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- PDB-1sly: COMPLEX OF THE 70-KDA SOLUBLE LYTIC TRANSGLYCOSYLASE WITH BULGECIN A -

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Basic information

Entry
Database: PDB / ID: 1sly
TitleCOMPLEX OF THE 70-KDA SOLUBLE LYTIC TRANSGLYCOSYLASE WITH BULGECIN A
Components70-KDA SOLUBLE LYTIC TRANSGLYCOSYLASE
KeywordsGLYCOSYLTRANSFERASE / INHIBITOR-ENZYME COMPLEX / LYSOZYME / PEPTIDOGLYCAN / HYDROLASE / GLYCOSIDASE / PERIPLASMIC
Function / homology
Function and homology information


lytic endotransglycosylase activity / : / lytic transglycosylase activity / peptidoglycan metabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds / peptidoglycan catabolic process / peptidoglycan-based cell wall / cell wall organization / outer membrane-bounded periplasmic space / periplasmic space ...lytic endotransglycosylase activity / : / lytic transglycosylase activity / peptidoglycan metabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds / peptidoglycan catabolic process / peptidoglycan-based cell wall / cell wall organization / outer membrane-bounded periplasmic space / periplasmic space / lyase activity / membrane
Similarity search - Function
70-kda Soluble Lytic Transglycosylase; domain 1 / Bacterial muramidases / Lytic transglycosylase, superhelical linker domain / Lytic transglycosylase, superhelical linker / Soluble lytic murein transglycosylase L domain / Lytic transglycosylase, superhelical U-shaped / Lytic transglycosylase, superhelical linker domain superfamily / Methyltransferase, Methionine Synthase (B12-binding Domains); Chain A, domain 1 / Prokaryotic transglycosylase, active site / Prokaryotic transglycosylases signature. ...70-kda Soluble Lytic Transglycosylase; domain 1 / Bacterial muramidases / Lytic transglycosylase, superhelical linker domain / Lytic transglycosylase, superhelical linker / Soluble lytic murein transglycosylase L domain / Lytic transglycosylase, superhelical U-shaped / Lytic transglycosylase, superhelical linker domain superfamily / Methyltransferase, Methionine Synthase (B12-binding Domains); Chain A, domain 1 / Prokaryotic transglycosylase, active site / Prokaryotic transglycosylases signature. / Transglycosylase SLT domain 1 / Transglycosylase SLT domain / Lysozyme - #10 / Lysozyme / Alpha Horseshoe / Lysozyme-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-BLG / Soluble lytic murein transglycosylase / Soluble lytic murein transglycosylase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.8 Å
AuthorsThunnissen, A.M.W.H. / Kalk, K.H. / Rozeboom, H.J. / Dijkstra, B.W.
Citation
Journal: Biochemistry / Year: 1995
Title: Structure of the 70-kDa soluble lytic transglycosylase complexed with bulgecin A. Implications for the enzymatic mechanism.
Authors: Thunnissen, A.M. / Rozeboom, H.J. / Kalk, K.H. / Dijkstra, B.W.
#1: Journal: Proteins / Year: 1995
Title: The Catalytic Domain of a Bacterial Lytic Transglycosylase Defines a Novel Class of Lysozymes
Authors: Thunnissen, A.M. / Isaacs, N.W. / Dijkstra, B.W.
#2: Journal: Curr.Opin.Struct.Biol. / Year: 1994
Title: 'Holy' Proteins. II: The Soluble Lytic Transglycosylase
Authors: Dijkstra, B.W. / Thunnissen, A.M.
#3: Journal: Nature / Year: 1994
Title: Doughnut-Shaped Structure of a Bacterial Muramidase Revealed by X-Ray Crystallography
Authors: Thunnissen, A.M. / Dijkstra, A.J. / Kalk, K.H. / Rozeboom, H.J. / Engel, H. / Keck, W. / Dijkstra, B.W.
History
DepositionAug 2, 1995Processing site: BNL
Revision 1.0Aug 17, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_entry_details.has_protein_modification / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 70-KDA SOLUBLE LYTIC TRANSGLYCOSYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,1132
Polymers70,5611
Non-polymers5531
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.310, 88.470, 133.060
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 70-KDA SOLUBLE LYTIC TRANSGLYCOSYLASE / SLT70 / EXOMURAMIDASE


Mass: 70560.555 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
References: UniProt: P03810, UniProt: P0AGC3*PLUS, Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds
#2: Chemical ChemComp-BLG / 4-O-(4-O-SULFONYL-N-ACETYLGLUCOSAMININYL)-5-METHYLHYDROXY-L-PROLINE-TAURINE / BULGECIN A


Mass: 552.551 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H30N3O14S2
Compound detailsTHE STRUCTURE CONSISTS OF 3 DOMAINS: DOMAIN RESIDUES COMMENT U 1 - 361 ALPHA-SUPERHELIX TOPOLOGY L ...THE STRUCTURE CONSISTS OF 3 DOMAINS: DOMAIN RESIDUES COMMENT U 1 - 361 ALPHA-SUPERHELIX TOPOLOGY L 380 - 448 ALPHA-SUPERHELIX TOPOLOGY C 449 - 618 LYSOZYME-FOLD
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.35 Å3/Da / Density % sol: 63.2 %
Crystal
*PLUS
Density % sol: 63 %
Crystal grow
*PLUS
pH: 6.8 / Method: vapor diffusion, hanging drop / Details: Rozeboom, H. J., (1990) J. Mol. Biol., 212, 557.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
210 mMpotassium phosphate1drop
315-30 %ammonium sulfate1reservoir
40.1 Msodium acetate1reservoir

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 1.003
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 20, 1993
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.003 Å / Relative weight: 1
ReflectionResolution: 2.8→22 Å / Num. obs: 23903 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Rmerge(I) obs: 0.08

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
KBRANI(BIOMOL)data reduction
X-PLORmodel building
X-PLORrefinement
BIOMOL(KBRANI)data scaling
X-PLORphasing
RefinementResolution: 2.8→8 Å / σ(F): 2
Details: RESIDUES 371 - 377 ARE POORLY DEFINED BY THE ELECTRON DENSITY. THESE RESIDUES BELONG TO A LONG SURFACE LOOP THAT CONNECTS THE U- AND L-DOMAINS.
RfactorNum. reflection% reflection
Rfree0.268 --
Rwork0.185 --
obs0.185 20119 88.1 %
Displacement parametersBiso mean: 24.15 Å2
Refine analyzeLuzzati coordinate error obs: 0.35 Å / Luzzati sigma a obs: 0.4 Å
Refinement stepCycle: LAST / Resolution: 2.8→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4965 0 35 0 5000
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.015
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_deg2.9
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d21.4
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.4
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2.32
X-RAY DIFFRACTIONx_mcangle_it4
X-RAY DIFFRACTIONx_scbond_it4.5
X-RAY DIFFRACTIONx_scangle_it5.48
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1SLT70_BULGA_PARAM.DATSLT70_BULGA_TOPOL.DAT
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.8 Å / Num. reflection obs: 22746 / Rfactor obs: 0.195
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg21.4
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.4

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