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- PDB-5aa4: Crystal structure of MltF from Pseudomonas aeruginosa in complex ... -

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Basic information

Entry
Database: PDB / ID: 5aa4
TitleCrystal structure of MltF from Pseudomonas aeruginosa in complex with cell-wall tetrapeptide
Components(MEMBRANE-BOUND LYTIC MUREIN TRANSGLYCOSYLASE F) x 2
KeywordsLYASE / LYTIC TRANSGLYCOSILASE / CELL WALL RECYCLING
Function / homology
Function and homology information


: / lytic transglycosylase activity / peptidoglycan metabolic 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
Chem-6X4 / : / Membrane-bound lytic murein transglycosylase F / Membrane-bound lytic murein transglycosylase F
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)205,0035
Polymers204,5144
Non-polymers4901
Water2,882160
1
A: MEMBRANE-BOUND LYTIC MUREIN TRANSGLYCOSYLASE F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,6032
Polymers51,1131
Non-polymers4901
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: MEMBRANE-BOUND LYTIC MUREIN TRANSGLYCOSYLASE F


Theoretical massNumber of molelcules
Total (without water)51,1431
Polymers51,1431
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: MEMBRANE-BOUND LYTIC MUREIN TRANSGLYCOSYLASE F


Theoretical massNumber of molelcules
Total (without water)51,1131
Polymers51,1131
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: MEMBRANE-BOUND LYTIC MUREIN TRANSGLYCOSYLASE F


Theoretical massNumber of molelcules
Total (without water)51,1431
Polymers51,1431
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)66.116, 136.774, 138.098
Angle α, β, γ (deg.)90.00, 92.34, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 51113.395 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Strain: BWHPSA013 / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: A0A077JMS0, UniProt: A0A1I9GEN8*PLUS, Lyases; Carbon-oxygen lyases; Acting on polysaccharides
#2: Protein MEMBRANE-BOUND LYTIC MUREIN TRANSGLYCOSYLASE F / MUREIN LYTIC TRANGLYCOSILASE F


Mass: 51143.418 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Strain: BWHPSA013 / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: A0A077JMS0, UniProt: A0A1I9GEN9*PLUS, Lyases; Carbon-oxygen lyases; Acting on polysaccharides
#3: Chemical ChemComp-6X4 / [6-[[(2~{R})-1-azanyl-1-oxidanylidene-propan-2-yl]amino]-6-oxidanylidene-5-[[(4~{R})-5-oxidanyl-5-oxidanylidene-4-[[(2~{S})-2-[[(2~{R})-2-oxidanylpropanoyl]amino]propanoyl]amino]pentanoyl]amino]hexyl]azanium


Mass: 489.543 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H37N6O8
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 160 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsFIRST NINE AMINOACIDS FROM ERW72512 SEQUENCE ARE FROM PEPTIDE SIGNAL 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: 2.94 Å3/Da / Density % sol: 58.15 % / 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: 2.4→48.72 Å / Num. obs: 94338 / % possible obs: 98.5 % / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 13.8
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 6.7 % / Rmerge(I) obs: 1.04 / Mean I/σ(I) obs: 1.7 / % possible all: 99.9

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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: 2.4→48.569 Å / SU ML: 0.35 / σ(F): 1.33 / Phase error: 26.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2392 4680 5 %
Rwork0.1854 --
obs0.1881 94297 98.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→48.569 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13342 0 34 160 13536
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01613655
X-RAY DIFFRACTIONf_angle_d1.59718456
X-RAY DIFFRACTIONf_dihedral_angle_d17.7055139
X-RAY DIFFRACTIONf_chiral_restr0.0821944
X-RAY DIFFRACTIONf_plane_restr0.0082434
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.42730.31671740.30563003X-RAY DIFFRACTION100
2.4273-2.45580.32591950.27082971X-RAY DIFFRACTION100
2.4558-2.48580.29641650.26093015X-RAY DIFFRACTION100
2.4858-2.51730.30461740.25512981X-RAY DIFFRACTION100
2.5173-2.55040.3521520.25573060X-RAY DIFFRACTION100
2.5504-2.58530.2881460.25343014X-RAY DIFFRACTION100
2.5853-2.62220.35271410.25433024X-RAY DIFFRACTION100
2.6222-2.66140.31741610.25043026X-RAY DIFFRACTION100
2.6614-2.7030.33481440.25453010X-RAY DIFFRACTION100
2.703-2.74730.32721320.25653059X-RAY DIFFRACTION100
2.7473-2.79460.32551480.26813027X-RAY DIFFRACTION100
2.7946-2.84550.2971580.25323023X-RAY DIFFRACTION100
2.8455-2.90020.3321710.24793003X-RAY DIFFRACTION100
2.9002-2.95940.26281350.23433035X-RAY DIFFRACTION100
2.9594-3.02370.2921270.23143065X-RAY DIFFRACTION100
3.0237-3.0940.29381520.22593039X-RAY DIFFRACTION100
3.094-3.17140.28211820.22653012X-RAY DIFFRACTION100
3.1714-3.25710.27261630.2392987X-RAY DIFFRACTION100
3.2571-3.35290.29961570.23813048X-RAY DIFFRACTION100
3.3529-3.46110.26421190.21993101X-RAY DIFFRACTION100
3.4611-3.58480.28741690.20952964X-RAY DIFFRACTION100
3.5848-3.72830.3129970.19921774X-RAY DIFFRACTION58
3.7283-3.89790.22661220.1823101X-RAY DIFFRACTION100
3.8979-4.10330.20261840.15932982X-RAY DIFFRACTION100
4.1033-4.36020.19761820.15053002X-RAY DIFFRACTION100
4.3602-4.69660.19541730.13453046X-RAY DIFFRACTION100
4.6966-5.16880.21551690.14123029X-RAY DIFFRACTION100
5.1688-5.91560.22591720.153042X-RAY DIFFRACTION100
5.9156-7.44870.2071600.15713063X-RAY DIFFRACTION100
7.4487-48.57920.14291560.11923111X-RAY DIFFRACTION100

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