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- PDB-1qut: THE SOLUBLE LYTIC TRANSGLYCOSYLASE SLT35 FROM ESCHERICHIA COLI IN... -

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Entry
Database: PDB / ID: 1qut
TitleTHE SOLUBLE LYTIC TRANSGLYCOSYLASE SLT35 FROM ESCHERICHIA COLI IN COMPLEX WITH N-ACETYLGLUCOSAMINE
ComponentsLYTIC MUREIN TRANSGLYCOSYLASE B
KeywordsHYDROLASE / ALPHA-HELICAL PROTEIN WITH A FIVE-STRANDED ANTIPARALLEL BETA-STRAND
Function / homology
Function and homology information


lytic endotransglycosylase activity / : / peptidoglycan lytic transglycosylase activity / sodium ion binding / peptidoglycan catabolic process / cell outer membrane / cell wall organization / outer membrane-bounded periplasmic space / calcium ion binding
Similarity search - Function
Bacterial muramidase / Lytic transglycosylase MltB / Transglycosylase SLT domain 2 / Membrane-bound lytic murein transglycosylase B-like / Transglycosylase SLT domain / Helicase, Ruva Protein; domain 3 / Lysozyme - #10 / Lysozyme / Lysozyme-like domain superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile. ...Bacterial muramidase / Lytic transglycosylase MltB / Transglycosylase SLT domain 2 / Membrane-bound lytic murein transglycosylase B-like / Transglycosylase SLT domain / Helicase, Ruva Protein; domain 3 / Lysozyme - #10 / Lysozyme / Lysozyme-like domain superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile. / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Membrane-bound lytic murein transglycosylase B
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 2.44 Å
Authorsvan Asselt, E.J. / Dijkstra, A.J. / Kalk, K.H. / Takacs, B. / Keck, W. / Dijkstra, B.W.
Citation
Journal: Structure Fold.Des. / Year: 1999
Title: Crystal structure of Escherichia coli lytic transglycosylase Slt35 reveals a lysozyme-like catalytic domain with an EF-hand.
Authors: van Asselt, E.J. / Dijkstra, A.J. / Kalk, K.H. / Takacs, B. / Keck, W. / Dijkstra, B.W.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1998
Title: Accelerated X-ray structure elucidation of a 36 kDa muramidase/ transglycosylase using wARP
Authors: van Asselt, E.J. / Perrakis, A. / Kalk, K.H. / Lamzin, V.S. / Dijkstra, B.W.
History
DepositionJul 3, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 15, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Nov 29, 2017Group: Database references / Category: pdbx_database_related
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Nov 3, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / 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 / _struct_ref_seq_dif.details
Revision 1.6Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LYTIC MUREIN TRANSGLYCOSYLASE B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,3243
Polymers36,0801
Non-polymers2442
Water3,657203
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.330, 67.848, 98.629
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121

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Components

#1: Protein LYTIC MUREIN TRANSGLYCOSYLASE B / E.C.3.2.1.- / MUREIN HYDROLASE B / 35 KD SOLUBLE LYTIC TRANSGLYCOSYLASE / SLT35


Mass: 36079.660 Da / Num. of mol.: 1 / Fragment: SLT35 / Mutation: L40M, L41V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Cellular location: PERIPLASM / Cellular location (production host): PERIPLASM / Production host: Escherichia coli (E. coli)
References: UniProt: P41052, Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds
#2: 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
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 54.5 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: BICINE-NAOH, PEG 20K, ISOPROPANOL, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal
*PLUS
Density % sol: 55 %
Crystal grow
*PLUS
Method: unknown / PH range low: 8.5 / PH range high: 7.8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.1 MBicine-NaOH11
20-6 %PEG2000011

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418
DetectorType: MAC Science DIP-2000H / Detector: IMAGE PLATE / Date: Oct 28, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.44→25 Å / Num. obs: 14836 / % possible obs: 98.4 % / Observed criterion σ(I): -3 / Redundancy: 3.3 % / Biso Wilson estimate: 19.5 Å2 / Rmerge(I) obs: 0.104 / Net I/σ(I): 11.1
Reflection shellResolution: 2.44→2.48 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.316 / % possible all: 84
Reflection
*PLUS
Num. measured all: 49117

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Processing

Software
NameVersionClassification
X-PLOR3.843model building
X-PLOR3.843refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.843phasing
RefinementResolution: 2.44→20 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 100000 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.256 1483 10.1 %RANDOM
Rwork0.191 ---
obs0.195 14679 97.3 %-
all-14679 --
Displacement parametersBiso mean: 21.9 Å2
Baniso -1Baniso -2Baniso -3
1--0.3 Å20 Å20 Å2
2---3.98 Å20 Å2
3---4.28 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.37 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 2.44→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2476 0 16 203 2695
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.2
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d22.1
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.05
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.651.5
X-RAY DIFFRACTIONx_mcangle_it2.562
X-RAY DIFFRACTIONx_scbond_it2.672
X-RAY DIFFRACTIONx_scangle_it3.82.5
LS refinement shellResolution: 2.44→2.55 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.348 174 10.7 %
Rwork0.249 1445 -
obs--87 %
Software
*PLUS
Name: X-PLOR / Version: 3.843 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 10.1 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 21.9 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_angle_deg1.2
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg22.1
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.05
X-RAY DIFFRACTIONx_mcbond_it1.5
X-RAY DIFFRACTIONx_scbond_it2
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.348 / % reflection Rfree: 10.7 % / Rfactor Rwork: 0.249

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