcangle_it7.5789.6683062
X-RAY DIFFRACTIONr_mcangle_other7.5779.6683063
X-RAY DIFFRACTIONr_scbond_it5.8487.1452751
X-RAY DIFFRACTIONr_scbond_other5.8477.1452752
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.65210.4543998
X-RAY DIFFRACTIONr_long_range_B_refined11.32775.4226042
X-RAY DIFFRACTIONr_long_range_B_other11.32875.4126041
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.336 112 -
Rwork0.307 2098 -
obs--100 %

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