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- PDB-4hjz: 1.9 A Crystal structure of E. coli MltE-E64Q with bound chitopentaose -

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Basic information

Entry
Database: PDB / ID: 4hjz
Title1.9 A Crystal structure of E. coli MltE-E64Q with bound chitopentaose
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 / MOLECULAR REPLACEMENT / Resolution: 1.9 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: 3T21
Revision 1.0Oct 24, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 31, 2012Group: Database references
Revision 1.2Dec 26, 2012Group: Database references
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 / 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.type_symbol / _chem_comp.name / _chem_comp.type / _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_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,5496
Polymers45,6142
Non-polymers1,9364
Water8,953497
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A: Endo-type membrane-bound lytic murein transglycosylase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,8763
Polymers22,8071
Non-polymers1,0692
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)23,6733
Polymers22,8071
Non-polymers8662
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)72.013, 34.322, 77.516
Angle α, β, γ (deg.)90.000, 105.870, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 22806.760 Da / Num. of mol.: 2 / Fragment: UNP residues 17-203 / Mutation: E64Q
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: pBADnLIC-mltE / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3)
References: UniProt: P0C960, Lyases; Carbon-oxygen lyases; Acting on polysaccharides
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1033.979 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,5,4/[a2122h-1b_1-5_2*NCC/3=O]/1-1-1-1-1/a4-b1_b4-c1_c4-d1_d4-e1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}}}LINUCSPDB-CARE
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 830.786 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,4,3/[a2122h-1b_1-5_2*NCC/3=O]/1-1-1-1/a4-b1_b4-c1_c4-d1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}}LINUCSPDB-CARE
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 497 / 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: 2.02 Å3/Da / Density % sol: 39.11 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.2 M succinic acid, pH 5.5, 15% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM16 / Wavelength: 0.984 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Feb 23, 2009 / Details: Rd coated toroidal mirror
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.984 Å / Relative weight: 1
ReflectionResolution: 1.9→74.562 Å / Num. all: 28825 / Num. obs: 28825 / % possible obs: 98.7 % / Redundancy: 3.5 % / Rsym value: 0.067 / Net I/σ(I): 12.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.9-22.90.21721103538600.21792.8
2-2.123.50.1624.61382639430.16299.3
2.12-2.273.60.1245.91355937680.12499.5
2.27-2.453.70.1027.31285635100.10299.6
2.45-2.693.70.0798.51196332350.07999.9
2.69-33.70.06410.11085429370.06499.9
3-3.473.70.05112.5963426250.05199.9
3.47-4.253.60.04513803622120.04599.9
4.25-6.013.60.04712.7626117380.04799.9
6.01-37.2813.40.03515.934139970.03599.2

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Processing

Software
NameVersionClassificationNB
SCALA3.3.9data scaling
PHENIX1.8_1069refinement
PDB_EXTRACT3.11data extraction
MxCuBEdata collection
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3T36

3t36


Resolution: 1.9→37.281 Å / Occupancy max: 1 / Occupancy min: 0.46 / FOM work R set: 0.8183 / SU ML: 0.23 / σ(F): 1.34 / Phase error: 25.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2619 1469 5.1 %RANDOM
Rwork0.2053 ---
obs0.2083 28810 98.4 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 69.18 Å2 / Biso mean: 18.3714 Å2 / Biso min: 6.21 Å2
Refinement stepCycle: LAST / Resolution: 1.9→37.281 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2804 0 130 497 3431
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013041
X-RAY DIFFRACTIONf_angle_d1.2444154
X-RAY DIFFRACTIONf_chiral_restr0.064476
X-RAY DIFFRACTIONf_plane_restr0.006533
X-RAY DIFFRACTIONf_dihedral_angle_d24.4261191
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9-1.96790.29221200.24472392251288
1.9679-2.04670.28661370.22942723286098
2.0467-2.13980.30071450.219127492894100
2.1398-2.25260.26691590.210827322891100
2.2526-2.39370.29491540.214927262880100
2.3937-2.57850.28121560.199827712927100
2.5785-2.83790.26961380.206527832921100
2.8379-3.24840.25841240.195927892913100
3.2484-4.09180.21581570.176427972954100
4.0918-37.28810.25741790.216428793058100
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)
11.83920.5776-0.57231.1293-0.58442.4451-0.10020.20070.0611-0.55660.0257-0.2143-0.05260.07660.06110.2757-0.01060.04590.14570.01180.099112.224427.47442.522
25.06934.5798-1.27594.2666-2.01526.10810.0976-0.34330.16120.1177-0.20630.062-0.0052-0.18840.10570.07990.0196-0.0270.1274-0.02870.09988.12633.517662.033
32.7197-0.35630.57452.12470.12982.08680.0114-0.2686-0.2412-0.01270.07150.0491-0.00380.0446-0.06960.1166-0.00710.00030.07720.01650.03436.054829.882952.8288
41.673-0.38460.30292.1107-0.71581.6812-0.02460.05140.019-0.21750.04580.055-0.1547-0.1625-0.020.2417-0.0004-0.06590.13910.0020.077-1.616739.532940.8212
52.0753-0.3732-0.10112.0489-0.21142.0766-0.1105-0.2733-0.05980.46750.067-0.05260.1174-0.0570.03360.13870.0023-0.00660.10840.0160.07670.959923.322982.2908
63.8713-0.90561.25932.2564-2.91214.12660.08570.3579-0.0653-0.2935-0.0844-0.10360.05550.0710.01120.15180.00310.00570.11510.0110.05377.660817.261863.3614
70.1128-0.1036-0.42321.74760.18981.5931-0.07130.12280.1150.05810.0466-0.03030.0620.07280.03310.05380.01630.00590.07810.01580.08791.324121.163170.2368
81.91370.717-0.10342.3674-0.03722.1151-0.0155-0.0538-0.04580.10340.00340.19720.1314-0.13210.00680.07160.0140.03980.0901-0.00250.1708-11.779711.324776.4603
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 21 through 84 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 85 through 101 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 102 through 136 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 137 through 203 )A0
5X-RAY DIFFRACTION5chain 'B' and (resid 21 through 84 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 85 through 101 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 102 through 136 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 137 through 203 )B0

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