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- PDB-4chx: Crystal structure of MltC in complex with disaccharide pentapepti... -

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Entry
Database: PDB / ID: 4chx
TitleCrystal structure of MltC in complex with disaccharide pentapeptide DHl89
Components
  • Membrane-bound lytic murein transglycosylase C
  • NAG-ANHMUR-PENTAPEPTIDE
KeywordsLYASE
Function / homology
Function and homology information


lytic endotransglycosylase activity / : / peptidoglycan lytic transglycosylase activity / 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 ...lytic endotransglycosylase activity / : / peptidoglycan lytic transglycosylase activity / 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
Chem-AH0 / Membrane-bound lytic murein transglycosylase C
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsArtola-Recolons, C. / Bernardo-Garcia, N. / 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
DepositionDec 4, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 23, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 1, 2014Group: Database references
Revision 1.2Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / pdbx_chem_comp_identifier ...chem_comp / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.0Dec 7, 2022Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_2 / entity / entity_name_com / entity_poly / entity_poly_seq / entity_src_gen / entity_src_nat / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / pdbx_struct_mod_residue / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / pdbx_validate_torsion / struct_asym / struct_conn / struct_mon_prot_cis / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_name_com.name / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_seq_type / _entity_src_nat.pdbx_beg_seq_num / _entity_src_nat.pdbx_end_seq_num / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_mod_residue.label_seq_id / _struct_conn.pdbx_dist_value / _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.ptnr1_label_seq_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 / _struct_conn.ptnr2_label_seq_id / _struct_mon_prot_cis.label_seq_id / _struct_mon_prot_cis.pdbx_label_seq_id_2 / _struct_ref.db_code / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.seq_align_end / _struct_ref_seq_dif.details / _struct_ref_seq_dif.pdbx_seq_db_accession_code
Revision 3.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / pdbx_validate_rmsd_angle / pdbx_validate_torsion / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id
Revision 3.1Jan 31, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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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
C: NAG-ANHMUR-PENTAPEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,5475
Polymers77,0513
Non-polymers4962
Water1,838102
1
A: Membrane-bound lytic murein transglycosylase C
C: NAG-ANHMUR-PENTAPEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,2884
Polymers38,7922
Non-polymers4962
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1840 Å2
ΔGint-7.9 kcal/mol
Surface area18700 Å2
MethodPQS
2
B: Membrane-bound lytic murein transglycosylase C


Theoretical massNumber of molelcules
Total (without water)38,2591
Polymers38,2591
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.160, 115.000, 61.280
Angle α, β, γ (deg.)90.00, 93.21, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Membrane-bound lytic murein transglycosylase C / Murein lyase C


Mass: 38259.070 Da / Num. of mol.: 2 / Fragment: RESIDUES 20-359 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: mltC, yggZ, b2963, JW5481 / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: P0C066, Lyases; Carbon-oxygen lyases; Acting on polysaccharides
#2: Protein/peptide NAG-ANHMUR-PENTAPEPTIDE


Mass: 532.544 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SYNTHETIC CONSTRUCT (others)
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Chemical ChemComp-AH0 / 2-(2-ACETYLAMINO-4-HYDROXY-6,8-DIOXA-BICYCLO[3.2.1]OCT-3-YLOXY)-PROPIONIC ACID / 1,6-anhydro-N-acetylmuramic acid


Mass: 275.255 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H17NO7
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 102 / 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: 8

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Sample preparation

CrystalDensity Matthews: 2.28 Å3/Da / Density % sol: 45.97 % / 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: ID23-2 / Wavelength: 0.8729
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 7, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8729 Å / Relative weight: 1
ReflectionResolution: 2.45→50.08 Å / Num. obs: 25551 / % possible obs: 100 % / Observed criterion σ(I): 3 / Redundancy: 3.7 % / Biso Wilson estimate: 30.61 Å2 / Rmerge(I) obs: 0.18 / Net I/σ(I): 7.2
Reflection shellResolution: 2.45→2.58 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.93 / Mean I/σ(I) obs: 1.5 / % possible all: 100

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Processing

Software
NameClassification
PHENIXmodel building
SCALAdata scaling
iMOSFLMphasing
SCALAphasing
MOLREPphasing
PHENIXphasing
PHENIXrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4C5F

4c5f


Resolution: 2.45→45.916 Å / SU ML: 0.34 / σ(F): 1.36 / Phase error: 25.57 / Stereochemistry target values: ML
Details: ATOMS IN THE SUGAR RINGS OF THE LIGAND WERE REFINED WITH ZERO OCCUPANCY AS THE ELECTRON DENSITY OF THAT PART WAS NOT SEEN.
RfactorNum. reflection% reflection
Rfree0.2485 2008 7.9 %
Rwork0.1918 --
obs0.1963 25521 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.45→45.916 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5223 0 0 102 5325
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015327
X-RAY DIFFRACTIONf_angle_d1.4217222
X-RAY DIFFRACTIONf_dihedral_angle_d16.1911952
X-RAY DIFFRACTIONf_chiral_restr0.06808
X-RAY DIFFRACTIONf_plane_restr0.008939
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4501-2.51130.3421480.29591673X-RAY DIFFRACTION100
2.5113-2.57920.33661350.25031646X-RAY DIFFRACTION100
2.5792-2.65510.30651440.24581723X-RAY DIFFRACTION100
2.6551-2.74080.31161320.23581646X-RAY DIFFRACTION100
2.7408-2.83870.26991520.23231657X-RAY DIFFRACTION100
2.8387-2.95240.30931410.21811721X-RAY DIFFRACTION100
2.9524-3.08670.30121430.22141641X-RAY DIFFRACTION100
3.0867-3.24940.27711500.2131681X-RAY DIFFRACTION100
3.2494-3.45290.29661410.19391677X-RAY DIFFRACTION100
3.4529-3.71940.21491390.16041678X-RAY DIFFRACTION100
3.7194-4.09350.19181480.15321687X-RAY DIFFRACTION100
4.0935-4.68540.23421470.14721678X-RAY DIFFRACTION100
4.6854-5.90110.21871410.1671691X-RAY DIFFRACTION100
5.9011-45.92420.17711470.18351714X-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)
12.42760.77130.76231.54140.03172.64190.1027-0.2315-0.18060.1266-0.0018-0.07510.0324-0.2199-0.09720.1513-0.00560.02250.21590.05550.23215.9304-13.352831.2611
21.33860.61210.40521.6689-0.47480.8365-0.13170.13140.1273-0.25410.33660.46620.1707-0.2531-0.20350.2252-0.0410.01120.31060.09410.2599.1673-7.281218.7992
33.1851.3314-0.84943.6063-1.1952.3263-0.0711-0.03660.0372-0.0183-0.1488-0.0197-0.06330.30990.23610.18110.0069-0.0130.17910.05170.228331.836311.276223.856
43.01151.64661.67673.06192.5324.5993-1.1089-0.09210.3046-0.19840.22050.4756-0.5959-1.03990.6260.48930.2888-0.2830.5056-0.1060.4419-9.533348.9841-2.908
52.10930.39230.55852.44190.69821.4484-0.5424-0.60470.7767-0.4538-0.42960.049-0.8629-1.230.52060.52580.3911-0.19240.422-0.30330.3757-0.408150.18145.0695
61.38281.21230.56722.20680.05482.1844-0.3466-0.24440.7004-0.7162-0.5690.6402-0.8655-0.92080.46570.28750.4465-0.01940.4284-0.49170.3261.535452.73814.9638
72.30360.99841.62530.720.79471.61650.3955-0.4895-0.24510.5105-0.77690.31690.2356-1.45650.26630.16220.06120.14210.746-0.29330.3213-0.227641.279618.5684
81.12541.02720.70491.83720.02371.5663-0.1164-0.12150.2711-0.1653-0.29950.3761-0.5289-0.57550.41040.36390.1393-0.09820.3214-0.12250.37057.432255.404616.7539
92.18231.32681.0734.14850.58292.54830.4191-0.4308-0.03980.4717-0.1174-0.25920.9756-0.7193-0.10540.4723-0.1719-0.04550.38040.04570.13447.24524.239311.7532
103.4829-0.74991.09184.50680.55263.17140.1011-0.09270.2445-0.1383-0.1767-0.10560.631-0.32030.01680.2927-0.02260.09240.22110.01670.17256.827529.74193.1455
111.49871.6282-0.25235.63260.29610.4166-0.0656-0.0198-0.1163-1.18140.24710.6660.8707-1.0639-0.030.5381-0.1811-0.09620.48160.01590.311-3.9325.8071-3.4177
122.89151.13680.67332.22990.17733.17320.4367-0.4956-0.2703-0.9313-0.40680.65751.0001-1.1297-0.00550.6367-0.2588-0.10910.49470.00960.2969-3.001522.33970.8364
131.6181-0.16240.3281.98470.25232.33930.08720.7623-0.3926-1.6646-0.0534-0.39820.69270.0068-0.10641.44840.09860.12750.4398-0.03140.166612.407718.5114-14.5745
141.48570.8637-0.13672.38230.574.73970.30920.31230.5388-0.8898-0.3829-0.48160.61220.8604-0.0120.6450.15390.26090.46660.08340.325618.225627.6299-6.5324
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 52 )
5X-RAY DIFFRACTION5CHAIN B AND (RESID 53 THROUGH 79 )
6X-RAY DIFFRACTION6CHAIN B AND (RESID 80 THROUGH 108 )
7X-RAY DIFFRACTION7CHAIN B AND (RESID 109 THROUGH 147 )
8X-RAY DIFFRACTION8CHAIN B AND (RESID 148 THROUGH 183 )
9X-RAY DIFFRACTION9CHAIN B AND (RESID 184 THROUGH 203 )
10X-RAY DIFFRACTION10CHAIN B AND (RESID 204 THROUGH 228 )
11X-RAY DIFFRACTION11CHAIN B AND (RESID 229 THROUGH 248 )
12X-RAY DIFFRACTION12CHAIN B AND (RESID 249 THROUGH 279 )
13X-RAY DIFFRACTION13CHAIN B AND (RESID 280 THROUGH 325 )
14X-RAY DIFFRACTION14CHAIN B AND (RESID 326 THROUGH 359 )

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