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- PDB-6fcr: The X-ray Structure of Lytic Transglycosylase Slt inactive mutant... -

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Basic information

Entry
Database: PDB / ID: 6fcr
TitleThe X-ray Structure of Lytic Transglycosylase Slt inactive mutant E503Q from Pseudomonas aeruginosa in complex with NAG-NAMtetrapeptide-NAG-anhNAMtetrapeptide
Components
  • ALA-DGL-API-DAL
  • Soluble lytic murein 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 / Soluble lytic murein transglycosylase L domain / Lytic transglycosylase, superhelical U-shaped / Lytic transglycosylase, superhelical linker domain superfamily / Transglycosylase SLT domain 1 / Transglycosylase SLT domain / Lysozyme-like domain superfamily
Similarity search - Domain/homology
ACETATE ION / Chem-AH0 / polypeptide(D) / Transglycosylase SLT domain-containing protein / Probable soluble lytic transglycosylase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 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 21, 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 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 / _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.ptnr2_auth_asym_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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Mar 30, 2022Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / pdbx_audit_support / struct_conn
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 / _struct_conn.pdbx_leaving_atom_flag
Revision 3.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / pdbx_validate_rmsd_bond / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id
Revision 3.1Jan 17, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Soluble lytic murein transglycosylase
F: ALA-DGL-API-DAL
G: ALA-DGL-API-DAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,4007
Polymers71,2743
Non-polymers1,1264
Water2,270126
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4180 Å2
ΔGint30 kcal/mol
Surface area28050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)166.703, 166.703, 55.378
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, 4 molecules AFG

#1: Protein Soluble lytic murein transglycosylase


Mass: 70350.688 Da / Num. of mol.: 1 / Mutation: E503Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: slt, AOY09_04369, PAMH19_2049 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A069QJX4, UniProt: Q9HZI6*PLUS, Lyases; Carbon-oxygen lyases; Acting on polysaccharides
#2: Polypeptide(D) ALA-DGL-API-DAL


Mass: 461.466 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Production host: Escherichia coli (E. coli)
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-N-acetyl-beta-muramic acid-(1-4)-2-acetamido-2-deoxy- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-N-acetyl-beta-muramic acid-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 699.656 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4MurNAc1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a2122h-1b_1-5_2*NCC/3=O_3*OC^RCO/4=O/3C]/1-2-1/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(3+1)][<C3O1>]{}[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE

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Non-polymers , 4 types, 129 molecules

#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: 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
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 126 / 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: 3.16 Å3/Da / Density % sol: 61.04 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 80mM Tris pH 8.5, 12% PEG 8000 and 160mM calcium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97926 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 2.75→144.37 Å / Num. obs: 23200 / % possible obs: 99.92 % / Redundancy: 9.7 % / Rpim(I) all: 0.052 / Net I/σ(I): 9.65
Reflection shellResolution: 2.75→2.85 Å / Rpim(I) all: 0.53

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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: 2.75→144.37 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.926 / SU B: 31.867 / SU ML: 0.294 / Cross valid method: THROUGHOUT / ESU R: 1.178 / ESU R Free: 0.334 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24492 1146 4.9 %RANDOM
Rwork0.19111 ---
obs0.19377 22044 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 66.562 Å2
Baniso -1Baniso -2Baniso -3
1-0.54 Å20.27 Å20 Å2
2--0.54 Å20 Å2
3----1.76 Å2
Refinement stepCycle: 1 / Resolution: 2.75→144.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4972 0 138 131 5241
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0195237
X-RAY DIFFRACTIONr_bond_other_d0.0020.024800
X-RAY DIFFRACTIONr_angle_refined_deg1.3021.9757107
X-RAY DIFFRACTIONr_angle_other_deg0.967311062
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.175612
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.09822.471263
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.52315846
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.861559
X-RAY DIFFRACTIONr_chiral_restr0.0690.2757
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215823
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021184
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_it1.5545.7832452
X-RAY DIFFRACTIONr_mcbond_other1.5515.7832450
X-RAY DIFFRACTIONr_mcangle_it2.6378.6713062
X-RAY DIFFRACTIONr_mcangle_other2.6378.6723063
X-RAY DIFFRACTIONr_scbond_it1.5856.0042785
X-RAY DIFFRACTIONr_scbond_other1.5856.0052786
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.7758.9174046
X-RAY DIFFRACTIONr_long_range_B_refined4.84367.4436073
X-RAY DIFFRACTIONr_long_range_B_other4.84367.4476074
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.75→2.822 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.407 92 -
Rwork0.356 1604 -
obs--99.76 %
Refinement TLS params.Method: refined / Origin x: 68.2798 Å / Origin y: -12.0916 Å / Origin z: -8.0797 Å
111213212223313233
T0.0121 Å2-0.0039 Å2-0.0146 Å2-0.013 Å20.0077 Å2--0.1521 Å2
L0.1426 °2-0.0582 °2-0.1121 °2-0.5246 °20.0725 °2--0.1068 °2
S-0.0023 Å °0.0063 Å °-0.003 Å °-0.0235 Å °0.023 Å °0.086 Å °-0.0077 Å °0.0069 Å °-0.0207 Å °

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