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- PDB-5aa2: Crystal structure of MltF from Pseudomonas aeruginosa in complex ... -

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Basic information

Entry
Database: PDB / ID: 5aa2
TitleCrystal structure of MltF from Pseudomonas aeruginosa in complex with NAM-pentapeptide.
Components
  • (MEMBRANE-BOUND LYTIC MUREIN TRANSGLYCOSYLASE ...) x 3
  • N-ACETYLGLUCOSAMINE-1,6-ANHYDRO-N-ACETYLMURAMIC ACID L-ALA-D-GLU-M-DAP-D-ALA-D-ALA
KeywordsLYASE / LYTIC TRANSGLYCOSILASE / CELL WALL RECYCLING / PSEUDOMONAS AERUGINOSA
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: 2.8 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 1.1May 3, 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)225,8777
Polymers225,8065
Non-polymers712
Water1,27971
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)57,0863
Polymers57,0502
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: MEMBRANE-BOUND LYTIC MUREIN TRANSGLYCOSYLASE F


Theoretical massNumber of molelcules
Total (without water)56,2391
Polymers56,2391
Non-polymers00
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)56,2962
Polymers56,2611
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: MEMBRANE-BOUND LYTIC MUREIN TRANSGLYCOSYLASE F


Theoretical massNumber of molelcules
Total (without water)56,2571
Polymers56,2571
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.585, 135.652, 137.459
Angle α, β, γ (deg.)90.00, 92.06, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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MEMBRANE-BOUND LYTIC MUREIN TRANSGLYCOSYLASE ... , 3 types, 4 molecules ACBD

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


Mass: 56260.512 Da / Num. of mol.: 2 / 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 MEMBRANE-BOUND LYTIC MUREIN TRANSGLYCOSYLASE F / MUREIN LYASE F


Mass: 56238.547 Da / Num. of mol.: 1 / 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
#3: Protein MEMBRANE-BOUND LYTIC MUREIN TRANSGLYCOSYLASE F / MUREIN LYASE F


Mass: 56256.520 Da / Num. of mol.: 1 / 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

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Protein/peptide , 1 types, 1 molecules E

#4: 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) / Strain: BWHPSA013

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Non-polymers , 2 types, 73 molecules

#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 71 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsN-ACETYLMURAMIC ACID L-ALA-D-GLU-M-DAP-D-ALA-D-ALA (PEP): NO ELECTRON DENSITY WAS OBSERVED FOR THE ...N-ACETYLMURAMIC ACID L-ALA-D-GLU-M-DAP-D-ALA-D-ALA (PEP): NO ELECTRON DENSITY WAS OBSERVED FOR THE N-ACETYLMURAMIC MOIETY AND WAS NOT INCLUDED IN THE MODEL.
Sequence detailsFIRST NINE AMINOACIDS FROM ERW72512 CORRESPONDS TO THE SIGNAL PEPTIDE AND ARE 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: 2.88 Å3/Da / Density % sol: 57.27 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97934
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: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.7→48.25 Å / Num. obs: 59073 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 63.84 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 5.1
Reflection shellResolution: 2.7→2.75 Å / Redundancy: 3.1 % / Rmerge(I) obs: 1.5 / Mean I/σ(I) obs: 0.5 / % possible all: 99.5

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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: 2.8→48.261 Å / SU ML: 0.45 / σ(F): 1.34 / Phase error: 25.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2354 3151 5.3 %
Rwork0.1672 --
obs0.1709 59065 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.8→48.261 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13397 0 2 71 13470
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00813716
X-RAY DIFFRACTIONf_angle_d1.14518535
X-RAY DIFFRACTIONf_dihedral_angle_d17.5825162
X-RAY DIFFRACTIONf_chiral_restr0.0431955
X-RAY DIFFRACTIONf_plane_restr0.0052442
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.84180.32251560.27492463X-RAY DIFFRACTION100
2.8418-2.88620.36871320.27992388X-RAY DIFFRACTION100
2.8862-2.93350.33631310.27022392X-RAY DIFFRACTION100
2.9335-2.98410.39021190.26852468X-RAY DIFFRACTION100
2.9841-3.03830.33361320.23632388X-RAY DIFFRACTION100
3.0383-3.09680.34191260.22832443X-RAY DIFFRACTION100
3.0968-3.160.34251400.21572431X-RAY DIFFRACTION100
3.16-3.22870.29931430.22412418X-RAY DIFFRACTION100
3.2287-3.30380.2761500.212397X-RAY DIFFRACTION100
3.3038-3.38640.32521310.21892433X-RAY DIFFRACTION100
3.3864-3.47790.25951560.20652418X-RAY DIFFRACTION100
3.4779-3.58020.26861290.19172452X-RAY DIFFRACTION100
3.5802-3.69570.29431220.18232431X-RAY DIFFRACTION100
3.6957-3.82780.27491430.16662420X-RAY DIFFRACTION100
3.8278-3.98090.21711300.15142429X-RAY DIFFRACTION100
3.9809-4.1620.23171410.14212431X-RAY DIFFRACTION100
4.162-4.38130.19621470.13122453X-RAY DIFFRACTION100
4.3813-4.65560.15991250.11952416X-RAY DIFFRACTION100
4.6556-5.01470.1981870.12062416X-RAY DIFFRACTION100
5.0147-5.51870.17031250.13192432X-RAY DIFFRACTION100
5.5187-6.31580.21031440.14442425X-RAY DIFFRACTION100
6.3158-7.95150.17561160.1572470X-RAY DIFFRACTION99
7.9515-48.26830.18521260.14532500X-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)
12.03790.27650.1931.676-1.00212.52110.001-0.3083-0.04130.1565-0.1414-0.2242-0.21750.07490.10570.2993-0.0217-0.01040.28830.00360.31927.9504-10.668973.7225
21.43610.1870.96140.2442-0.25612.2842-0.1006-0.09480.17690.3199-0.0472-0.17620.4615-0.5337-0.17130.48830.0344-0.02920.3762-0.12470.54255.693414.950161.8764
31.17570.36430.01381.4855-0.41620.9325-0.17340.08130.1385-0.19390.0747-0.13730.10890.07330.08450.227-0.00660.01680.30480.0030.30089.01067.676847.3741
41.698-0.9815-0.11732.5488-0.27251.54270.0295-0.10250.2717-0.14130.0476-0.2579-0.5022-0.0844-0.0690.57820.0027-0.00340.2983-0.01780.318130.927350.440118.7776
52.1157-1.29450.35742.18780.83971.0866-0.2169-0.72550.29080.11680.0732-0.552-0.1278-0.11250.10470.31770.041-0.02740.3968-0.05680.441846.134927.840147.2971
61.4107-0.35330.40651.4357-0.13991.7148-0.0878-0.16360.1843-0.09430.0411-0.09230.1203-0.17980.03390.2697-0.02410.00890.32280.00510.343234.474426.898336.41
72.00390.9098-0.27743.2659-1.11881.4974-0.11650.1336-0.2735-0.35880.0958-0.08130.2126-0.0658-0.00410.32450.0183-0.02090.2496-0.03550.275-18.2847-33.188256.5226
81.41180.4744-0.611.5659-0.352.5747-0.22380.20170.008-0.45050.12060.02260.0259-0.34490.07870.43080.0361-0.03790.28630.02260.3204-29.0169-9.696938.8214
91.7583-0.92510.09521.5636-0.40771.90990.16360.37360.2002-0.4214-0.1188-0.103-0.0641-0.4534-0.05950.72380.06590.00560.5113-0.01870.350836.168227.4424-11.1981
101.1781-0.42940.09012.0680.24242.4878-0.035-0.02470.0212-0.38360.0164-0.26980.3305-0.0150.02910.525-0.02750.03230.30870.04080.327254.02367.64544.1619
110.4292-0.00720.15450.40460.09680.0680.00110.6399-0.3537-0.05330.3233-0.6208-0.26660.2850.02430.92470.28570.25871.03950.04971.417216.17215.840721.0716
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 28 THROUGH 241 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 242 THROUGH 278 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 279 THROUGH 446 )
4X-RAY DIFFRACTION4CHAIN 'B' AND (RESID 30 THROUGH 252 )
5X-RAY DIFFRACTION5CHAIN 'B' AND (RESID 253 THROUGH 304 )
6X-RAY DIFFRACTION6CHAIN 'B' AND (RESID 305 THROUGH 445 )
7X-RAY DIFFRACTION7CHAIN 'C' AND (RESID 28 THROUGH 263 )
8X-RAY DIFFRACTION8CHAIN 'C' AND (RESID 264 THROUGH 445 )
9X-RAY DIFFRACTION9CHAIN 'D' AND (RESID 30 THROUGH 240 )
10X-RAY DIFFRACTION10CHAIN 'D' AND (RESID 241 THROUGH 445 )
11X-RAY DIFFRACTION11CHAIN 'E' AND (RESID 1 THROUGH 3 )

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