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- PDB-3t36: Crystal structure of lytic transglycosylase MltE from Eschericha coli -

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Basic information

Entry
Database: PDB / ID: 3t36
TitleCrystal structure of lytic transglycosylase MltE from Eschericha coli
ComponentsEndo-type membrane-bound lytic murein transglycosylase A
KeywordsLYASE / goose type lysozyme-like structure / 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
Endo-type membrane-bound lytic murein transglycosylase A
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.25 Å
AuthorsFibriansah, G. / Gliubich, F.I. / Thunnissen, A.-M.W.H.
CitationJournal: Biochemistry / Year: 2012
Title: On the Mechanism of Peptidoglycan Binding and Cleavage by the endo-Specific Lytic Transglycosylase MltE from Escherichia coli.
Authors: Fibriansah, G. / Gliubich, F.I. / Thunnissen, A.M.
History
DepositionJul 24, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 25, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 31, 2012Group: Database references
Revision 1.2Dec 26, 2012Group: Database references
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.5Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_ref_seq_dif.details / _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: Endo-type membrane-bound lytic murein transglycosylase A
B: Endo-type membrane-bound lytic murein transglycosylase A
C: Endo-type membrane-bound lytic murein transglycosylase A
D: Endo-type membrane-bound lytic murein transglycosylase A
E: Endo-type membrane-bound lytic murein transglycosylase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,3298
Polymers111,0415
Non-polymers2883
Water7,566420
1
A: Endo-type membrane-bound lytic murein transglycosylase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3042
Polymers22,2081
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Endo-type membrane-bound lytic murein transglycosylase A


Theoretical massNumber of molelcules
Total (without water)22,2081
Polymers22,2081
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Endo-type membrane-bound lytic murein transglycosylase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3042
Polymers22,2081
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Endo-type membrane-bound lytic murein transglycosylase A


Theoretical massNumber of molelcules
Total (without water)22,2081
Polymers22,2081
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Endo-type membrane-bound lytic murein transglycosylase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3042
Polymers22,2081
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)77.764, 94.925, 160.494
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 22208.146 Da / Num. of mol.: 5 / Fragment: UNP residues 17-203
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: emtA, mltE, sltZ, ycgP, b1193, JW5821 / Plasmid: pMT429-emtA / Production host: Escherichia coli (E. coli) / Strain (production host): XL1-Blue
References: UniProt: P0C960, Lyases; Carbon-oxygen lyases; Acting on polysaccharides
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 420 / 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: 2.67 Å3/Da / Density % sol: 53.89 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M lithium sulfate, 15% PEG8000, 20 mM HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.835 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jul 1, 1998
RadiationMonochromator: horizontally focusing / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.835 Å / Relative weight: 1
ReflectionResolution: 2.25→24.77 Å / Num. obs: 56663

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.25→24.77 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.925 / Occupancy max: 1 / Occupancy min: 1 / SU B: 4.703 / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.265 / ESU R Free: 0.201 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2235 5691 10.1 %RANDOM
Rwork0.1888 ---
obs0.1923 56611 99.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 66.55 Å2 / Biso mean: 27.2748 Å2 / Biso min: 10.14 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.25→24.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7077 0 15 420 7512
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0227248
X-RAY DIFFRACTIONr_bond_other_d0.0010.024919
X-RAY DIFFRACTIONr_angle_refined_deg1.1741.9669856
X-RAY DIFFRACTIONr_angle_other_deg0.862312036
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0815917
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.79624.531309
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.804151201
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3291545
X-RAY DIFFRACTIONr_chiral_restr0.0650.21072
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0218103
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021350
X-RAY DIFFRACTIONr_mcbond_it0.5611.54610
X-RAY DIFFRACTIONr_mcbond_other0.1141.51839
X-RAY DIFFRACTIONr_mcangle_it1.11327391
X-RAY DIFFRACTIONr_scbond_it1.93932638
X-RAY DIFFRACTIONr_scangle_it3.3024.52465
LS refinement shellResolution: 2.25→2.308 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.262 393 -
Rwork0.205 3708 -
all-4101 -
obs--98.89 %

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