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

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Basic information

Entry
Database: PDB / ID: 6fcq
TitleThe X-ray Structure of Lytic Transglycosylase Slt inactive mutant E503Q from Pseudomonas aeruginosa in complex with Bulgecin A
ComponentsSoluble 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 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
BULGECIN A / Transglycosylase SLT domain-containing protein / Probable soluble lytic transglycosylase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsBatuecas, M.T. / Dominguez-Gil, T. / Hermoso, J.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD) 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 1.2Mar 30, 2022Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization
Revision 1.3Jan 17, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Soluble lytic murein transglycosylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,9943
Polymers70,3511
Non-polymers6442
Water1,36976
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1080 Å2
ΔGint-6 kcal/mol
Surface area29290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)165.715, 165.715, 55.884
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

#1: Protein Soluble lytic murein transglycosylase


Mass: 70350.688 Da / Num. of mol.: 1 / Fragment: UNP residues 30-642 / 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: Chemical ChemComp-BUL / BULGECIN A


Mass: 551.543 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H29N3O14S2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / Source method: isolated from a natural source / Formula: H2O
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: 3.15 Å3/Da / Density % sol: 60.94 %
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: 0.97953 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 24, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97953 Å / Relative weight: 1
ReflectionResolution: 3.1→143.51 Å / Num. obs: 15755 / % possible obs: 97.11 % / Redundancy: 16.5 % / Rpim(I) all: 0.037 / Net I/σ(I): 16.53
Reflection shellResolution: 3.1→3.21 Å

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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: 3.1→143.51 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.946 / SU B: 18.364 / SU ML: 0.301 / Cross valid method: THROUGHOUT / ESU R Free: 0.405 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21683 812 5.2 %RANDOM
Rwork0.18136 ---
obs0.18313 14943 97.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 92.669 Å2
Baniso -1Baniso -2Baniso -3
1-1.25 Å20.63 Å20 Å2
2--1.25 Å20 Å2
3----4.07 Å2
Refinement stepCycle: 1 / Resolution: 3.1→143.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4972 0 41 76 5089
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0195154
X-RAY DIFFRACTIONr_bond_other_d0.0020.024724
X-RAY DIFFRACTIONr_angle_refined_deg1.2611.9556996
X-RAY DIFFRACTIONr_angle_other_deg0.978310886
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.535616
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.63622.528265
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.27315849
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3341559
X-RAY DIFFRACTIONr_chiral_restr0.0630.2737
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0215781
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021180
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_it3.1439.3532458
X-RAY DIFFRACTIONr_mcbond_other3.1439.3532457
X-RAY DIFFRACTIONr_mcangle_it5.22714.0263073
X-RAY DIFFRACTIONr_mcangle_other5.22614.0263074
X-RAY DIFFRACTIONr_scbond_it2.7759.522696
X-RAY DIFFRACTIONr_scbond_other2.7719.522696
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.76514.1713923
X-RAY DIFFRACTIONr_long_range_B_refined8.0726082
X-RAY DIFFRACTIONr_long_range_B_other8.0726083
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.1→3.18 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 67 -
Rwork0.302 1104 -
obs--98.9 %

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