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- PDB-8rhf: Lytic Transglycosylase MltD of Pseudomonas aeruginosa bound to th... -

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Basic information

Entry
Database: PDB / ID: 8rhf
TitleLytic Transglycosylase MltD of Pseudomonas aeruginosa bound to the Natural Product Bulgecin A, with two LysM domains
ComponentsLysM peptidoglycan-binding domain-containing protein
KeywordsLYASE / Lytic transglycosylase / Bacterial cell-wall / bulgecin A
Function / homology
Function and homology information


Lyases; Carbon-oxygen lyases; Acting on polysaccharides / lytic endotransglycosylase activity / peptidoglycan metabolic process / membrane
Similarity search - Function
Lytic murein transglycosylase D , lipid attachment domain / MltD lipid attachment motif / Prokaryotic transglycosylase, active site / Prokaryotic transglycosylases signature. / Transglycosylase SLT domain 1 / Transglycosylase SLT domain / Lysin motif / LysM domain superfamily / LysM domain / LysM domain profile. ...Lytic murein transglycosylase D , lipid attachment domain / MltD lipid attachment motif / Prokaryotic transglycosylase, active site / Prokaryotic transglycosylases signature. / Transglycosylase SLT domain 1 / Transglycosylase SLT domain / Lysin motif / LysM domain superfamily / LysM domain / LysM domain profile. / LysM domain / Lysozyme-like domain superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
Chem-BLG / DI(HYDROXYETHYL)ETHER / LysM peptidoglycan-binding domain-containing protein
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsMiguel-Ruano, V. / Hermoso, J.A.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and UniversitiesBFU2017-90030-P Spain
CitationJournal: Int.J.Biol.Macromol. / Year: 2024
Title: Structural characterization of lytic transglycosylase MltD of Pseudomonas aeruginosa, a target for the natural product bulgecin A.
Authors: Miguel-Ruano, V. / Feltzer, R. / Batuecas, M.T. / Ramachandran, B. / El-Araby, A.M. / Avila-Cobian, L.F. / De Benedetti, S. / Mobashery, S. / Hermoso, J.A.
History
DepositionDec 15, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 17, 2024Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2024Group: Database references / Category: citation / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: LysM peptidoglycan-binding domain-containing protein
A: LysM peptidoglycan-binding domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,26118
Polymers77,1592
Non-polymers2,10216
Water6,846380
1
B: LysM peptidoglycan-binding domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,69610
Polymers38,5791
Non-polymers1,1179
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: LysM peptidoglycan-binding domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,5658
Polymers38,5791
Non-polymers9867
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.753, 116.527, 121.101
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 LysM peptidoglycan-binding domain-containing protein / Membrane-bound lytic murein transglycosylase D / Murein transglycosylase


Mass: 38579.418 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: His tag and TEV cleavage site in the N-t region. MltD contruction from residues 76 to 393
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria)
Gene: mltD, CAZ10_25765, CGU42_31890, GNQ48_00460, GUL26_19730, IPC1295_05870, PAERUG_P19_London_7_VIM_2_05_10_06006
Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 DE3
References: UniProt: A0A0C7CWY9, Lyases; Carbon-oxygen lyases; Acting on polysaccharides
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-BLG / 4-O-(4-O-SULFONYL-N-ACETYLGLUCOSAMININYL)-5-METHYLHYDROXY-L-PROLINE-TAURINE / BULGECIN A


Mass: 552.551 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H30N3O14S2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 380 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.13 Å3/Da / Density % sol: 42.32 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M MES pH 6.5, 25% w/v PEG 550 MME, and 10 mM zinc sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 20, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.95→60.62 Å / Num. obs: 52231 / % possible obs: 83.04 % / Redundancy: 12.47 % / CC1/2: 0.997 / Net I/σ(I): 12.2
Reflection shellResolution: 1.95→2 Å / Mean I/σ(I) obs: 1.476 / Num. unique obs: 2611 / CC1/2: 0.5522

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Processing

Software
NameVersionClassification
REFMAC5.8.0411refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→60.62 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.942 / SU B: 8.046 / SU ML: 0.122 / Cross valid method: THROUGHOUT / ESU R: 0.186 / ESU R Free: 0.161 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22832 2375 4.9 %RANDOM
Rwork0.1857 ---
obs0.18782 46272 98.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.083 Å2
Baniso -1Baniso -2Baniso -3
1--0.77 Å20 Å2-0 Å2
2---0.23 Å20 Å2
3---1.01 Å2
Refinement stepCycle: 1 / Resolution: 1.95→60.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5352 0 54 380 5786
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0125548
X-RAY DIFFRACTIONr_bond_other_d0.0010.0165150
X-RAY DIFFRACTIONr_angle_refined_deg1.3941.6567534
X-RAY DIFFRACTIONr_angle_other_deg0.4691.57111810
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.225655
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.176562
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.1610902
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.070.2819
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026616
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021380
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_it2.5532.6982629
X-RAY DIFFRACTIONr_mcbond_other2.5522.6982630
X-RAY DIFFRACTIONr_mcangle_it3.9174.8223279
X-RAY DIFFRACTIONr_mcangle_other3.9164.8223280
X-RAY DIFFRACTIONr_scbond_it3.2783.1112919
X-RAY DIFFRACTIONr_scbond_other3.2783.1112917
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.3045.4944256
X-RAY DIFFRACTIONr_long_range_B_refined8.14835.616539
X-RAY DIFFRACTIONr_long_range_B_other8.14735.66540
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 155 -
Rwork0.269 2969 -
obs--87.93 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.06620.00160.08770.4784-0.5770.8312-0.0173-0.04350.0069-0.1944-0.0579-0.05950.25760.01460.07520.22660.02420.02170.0783-0.00960.0114-8.2335-7.4067-20.2181
20.36730.20990.06990.29-0.17990.3952-0.0383-0.0297-0.00150.02840.0339-0.0071-0.0802-0.05990.00440.07610.0262-0.02210.109-0.02070.046-20.305811.9148-12.0714
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B62 - 552
2X-RAY DIFFRACTION2A60 - 653

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