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- PDB-4hjv: Crystal structure of E. coli MltE with bound bulgecin and murodip... -

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Basic information

Entry
Database: PDB / ID: 4hjv
TitleCrystal structure of E. coli MltE with bound bulgecin and murodipeptide
ComponentsEndo-type membrane-bound lytic murein transglycosylase A
KeywordsLYASE/LYASE INHIBITOR / goose type lysozyme-like structure / lytic transglycosylase / LYASE-LYASE INHIBITOR complex
Function / homology
Function and homology information


: / lytic endotransglycosylase activity / peptidoglycan lytic transglycosylase activity / peptidoglycan metabolic process / cell outer membrane / cell wall organization / cell wall macromolecule catabolic process / cell division
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 / Lysozyme-like domain superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile. / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-BLG / Endo-type membrane-bound lytic murein transglycosylase A
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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
DepositionOct 14, 2012Deposition site: RCSB / Processing site: RCSB
SupersessionOct 24, 2012ID: 3T4I
Revision 1.0Oct 24, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 31, 2012Group: Database references
Revision 1.2Dec 26, 2012Group: Database references
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / diffrn_source / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / 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_ref_seq_dif / 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.occupancy / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_assembly_gen.asym_id_list / _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 / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: 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)115,02915
Polymers111,0415
Non-polymers3,98810
Water8,593477
1
A: Endo-type membrane-bound lytic murein transglycosylase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2573
Polymers22,2081
Non-polymers1,0492
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Endo-type membrane-bound lytic murein transglycosylase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8573
Polymers22,2081
Non-polymers6492
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)23,3534
Polymers22,2081
Non-polymers1,1453
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Endo-type membrane-bound lytic murein transglycosylase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2573
Polymers22,2081
Non-polymers1,0492
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)78.778, 94.853, 162.016
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Endo-type membrane-bound lytic murein transglycosylase A / 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: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-N-acetyl-beta-muramic acid


Type: oligosaccharide / Mass: 496.463 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4MurNAc1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O_3*OC^RCO/4=O/3C][a2122h-1b_1-5_2*NCC/3=O]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(3+1)][<C3O2>]{}[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#3: Chemical
ChemComp-BLG / 4-O-(4-O-SULFONYL-N-ACETYLGLUCOSAMININYL)-5-METHYLHYDROXY-L-PROLINE-TAURINE / BULGECIN A


Mass: 552.551 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H30N3O14S2
#4: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 477 / 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: 2.73 Å3/Da / Density % sol: 54.87 %
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: 0.842 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jul 1, 1998 / Details: mirror
RadiationMonochromator: Si(111), horizontally focusing / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.842 Å / Relative weight: 1
ReflectionResolution: 2.3→23 Å / Num. obs: 54621 / % possible obs: 98.2 % / Redundancy: 4.3 % / Rsym value: 0.063 / Net I/σ(I): 13.1

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
MOLREPphasing
PHENIX(phenix.refine: 1.8_1069)refinement
DENZOdata reduction
SCALEPACKdata scaling
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3T36

3t36


Resolution: 2.3→22.758 Å / SU ML: 0.2 / σ(F): 1.34 / Phase error: 19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.203 5514 10.12 %
Rwork0.1627 --
obs0.1668 54478 99.7 %
Solvent computationShrinkage radii: 1 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→22.758 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7069 0 257 477 7803
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0097503
X-RAY DIFFRACTIONf_angle_d1.18510222
X-RAY DIFFRACTIONf_dihedral_angle_d17.2132874
X-RAY DIFFRACTIONf_chiral_restr0.0761137
X-RAY DIFFRACTIONf_plane_restr0.0061311
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.38220.24175450.18874789X-RAY DIFFRACTION99
2.3822-2.47750.23645660.17374816X-RAY DIFFRACTION100
2.4775-2.59010.2155650.16034811X-RAY DIFFRACTION100
2.5901-2.72640.21765520.16694880X-RAY DIFFRACTION100
2.7264-2.89690.21525490.16464850X-RAY DIFFRACTION100
2.8969-3.12010.23215450.16984882X-RAY DIFFRACTION100
3.1201-3.43310.21425480.17364924X-RAY DIFFRACTION100
3.4331-3.92770.19335090.1644956X-RAY DIFFRACTION100
3.9277-4.94010.17235420.14235000X-RAY DIFFRACTION100
4.9401-22.75930.18985930.16215056X-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)
12.8108-0.01120.22552.0208-0.6261.3002-0.0625-0.1006-0.07210.1640.0173-0.1883-0.0195-0.09850.03850.2655-0.003-0.06220.2538-0.05650.209357.018841.324955.6201
21.56410.18410.24952.1087-0.1532.2588-0.0071-0.04780.0912-0.02010.10630.1224-0.0587-0.0934-0.10260.156-0.0072-0.02110.1854-0.01620.232548.031568.424433.9489
31.9341-0.3049-0.63792.5553-0.66053.31640.13660.04570.27480.1001-0.1728-0.1474-0.36720.29070.02330.1711-0.02340.00240.24780.01710.220614.888351.655459.8174
42.2709-0.0951-0.72771.9857-0.13343.2669-0.10720.2702-0.1602-0.0894-0.01820.3295-0.0451-0.26640.11570.27370.0535-0.06140.33180.04420.42278.100555.37424.6002
52.528-0.1524-0.02812.2685-0.08924.4356-0.07480.0131-0.2409-0.1301-0.0366-0.19860.59260.23070.09310.33720.0444-0.00040.21710.01950.212942.256287.698467.8952
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 20 through 203 )
2X-RAY DIFFRACTION2chain 'B' and (resid 19 through 203 )
3X-RAY DIFFRACTION3chain 'C' and (resid 19 through 203 )
4X-RAY DIFFRACTION4chain 'D' and (resid 22 through 203 )
5X-RAY DIFFRACTION5chain 'E' and (resid 19 through 203 )

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