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

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Basic information

Entry
Database: PDB / ID: 8rhe
TitleLytic Transglycosylase MltD of Pseudomonas aeruginosa bound to the Natural Product Bulgecin A
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 / 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
A: LysM peptidoglycan-binding domain-containing protein
B: LysM peptidoglycan-binding domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,5919
Polymers77,1592
Non-polymers1,4327
Water4,306239
1
A: LysM peptidoglycan-binding domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,2634
Polymers38,5791
Non-polymers6833
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: LysM peptidoglycan-binding domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,3285
Polymers38,5791
Non-polymers7494
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.224, 113.408, 116.858
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: HIS / Beg label comp-ID: HIS / End auth comp-ID: ASP / End label comp-ID: ASP / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 62 - 338 / Label seq-ID: 7 - 283

Dom-ID
1
2

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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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: Histidine Tag and TEV site in the N-T region. MltD construction from 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-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
#3: Chemical
ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 239 / 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: 1.94 Å3/Da / Density % sol: 36.66 %
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 5, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.95→42.18 Å / Num. obs: 49604 / % possible obs: 89.8 % / Redundancy: 6 % / CC1/2: 0.999 / Net I/σ(I): 11.4
Reflection shellResolution: 1.95→1.99 Å / Mean I/σ(I) obs: 1.264 / Num. unique obs: 2480 / CC1/2: 0.4712

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Processing

Software
NameVersionClassification
REFMAC5.8.0411refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→42.18 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.954 / SU B: 8.355 / SU ML: 0.118 / Cross valid method: FREE R-VALUE / ESU R: 0.173 / ESU R Free: 0.143
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.213 2194 4.912 %
Rwork0.1905 42476 -
all0.192 --
obs-44670 99.81 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 44.818 Å2
Baniso -1Baniso -2Baniso -3
1--0.086 Å20 Å2-0 Å2
2--0.202 Å2-0 Å2
3----0.116 Å2
Refinement stepCycle: LAST / Resolution: 1.95→42.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4457 0 75 239 4771
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0124720
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164358
X-RAY DIFFRACTIONr_angle_refined_deg1.0511.6526438
X-RAY DIFFRACTIONr_angle_other_deg0.3591.5679999
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6875568
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.381547
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg1.86658
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.12310758
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.29210245
X-RAY DIFFRACTIONr_chiral_restr0.0540.2697
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025683
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021177
X-RAY DIFFRACTIONr_nbd_refined0.2150.21083
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1820.23997
X-RAY DIFFRACTIONr_nbtor_refined0.1790.22337
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0730.22471
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1750.2225
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0430.21
X-RAY DIFFRACTIONr_metal_ion_refined0.1180.27
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2160.231
X-RAY DIFFRACTIONr_nbd_other0.1970.2116
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1350.214
X-RAY DIFFRACTIONr_mcbond_it2.0133.4372256
X-RAY DIFFRACTIONr_mcbond_other2.0123.4372257
X-RAY DIFFRACTIONr_mcangle_it3.2746.1612828
X-RAY DIFFRACTIONr_mcangle_other3.2736.1612829
X-RAY DIFFRACTIONr_scbond_it2.4563.772464
X-RAY DIFFRACTIONr_scbond_other2.4533.772462
X-RAY DIFFRACTIONr_scangle_it4.1336.7633610
X-RAY DIFFRACTIONr_scangle_other4.1336.7633611
X-RAY DIFFRACTIONr_lrange_it6.81737.2495559
X-RAY DIFFRACTIONr_lrange_other6.78536.4945506
X-RAY DIFFRACTIONr_ncsr_local_group_10.1280.058891
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.128420.05008
12AX-RAY DIFFRACTIONLocal ncs0.128420.05008
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.95-2.0010.3091700.31930170.31832380.9240.92598.42490.306
2.001-2.0550.2821440.27430790.27532230.9410.9491000.252
2.055-2.1150.2831510.24928810.2530320.9410.9571000.226
2.115-2.180.2491270.23828980.23930250.9560.9621000.211
2.18-2.2510.2411410.2227680.22129090.9670.9681000.192
2.251-2.330.2471390.19526580.19828000.9610.97699.89290.171
2.33-2.4170.21510.19525920.19627430.9710.9771000.17
2.417-2.5160.2051090.18425230.18426320.9690.981000.16
2.516-2.6270.2181360.19123770.19325140.9690.97999.96020.167
2.627-2.7550.2121180.18322790.18423970.9690.981000.163
2.755-2.9030.2211130.18422170.18623300.9650.981000.169
2.903-3.0780.2461090.18920710.19121810.9640.97899.95420.176
3.078-3.290.237960.18619650.18820620.9640.97999.95150.177
3.29-3.5510.214860.18218350.18419250.9690.98199.79220.179
3.551-3.8880.194860.16416950.16617840.9780.98399.83180.166
3.888-4.3420.179860.15315440.15416300.9790.9861000.161
4.342-5.0050.175780.16213750.16314590.9830.98599.58880.173
5.005-6.1080.206790.211590.212400.9760.98299.83870.21
6.108-8.5490.24430.2049480.2069940.9740.97899.69820.221
8.549-42.180.163310.1945810.1926160.9860.97699.35060.216
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)
10.43170.0045-0.01230.31130.14410.51890.0334-0.0128-0.02630.0221-0.02750.0171-0.06750.0456-0.00590.0431-0.0127-0.00530.03960.02570.058316.39118.632911.5597
20.54610.0152-0.92810.8784-0.46242.0047-0.25570.0051-0.0644-0.10350.0154-0.04940.5173-0.01520.24020.16330.02940.08520.06210.06150.125711.4698-4.108328.5035
Refinement TLS groupSelection: ALL

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