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- PDB-4cfp: Crystal structure of MltC in complex with tetrasaccharide at 2.15... -

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Basic information

Entry
Database: PDB / ID: 4cfp
TitleCrystal structure of MltC in complex with tetrasaccharide at 2.15 A resolution
ComponentsMEMBRANE-BOUND LYTIC MUREIN TRANSGLYCOSYLASE C
KeywordsLYASE
Function / homology
Function and homology information


lytic endotransglycosylase activity / : / peptidoglycan lytic transglycosylase activity / peptidoglycan metabolic process / hydrolase activity, acting on glycosyl bonds / cellular response to antibiotic / peptidoglycan catabolic process / cell outer membrane / cell wall organization / cell wall macromolecule catabolic process ...lytic endotransglycosylase activity / : / peptidoglycan lytic transglycosylase activity / peptidoglycan metabolic process / hydrolase activity, acting on glycosyl bonds / cellular response to antibiotic / peptidoglycan catabolic process / cell outer membrane / cell wall organization / cell wall macromolecule catabolic process / outer membrane-bounded periplasmic space / cellular response to oxidative stress / cell division
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 / Lysozyme-like domain superfamily ...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 / Lysozyme-like domain superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile. / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
CITRIC ACID / Membrane-bound lytic murein transglycosylase C / Membrane-bound lytic murein transglycosylase C
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsBernardo-Garcia, N. / Artola-Recolons, C. / 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
DepositionNov 19, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 23, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 1, 2014Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1May 8, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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 C
B: MEMBRANE-BOUND LYTIC MUREIN TRANSGLYCOSYLASE C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,9706
Polymers76,5182
Non-polymers2,4524
Water3,657203
1
A: MEMBRANE-BOUND LYTIC MUREIN TRANSGLYCOSYLASE C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,5303
Polymers38,2591
Non-polymers1,2712
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: MEMBRANE-BOUND LYTIC MUREIN TRANSGLYCOSYLASE C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,4403
Polymers38,2591
Non-polymers1,1812
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.510, 114.330, 61.771
Angle α, β, γ (deg.)90.00, 93.28, 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: 38259.070 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: C5A0N2, UniProt: P0C066*PLUS, Lyases; Carbon-oxygen lyases; Acting on polysaccharides
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-N-acetyl-beta-muramic acid-(1-4)-2-acetamido-2-deoxy- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-N-acetyl-beta-muramic acid-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-methyl 2-acetamido-3-O-[(1R)-1-carboxyethyl]-2-deoxy-beta-D-glucopyranoside


Type: oligosaccharide / Mass: 988.937 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/3,4,3/[a2122h-1b_1-5_1*OC_2*NCC/3=O_3*OC^RCO/4=O/3C][a2122h-1b_1-5_2*NCC/3=O][a2122h-1b_1-5_2*NCC/3=O_3*OC^RCO/4=O/3C]/1-2-3-2/a4-b1_b4-c1_c4-d1WURCSPDB2Glycan 1.1.0
[][methyl]{[(1+1)][b-D-GlcpNAc]{[(3+1)][<C3O2>]{}[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(3+1)][<C3O2>]{}[(4+1)][b-D-GlcpNAc]{}}}}}LINUCSPDB-CARE
#3: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#4: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 203 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.28 Å3/Da / Density % sol: 46.08 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9794
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.15→49.43 Å / Num. obs: 37159 / % possible obs: 99.7 % / Observed criterion σ(I): 6 / Redundancy: 5.4 % / Biso Wilson estimate: 28.22 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 6.6
Reflection shellResolution: 2.15→2.33 Å / Redundancy: 5 % / Mean I/σ(I) obs: 1.9 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: NONE

Resolution: 2.15→49.429 Å / SU ML: 0.34 / σ(F): 1.34 / Phase error: 29.4 / Stereochemistry target values: ML
Details: POOR ELECTRON DENSITY IN CHAIN A RESIDUES 310-326, PRESENTING HIGH B-FACTORS.
RfactorNum. reflection% reflection
Rfree0.2678 1856 5 %
Rwork0.1912 --
obs0.1951 37109 99.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.15→49.429 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5154 0 168 203 5525
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085428
X-RAY DIFFRACTIONf_angle_d1.1747360
X-RAY DIFFRACTIONf_dihedral_angle_d16.3181967
X-RAY DIFFRACTIONf_chiral_restr0.051834
X-RAY DIFFRACTIONf_plane_restr0.005945
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.20820.32311540.26832683X-RAY DIFFRACTION100
2.2082-2.27310.34511380.27512701X-RAY DIFFRACTION100
2.2731-2.34650.33851450.25632702X-RAY DIFFRACTION100
2.3465-2.43040.32521380.24422695X-RAY DIFFRACTION100
2.4304-2.52770.35621180.23192722X-RAY DIFFRACTION100
2.5277-2.64270.2981270.22262735X-RAY DIFFRACTION99
2.6427-2.7820.29361430.22372696X-RAY DIFFRACTION99
2.782-2.95630.36211320.21972740X-RAY DIFFRACTION100
2.9563-3.18450.32721590.21582678X-RAY DIFFRACTION100
3.1845-3.50490.29681360.19292732X-RAY DIFFRACTION100
3.5049-4.01190.24341490.15382706X-RAY DIFFRACTION100
4.0119-5.05380.18321530.13532729X-RAY DIFFRACTION100
5.0538-49.44190.20671640.15052734X-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)
10.0063-0.00880.01230.0798-0.05910.0353-0.1575-0.00240.2214-0.0974-0.0925-0.0915-0.0388-0.1721-0.18880.50260.1538-0.29480.1989-0.03920.2895-29.154431.15791.6986
20.23380.0161-0.02010.154-0.03630.6285-0.4769-0.08540.32160.0356-0.16090.0698-0.4906-0.2441-0.41640.33650.1151-0.19840.2898-0.18680.3073-22.175530.641717.1768
30.5404-0.00680.11870.2331-0.19180.23650.0779-0.03880.3457-0.3697-0.11420.10530.6287-0.1024-0.00460.3861-0.0244-0.03610.16490.0873-0.0222-17.41595.983-3.4693
40.15980.0535-0.01150.2696-0.04230.1053-0.0269-0.0261-0.0684-0.03140.03690.0533-0.0154-0.011600.1334-0.0079-0.00740.1260.0420.1776-12.7436-31.837826.9558
50.20570.049-0.04990.2463-0.17620.1286-0.02740.03160.00310.0129-0.02810.0628-0.03390.0478-0.00170.131-0.01320.03110.15120.04540.17164.3794-6.858723.4283
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 33 THROUGH 79 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 80 THROUGH 183 )
3X-RAY DIFFRACTION3CHAIN A AND (RESID 184 THROUGH 359 )
4X-RAY DIFFRACTION4CHAIN B AND (RESID 33 THROUGH 183 )
5X-RAY DIFFRACTION5CHAIN B AND (RESID 184 THROUGH 359 )

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