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- PDB-1qte: CRYSTAL STRUCTURE OF THE 70 KDA SOLUBLE LYTIC TRANSGLYCOSYLASE SL... -

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Basic information

Entry
Database: PDB / ID: 1qte
TitleCRYSTAL STRUCTURE OF THE 70 KDA SOLUBLE LYTIC TRANSGLYCOSYLASE SLT70 FROM ESCHERICHIA COLI AT 1.90 A RESOLUTION IN COMPLEX WITH A 1,6-ANHYDROMUROTRIPEPTIDE
ComponentsSOLUBLE LYTIC TRANSGLYCOSYLASE SLT70
KeywordsHYDROLASE / ALPHA-SUPERHELIX
Function / homology
Function and homology information


lytic endotransglycosylase activity / : / lytic transglycosylase activity / hydrolase activity, hydrolyzing O-glycosyl compounds / peptidoglycan catabolic process / peptidoglycan-based cell wall / cell wall organization / outer membrane-bounded periplasmic space / 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
ACETATE ION / Chem-AH0 / ALANINE / D-ALANINE / : / Soluble lytic murein transglycosylase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.9 Å
Authorsvan Asselt, E.J. / Thunnissen, A.-M.W.H. / Dijkstra, B.W.
CitationJournal: J.Mol.Biol. / Year: 1999
Title: High resolution crystal structures of the Escherichia coli lytic transglycosylase Slt70 and its complex with a peptidoglycan fragment.
Authors: van Asselt, E.J. / Thunnissen, A.M. / Dijkstra, B.W.
History
DepositionJun 27, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 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 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / 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 / _struct_conn.pdbx_leaving_atom_flag
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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: SOLUBLE LYTIC TRANSGLYCOSYLASE SLT70
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,89123
Polymers70,5451
Non-polymers2,34722
Water15,745874
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.266, 87.514, 132.947
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

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein SOLUBLE LYTIC TRANSGLYCOSYLASE SLT70 / E.C.3.2.1.-


Mass: 70544.516 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: COMPLEXED WITH 1,6-ANHYDROMUROTRIPEPTIDE, DAL-ALA-AH0
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)
References: PIR: S56616, UniProt: P0AGC3*PLUS, 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

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Non-polymers , 7 types, 895 molecules

#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-ALA / ALANINE


Type: L-peptide linking / Mass: 89.093 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO2
#6: Chemical ChemComp-DAL / D-ALANINE


Type: D-peptide linking / Mass: 89.093 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO2
#7: Chemical ChemComp-AH0 / 2-(2-ACETYLAMINO-4-HYDROXY-6,8-DIOXA-BICYCLO[3.2.1]OCT-3-YLOXY)-PROPIONIC ACID / 1,6-anhydro-N-acetylmuramic acid


Mass: 275.255 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H17NO7
#8: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 874 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 3.23 Å3/Da / Density % sol: 61.87 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5
Details: SODIUM ACETATE, AMMONIUM SULFATE, SODIUM AZIDE, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
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-IDDetails
115-30 %ammonium sulfate1reservoir
20.1 Msodium acetate1reservoirpH4.5-5.0
310 mg/mlprotein1drop
410 mMpotassium phosphate1droppH6.8

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.92
DetectorType: PRINCETON 2K / Detector: CCD / Date: Apr 9, 1995
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.9→15 Å / Num. obs: 57525 / % possible obs: 79.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Biso Wilson estimate: 16.3 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 17.9
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.148 / % possible all: 64.6
Reflection
*PLUS
Num. measured all: 193873
Reflection shell
*PLUS
% possible obs: 63.7 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
X-PLOR3.843refinement
X-PLORphasing
RefinementResolution: 1.9→15 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
Details: USED RESOLUTION-DEPENDENT WEIGHTING SCHEME, BULK SOLVENT MODEL, AND ANISOTROPIC B-FACTOR SCALING
RfactorNum. reflection% reflectionSelection details
Rfree0.197 2745 4.9 %RANDOM
Rwork0.171 ---
all0.173 56504 --
obs0.171 53759 77.9 %-
Displacement parametersBiso mean: 25.8 Å2
Baniso -1Baniso -2Baniso -3
1-13.34 Å20 Å20 Å2
2---7.04 Å20 Å2
3----6.31 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.15 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 1.9→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4964 0 137 874 5975
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
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_d19.9
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.19
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 1.9→1.96 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 12
RfactorNum. reflection% reflection
Rfree0.255 150 4.2 %
Rwork0.22 3402 -
obs--59.6 %
Refinement
*PLUS
Lowest resolution: 15 Å / Num. reflection obs: 56504 / Rfactor obs: 0.172
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg19.9
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.19
LS refinement shell
*PLUS
Rfactor Rwork: 0.22

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