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- PDB-4hjy: 2.4 A Crystal structure of E. coli MltE-E64Q with bound chitopentaose -

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Basic information

Entry
Database: PDB / ID: 4hjy
Title2.4 A Crystal structure of E. coli MltE-E64Q with bound chitopentaose
ComponentsEndo-type membrane-bound lytic murein transglycosylase A
KeywordsLYASE / goose 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
triacetyl-beta-chitotriose / Endo-type membrane-bound lytic murein transglycosylase A
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 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: 3T1Z
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 / entity_name_com / 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_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _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)47,2754
Polymers45,6142
Non-polymers1,6622
Water1,31573
1
A: Endo-type membrane-bound lytic murein transglycosylase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,8412
Polymers22,8071
Non-polymers1,0341
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)23,4342
Polymers22,8071
Non-polymers6281
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)71.540, 33.620, 75.220
Angle α, β, γ (deg.)90.000, 106.050, 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 / triacetyl-beta-chitotriose


Type: oligosaccharide, Oligosaccharide / Class: Inhibitor / Mass: 627.594 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: triacetyl-beta-chitotriose
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a2122h-1b_1-5_2*NCC/3=O]/1-1-1/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / 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: 1.91 Å3/Da / Density % sol: 35.46 %
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: ID14-4 / Wavelength: 0.9395 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 1, 2009 / Details: torodial focusing mirror
RadiationMonochromator: channel cut ESRF Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9395 Å / Relative weight: 1
ReflectionResolution: 2.4→72.288 Å / Num. all: 13461 / Num. obs: 13461 / % possible obs: 97.3 % / Redundancy: 3.1 % / Rsym value: 0.087 / Net I/σ(I): 8.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.4-2.533.10.4981.4601119190.49896.6
2.53-2.683.10.3452.1568118210.34597.4
2.68-2.873.10.2652.1541217500.26597.3
2.87-3.13.10.1763.8502816040.17697.5
3.1-3.393.10.1215.4475815160.12198.1
3.39-3.793.10.0778.3428013610.07797.8
3.79-4.383.10.05411.2376112160.05498.5
4.38-5.3730.04913306510170.04996.6
5.37-7.592.90.05511.122247740.05593.8
7.59-44.130.03315.814504830.03398.9

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Phasing

PhasingMethod: molecular replacement

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Processing

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

3t36


Resolution: 2.4→35.026 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8274 / SU ML: 0.3 / σ(F): 1.38 / Phase error: 24.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2609 1342 9.97 %RANDOM
Rwork0.1982 ---
obs0.2042 13455 97.08 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 128.61 Å2 / Biso mean: 44.7098 Å2 / Biso min: 1.85 Å2
Refinement stepCycle: LAST / Resolution: 2.4→35.026 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2804 0 114 73 2991
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012986
X-RAY DIFFRACTIONf_angle_d1.3274072
X-RAY DIFFRACTIONf_chiral_restr0.063466
X-RAY DIFFRACTIONf_plane_restr0.007522
X-RAY DIFFRACTIONf_dihedral_angle_d24.2191154
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 (%)
2.4-2.48580.35371110.27671191130296
2.4858-2.58530.28861490.24861201135097
2.5853-2.7030.31311230.22421184130797
2.703-2.84540.29721540.23221178133297
2.8454-3.02360.27731400.2061196133697
3.0236-3.25690.27211450.20441205135097
3.2569-3.58440.25621430.17991209135298
3.5844-4.10230.22131310.171235136699
4.1023-5.16590.23061190.17151237135697
5.1659-35.03020.25921270.20681277140495
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)
13.2346-0.0154-1.46574.6411-1.02852.8913-0.30350.7254-0.1354-1.76840.5643-0.35190.2120.1346-0.13820.8181-0.0538-0.06060.35340.08910.283714.647544.552540.4309
25.86661.55191.18482.8641-1.28755.9062-0.4195-0.30810.3647-0.1576-0.15950.04620.2144-0.62660.42810.3947-0.08730.03460.31750.00870.20438.325850.487259.516
35.771.7372-0.45213.279-0.11824.0173-0.3721-0.54980.1637-0.36840.24150.4430.3564-0.34960.12330.3094-0.0389-0.09260.13240.02140.32787.352846.542850.0433
42.38660.663-0.10564.2250.70143.5748-0.33890.42990.4039-1.36860.05920.8149-0.484-0.29380.27571.05560.0053-0.29940.42990.01490.40311.082556.315236.8953
53.30831.65191.09333.763-0.024.21290.0517-0.32450.21470.64980.14690.350.0077-0.2726-0.20890.1926-0.00780.05880.16480.00460.22251.244539.354679.434
69.90831.49961.13513.2557-1.87154.59630.15490.567-0.6237-0.71880.1304-0.1690.5286-0.3412-0.27550.37560.0036-0.01520.2958-0.04010.19288.728533.134360.9129
71.04-0.0749-1.41573.86821.64942.5611-0.19340.26230.58090.05910.14670.4556-0.00660.00860.01560.12910.00220.0090.22510.03180.3061.566437.304467.3744
82.91981.3085-0.53173.43530.77294.29870.0637-0.07760.19380.12880.02920.4840.3494-0.2531-0.10620.19470.02580.08290.25810.04640.4104-11.355727.262273.9014
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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