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- PDB-4c5f: Structure of Lytic Transglycosylase MltC from Escherichia coli at... -

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Basic information

Entry
Database: PDB / ID: 4c5f
TitleStructure of Lytic Transglycosylase MltC from Escherichia coli at 2.3 A resolution.
ComponentsMEMBRANE-BOUND LYTIC MUREIN TRANSGLYCOSYLASE C
KeywordsLYASE
Function / homology
Function and homology information


lytic endotransglycosylase activity / : / lytic transglycosylase activity / peptidoglycan metabolic process / hydrolase activity, acting on glycosyl bonds / peptidoglycan catabolic process / cell outer membrane / cell wall organization / cell wall macromolecule catabolic process / outer membrane-bounded periplasmic space / cellular response to oxidative stress
Similarity search - Function
Murein transglycosylase-C / Murein transglycosylase-C, N-terminal / Membrane-bound lytic murein transglycosylase C, N-terminal domain / Prokaryotic transglycosylase, active site / Prokaryotic transglycosylases signature. / Transglycosylase SLT domain 1 / Transglycosylase SLT domain / Lysozyme - #10 / Lysozyme / Prokaryotic membrane lipoprotein lipid attachment site profile. ...Murein transglycosylase-C / Murein transglycosylase-C, N-terminal / Membrane-bound lytic murein transglycosylase C, N-terminal domain / 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
Membrane-bound lytic murein transglycosylase C / Membrane-bound lytic murein transglycosylase C
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.34 Å
AuthorsArtola-Recolons, C. / Bernardo-Garcia, N. / Mobashery, S. / Hermoso, J.A.
CitationJournal: Acs Chem.Biol. / Year: 2014
Title: Structure and Cell Wall Cleavage by Modular Lytic Transglycosylase Mltc of Escherichia Coli.
Authors: Artola-Recolons, C. / Lee, M. / Bernardo-Garcia, N. / Blazquez, B. / Hesek, D. / Bartual, S.G. / Mahasenan, K.V. / Lastochkin, E. / Pi, H. / Boggess, B. / Meindl, K. / Uson, I. / Fisher, J.F. ...Authors: Artola-Recolons, C. / Lee, M. / Bernardo-Garcia, N. / Blazquez, B. / Hesek, D. / Bartual, S.G. / Mahasenan, K.V. / Lastochkin, E. / Pi, H. / Boggess, B. / Meindl, K. / Uson, I. / Fisher, J.F. / Mobashery, S. / Hermoso, J.A.
History
DepositionSep 11, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 23, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 1, 2014Group: Database references
Revision 1.2May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MEMBRANE-BOUND LYTIC MUREIN TRANSGLYCOSYLASE C
B: MEMBRANE-BOUND LYTIC MUREIN TRANSGLYCOSYLASE C


Theoretical massNumber of molelcules
Total (without water)76,5202
Polymers76,5202
Non-polymers00
Water1,874104
1
A: MEMBRANE-BOUND LYTIC MUREIN TRANSGLYCOSYLASE C


Theoretical massNumber of molelcules
Total (without water)38,2601
Polymers38,2601
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: MEMBRANE-BOUND LYTIC MUREIN TRANSGLYCOSYLASE C


Theoretical massNumber of molelcules
Total (without water)38,2601
Polymers38,2601
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.865, 114.651, 61.404
Angle α, β, γ (deg.)90.00, 93.47, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 38260.055 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: C5A0N2, UniProt: P0C066*PLUS, Lyases; Carbon-oxygen lyases; Acting on polysaccharides
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / 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: 20

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Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 47 % / Description: NONE
Crystal growDetails: 18% PEG 3350, 0.2M TRIAMMONIUM CITRATE PH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.74709
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 5, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.74709 Å / Relative weight: 1
ReflectionResolution: 2.33→45.66 Å / Num. obs: 28559 / % possible obs: 97.2 % / Observed criterion σ(I): 6 / Redundancy: 3.6 % / Biso Wilson estimate: 34.58 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 8.64
Reflection shellResolution: 2.33→2.46 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 1.8 / % possible all: 84.2

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 2.34→45.657 Å / SU ML: 0.39 / σ(F): 1.35 / Phase error: 31.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2555 1425 5 %
Rwork0.1913 --
obs0.1946 28475 98.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.34→45.657 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5214 0 0 104 5318
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0115320
X-RAY DIFFRACTIONf_angle_d1.267210
X-RAY DIFFRACTIONf_dihedral_angle_d13.6511966
X-RAY DIFFRACTIONf_chiral_restr0.056798
X-RAY DIFFRACTIONf_plane_restr0.007938
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3402-2.42380.3951250.2812362X-RAY DIFFRACTION87
2.4238-2.52090.34531220.27192742X-RAY DIFFRACTION99
2.5209-2.63560.3311390.26662684X-RAY DIFFRACTION97
2.6356-2.77450.32631600.24752735X-RAY DIFFRACTION99
2.7745-2.94830.31821610.23772722X-RAY DIFFRACTION100
2.9483-3.17590.32031240.23642741X-RAY DIFFRACTION99
3.1759-3.49540.28161490.20142744X-RAY DIFFRACTION100
3.4954-4.0010.23811560.16472737X-RAY DIFFRACTION100
4.001-5.03980.19951480.13952781X-RAY DIFFRACTION100
5.0398-45.66560.17171410.14812802X-RAY DIFFRACTION100
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)
1-0.00140.02090.0956-0.00560.05380.0435-0.212-0.27550.1785-0.2744-0.0252-0.09750.0906-0.273400.32930.1188-0.16160.3749-0.08670.3166-5.060510.401938.1902
2-0.21320.01790.33720.0290.0602-0.0202-0.0874-0.2914-0.0529-0.1393-0.18850.0192-0.0105-0.196100.26950.0266-0.08280.2668-0.10780.17444.94534.155948.0909
30.1015-0.00550.05290.04980.00040.18290.0491-0.1320.2564-0.3260.0626-0.00720.313-0.070100.4552-0.0446-0.00920.1810.03860.13275.6386-14.397225.1935
40.02110.07370.06830.017-0.1110.01030.0473-0.0053-0.02190.04070.0444-0.0531-0.0346-0.0548-00.1432-0.0020.00690.16180.04270.195711.1438-50.489159.6535
50.11470.18530.13060.2312-0.56450.3949-0.01230.0289-0.0211-0.0411-0.07960.0272-0.10020.0253-00.0998-0.02190.03870.15980.04210.204523.9735-32.729153.3585
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 33 THROUGH 127 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 128 THROUGH 203 )
3X-RAY DIFFRACTION3CHAIN A AND (RESID 204 THROUGH 359 )
4X-RAY DIFFRACTION4CHAIN B AND (RESID 33 THROUGH 147 )
5X-RAY DIFFRACTION5CHAIN B AND (RESID 148 THROUGH 359 )

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