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- PDB-6ghy: Structure of Lytic Transglycosylase MltE inactive mutant E64Q fro... -

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Basic information

Entry
Database: PDB / ID: 6ghy
TitleStructure of Lytic Transglycosylase MltE inactive mutant E64Q from E.coli
ComponentsEndo-type membrane-bound lytic murein transglycosylase A
KeywordsLYASE / Lytic Transglycosylase
Function / homology
Function and homology information


: / lytic endotransglycosylase activity / lytic transglycosylase activity / peptidoglycan metabolic process / cell outer membrane / cell wall organization / cell wall macromolecule catabolic process
Similarity search - Function
Endo-type membrane-bound lytic murein transglycosylase A / Prokaryotic transglycosylase, active site / Prokaryotic transglycosylases signature. / Transglycosylase SLT domain 1 / Transglycosylase SLT domain / Lysozyme - #10 / Lysozyme / Prokaryotic membrane lipoprotein lipid attachment site profile. / Lysozyme-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Endo-type membrane-bound lytic murein transglycosylase A
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.12 Å
AuthorsBatuecas, M.T. / Hermoso, J.A.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Economy and CompetitivenessBFU2014-59389-P Spain
CitationJournal: Biochemistry / Year: 2018
Title: A Structural Dissection of the Active Site of the Lytic Transglycosylase MltE from Escherichia coli.
Authors: Dik, D.A. / Batuecas, M.T. / Lee, M. / Mahasenan, K.V. / Marous, D.R. / Lastochkin, E. / Fisher, J.F. / Hermoso, J.A. / Mobashery, S.
History
DepositionMay 9, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 31, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Endo-type membrane-bound lytic murein transglycosylase A
A: Endo-type membrane-bound lytic murein transglycosylase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,1455
Polymers42,8272
Non-polymers3183
Water5,314295
1
B: Endo-type membrane-bound lytic murein transglycosylase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,6263
Polymers21,4131
Non-polymers2122
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: Endo-type membrane-bound lytic murein transglycosylase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,5192
Polymers21,4131
Non-polymers1061
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)121.488, 181.138, 34.829
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-499-

HOH

21B-527-

HOH

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Components

#1: Protein Endo-type membrane-bound lytic murein transglycosylase A / Peptidoglycan lytic endotransglycosylase


Mass: 21413.326 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: emtA, mltE, sltZ, ycgP, b1193, JW5821 / Production host: Escherichia coli (E. coli)
References: UniProt: P0C960, Lyases; Carbon-oxygen lyases; Acting on polysaccharides
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 295 / Source method: isolated from a natural source / Formula: H2O

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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: 2.24 Å3/Da / Density % sol: 45.02 %
Crystal growTemperature: 291 K / Method: batch mode / pH: 8.4
Details: 26% Polyethylene Glycol 4000, 0.2 M magnesium chloride and 0.1 M TRIS HCl (pH 8.4)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97242 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97242 Å / Relative weight: 1
ReflectionResolution: 2.12→39.55 Å / Num. obs: 22063 / % possible obs: 98.06 % / Redundancy: 4.2 % / Rpim(I) all: 0.047 / Net I/σ(I): 11
Reflection shellResolution: 2.12→2.19 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0232refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2Y8P

2y8p


Resolution: 2.12→39.55 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.929 / SU B: 0.003 / SU ML: 0 / Cross valid method: THROUGHOUT / ESU R: 0.173 / ESU R Free: 0.209 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24435 1112 5 %RANDOM
Rwork0.20279 ---
obs0.20489 20951 98.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 35.334 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.02 Å2
Refinement stepCycle: 1 / Resolution: 2.12→39.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2924 0 21 295 3240
LS refinement shellResolution: 2.12→2.175 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 92 -
Rwork0.277 1543 -
obs--99.09 %

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