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- PDB-5aa1: Crystal structure of MltF from Pseudomonas aeruginosa in complex ... -

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Basic information

Entry
Database: PDB / ID: 5aa1
TitleCrystal structure of MltF from Pseudomonas aeruginosa in complex with NAG-anhNAM-pentapeptide
Components
  • MEMBRANE-BOUND LYTIC MUREIN TRANSGLYCOSYLASE F
  • N-ACETYLGLUCOSAMINE-1,6-ANHYDRO-N-ACETYLMURAMIC ACID L-ALA-D-GLU-M-DAP-D-ALA-D-ALA
KeywordsLYASE / LYTIC TRANSGLYCOSILASE / CELL WALL RECYCLING
Function / homology
Function and homology information


: / peptidoglycan lytic transglycosylase activity / peptidoglycan catabolic process / cell outer membrane / cell wall organization / cell wall macromolecule catabolic process
Similarity search - Function
Membrane-bound lytic murein transglycosylase F / Prokaryotic transglycosylase, active site / Prokaryotic transglycosylases signature. / Transglycosylase SLT domain 1 / Transglycosylase SLT domain / Bacterial periplasmic substrate-binding proteins / Bacterial extracellular solute-binding proteins, family 3 / Solute-binding protein family 3/N-terminal domain of MltF / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 ...Membrane-bound lytic murein transglycosylase F / Prokaryotic transglycosylase, active site / Prokaryotic transglycosylases signature. / Transglycosylase SLT domain 1 / Transglycosylase SLT domain / Bacterial periplasmic substrate-binding proteins / Bacterial extracellular solute-binding proteins, family 3 / Solute-binding protein family 3/N-terminal domain of MltF / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / Lysozyme-like domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Membrane-bound lytic murein transglycosylase F
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.89 Å
AuthorsDominguez-Gil, T. / Acebron, I. / Hermoso, J.A.
CitationJournal: Structure / Year: 2016
Title: Activation by Allostery in Cell-Wall Remodeling by a Modular Membrane-Bound Lytic Transglycosylase from Pseudomonas aeruginosa.
Authors: Dominguez-Gil, T. / Lee, M. / Acebron-Avalos, I. / Mahasenan, K.V. / Hesek, D. / Dik, D.A. / Byun, B. / Lastochkin, E. / Fisher, J.F. / Mobashery, S. / Hermoso, J.A.
History
DepositionJul 23, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 12, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 22, 2017Group: Database references
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_validate_torsion / struct_conn / struct_site
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.1Jan 10, 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: MEMBRANE-BOUND LYTIC MUREIN TRANSGLYCOSYLASE F
B: MEMBRANE-BOUND LYTIC MUREIN TRANSGLYCOSYLASE F
C: MEMBRANE-BOUND LYTIC MUREIN TRANSGLYCOSYLASE F
D: MEMBRANE-BOUND LYTIC MUREIN TRANSGLYCOSYLASE F
E: N-ACETYLGLUCOSAMINE-1,6-ANHYDRO-N-ACETYLMURAMIC ACID L-ALA-D-GLU-M-DAP-D-ALA-D-ALA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)226,04910
Polymers225,8725
Non-polymers1775
Water2,324129
1
A: MEMBRANE-BOUND LYTIC MUREIN TRANSGLYCOSYLASE F
E: N-ACETYLGLUCOSAMINE-1,6-ANHYDRO-N-ACETYLMURAMIC ACID L-ALA-D-GLU-M-DAP-D-ALA-D-ALA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,0963
Polymers57,0602
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1340 Å2
ΔGint-7.4 kcal/mol
Surface area24020 Å2
MethodPQS
2
B: MEMBRANE-BOUND LYTIC MUREIN TRANSGLYCOSYLASE F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,3413
Polymers56,2711
Non-polymers712
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: MEMBRANE-BOUND LYTIC MUREIN TRANSGLYCOSYLASE F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,3062
Polymers56,2711
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: MEMBRANE-BOUND LYTIC MUREIN TRANSGLYCOSYLASE F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,3062
Polymers56,2711
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.853, 135.752, 138.030
Angle α, β, γ (deg.)90.00, 92.01, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
MEMBRANE-BOUND LYTIC MUREIN TRANSGLYCOSYLASE F / MUREIN LYASE F


Mass: 56270.547 Da / Num. of mol.: 4 / Fragment: UNP RESIDUES 8-490
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Strain: BWHPSA013 / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: Q9HXN1, Lyases; Carbon-oxygen lyases; Acting on polysaccharides
#2: Protein/peptide N-ACETYLGLUCOSAMINE-1,6-ANHYDRO-N-ACETYLMURAMIC ACID L-ALA-D-GLU-M-DAP-D-ALA-D-ALA


Mass: 789.784 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) PSEUDOMONAS AERUGINOSA (bacteria)
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 129 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsN-ACETYLGLUCOSAMINE-1,6-ANHYDRO-N-ACETYLMURAMIC ACID L-ALA-D-GLU-M-DAP-D-ALA-D-ALA (PEP): NO ...N-ACETYLGLUCOSAMINE-1,6-ANHYDRO-N-ACETYLMURAMIC ACID L-ALA-D-GLU-M-DAP-D-ALA-D-ALA (PEP): NO ELECTRON DENSITY WAS OBSERVED FOR N-ACETYLGLUCOSAMINE-1, 6-ANHYDRO-N-ACETYLMURAMIC ACID AND THEREFORE MODEL WAS NOT INCLUDED FOR THESE MOIETIES
Sequence detailsFIRST NINE AMINOACIDS IN ERW72512 SEQUENCE CORRESPONDS TO THE SIGNAL PEPTIDE AND WERE NOT INCLUDED ...FIRST NINE AMINOACIDS IN ERW72512 SEQUENCE CORRESPONDS TO THE SIGNAL PEPTIDE AND WERE NOT INCLUDED IN OUR CONSTRUCT.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.73 Å3/Da / Density % sol: 55.05 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Details: ELLIPTICALLY BENT MIRROR
RadiationMonochromator: SI(111) CHANNEL-CUT, CRYOCOOLED / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.89→47.25 Å / Num. obs: 52009 / % possible obs: 92.3 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 61.28 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 9.1
Reflection shellResolution: 2.8→2.89 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.95 / Mean I/σ(I) obs: 1.6 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 5A5X

5a5x


Resolution: 2.89→47.249 Å / SU ML: 0.48 / σ(F): 1.35 / Phase error: 26.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2427 2023 4.1 %
Rwork0.1676 --
obs0.1706 49825 91.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.89→47.249 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13408 0 5 129 13542
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00913699
X-RAY DIFFRACTIONf_angle_d1.35118519
X-RAY DIFFRACTIONf_dihedral_angle_d16.545159
X-RAY DIFFRACTIONf_chiral_restr0.0491953
X-RAY DIFFRACTIONf_plane_restr0.0062441
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.89-2.96230.38691570.28833711X-RAY DIFFRACTION100
2.9623-3.04230.41431580.27363678X-RAY DIFFRACTION100
3.0423-3.13190.32991590.24913734X-RAY DIFFRACTION100
3.1319-3.23290.36021510.25793666X-RAY DIFFRACTION99
3.2329-3.34840.35831540.25583634X-RAY DIFFRACTION99
3.3484-3.48250.3178890.2542019X-RAY DIFFRACTION54
3.4825-3.64090.27241450.18813600X-RAY DIFFRACTION98
3.6409-3.83280.2704990.16932452X-RAY DIFFRACTION98
3.8328-4.07280.23141150.14372706X-RAY DIFFRACTION72
4.0728-4.3870.19491600.12773714X-RAY DIFFRACTION100
4.387-4.82810.18851560.11443690X-RAY DIFFRACTION100
4.8281-5.52590.18391560.12253731X-RAY DIFFRACTION100
5.5259-6.95840.2091640.15193700X-RAY DIFFRACTION99
6.9584-47.25540.19691600.14273767X-RAY DIFFRACTION99
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)
14.8547-0.01120.33112.2143-0.96563.24410.0499-0.4767-0.00880.3049-0.1495-0.1236-0.22440.03820.09280.3432-0.0411-0.0090.35830.0240.39218.4311-18.926274.1431
21.16270.4370.08853.9413-0.35141.3964-0.19280.10590.15-0.19160.1758-0.10450.0603-0.02370.01980.22470.0053-0.00510.3878-0.00010.33258.13030.101848.6368
33.3063-1.3448-0.39913.5569-0.52541.85170.110.05510.4016-0.3077-0.0663-0.3844-0.3576-0.147-0.0380.6810.0080.02490.45380.00760.355931.812140.072216.8032
43.9251-3.77733.31255.116-3.47482.8293-0.3656-0.42220.48690.01420.2731-0.746-0.5678-0.15870.16520.68780.0868-0.0560.4919-0.12680.675737.565939.308836.1969
52.3959-1.10211.09442.7492-0.19034.794-0.0886-0.29560.2881-0.03930.0454-0.12410.1335-0.36650.04980.2514-0.02180.0310.3717-0.01220.423836.041617.330238.9883
62.85651.6807-0.6884.3751-1.15562.1915-0.0820.0719-0.3535-0.2277-0.0154-0.20820.17560.09990.06520.32220.0227-0.03360.31450.00120.311248.2792-42.567558.5319
70.13060.13510.10467.2734-6.49186.1354-0.2970.2358-0.1335-0.89180.0139-0.84060.3336-0.20210.51281.0796-0.1563-0.09190.67930.00270.530939.6549-29.64130.8879
82.55090.62490.55812.1358-0.82285.379-0.18550.1210.1194-0.52520.12520.00640.0822-0.34390.03820.44810.04080.01270.30550.04020.382236.8939-18.582441.6246
94.41010.7422-0.74272.9507-1.48415.22340.63160.87940.4465-0.741-0.5968-0.1604-0.36380.02830.02781.06970.26020.11780.66920.09430.524146.974918.8682-16.8152
102.1443-0.5676-0.1312.0765-1.14514.35710.21940.67740.0042-0.3507-0.26760.1461-0.4668-0.70570.05850.87420.1421-0.06660.7746-0.05150.429130.557318.3817-7.7758
110.2425-0.4380.52562.3807-2.77193.22520.10230.3479-0.0116-1.3384-0.0689-0.31750.1705-0.5104-0.04441.58230.19920.02980.71-0.04690.659441.47051.1825-12.5507
122.4744-0.4190.00533.92590.38633.6891-0.0582-0.0785-0.0187-0.120.1005-0.42540.3379-0.1513-0.04170.5357-0.05070.0030.40650.0410.366355.9599-1.72456.1323
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 29 THROUGH 251 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 252 THROUGH 446 )
3X-RAY DIFFRACTION3CHAIN 'B' AND (RESID 30 THROUGH 226 )
4X-RAY DIFFRACTION4CHAIN 'B' AND (RESID 227 THROUGH 274 )
5X-RAY DIFFRACTION5CHAIN 'B' AND (RESID 275 THROUGH 445 )
6X-RAY DIFFRACTION6CHAIN 'C' AND (RESID 28 THROUGH 241 )
7X-RAY DIFFRACTION7CHAIN 'C' AND (RESID 242 THROUGH 285 )
8X-RAY DIFFRACTION8CHAIN 'C' AND (RESID 286 THROUGH 446 )
9X-RAY DIFFRACTION9CHAIN 'D' AND (RESID 30 THROUGH 104 )
10X-RAY DIFFRACTION10CHAIN 'D' AND (RESID 105 THROUGH 237 )
11X-RAY DIFFRACTION11CHAIN 'D' AND (RESID 238 THROUGH 262 )
12X-RAY DIFFRACTION12CHAIN 'D' AND (RESID 263 THROUGH 446 )

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