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

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Basic information

Entry
Database: PDB / ID: 1qsa
TitleCRYSTAL STRUCTURE OF THE 70 KDA SOLUBLE LYTIC TRANSGLYCOSYLASE SLT70 FROM ESCHERICHIA COLI AT 1.65 ANGSTROMS RESOLUTION
ComponentsPROTEIN (SOLUBLE LYTIC TRANSGLYCOSYLASE SLT70)
KeywordsTRANSFERASE / ALPHA-SUPERHELIX
Function / homology
Function and homology information


lytic endotransglycosylase activity / : / peptidoglycan 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 / : / peptidoglycan 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 / Prokaryotic transglycosylase, active site / Prokaryotic transglycosylases signature. / Methyltransferase, Methionine Synthase (B12-binding Domains); Chain A, domain 1 ...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 / Prokaryotic transglycosylase, active site / Prokaryotic transglycosylases signature. / Methyltransferase, Methionine Synthase (B12-binding Domains); Chain A, domain 1 / Transglycosylase SLT domain 1 / Transglycosylase SLT domain / Lysozyme - #10 / Lysozyme / Lysozyme-like domain superfamily / Alpha Horseshoe / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ACETATE ION / Soluble lytic murein transglycosylase / Soluble lytic murein transglycosylase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.65 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 20, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 1, 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 6, 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 / 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 / _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: PROTEIN (SOLUBLE LYTIC TRANSGLYCOSYLASE SLT70)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,49722
Polymers70,5451
Non-polymers1,95321
Water17,817989
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.009, 87.477, 132.906
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 PROTEIN (SOLUBLE LYTIC TRANSGLYCOSYLASE SLT70)


Mass: 70544.516 Da / Num. of mol.: 1 / Fragment: FULL PROTEIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: 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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 989 / Source method: isolated from a natural source / Formula: H2O
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: 3.21 Å3/Da / Density % sol: 61.72 %
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: 1.65→34 Å / Num. all: 335588 / Num. obs: 100894 / % possible obs: 92.3 % / Redundancy: 3.3 % / Biso Wilson estimate: 16.8 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 23
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 2 % / Rmerge(I) obs: 0.255 / % possible all: 75.6
Reflection
*PLUS
Num. measured all: 335588
Reflection shell
*PLUS
% possible obs: 75.6 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
PHASESphasing
DMmodel building
X-PLORmodel building
X-PLOR3.843refinement
DMphasing
X-PLORphasing
RefinementResolution: 1.65→20 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
Details: RESOLUTION-DEPENDENT WEIGHTING SCHEME USED BULK SOLVENT MODEL USED, ANISOTROPIC B-FACTOR SCALING USED,
RfactorNum. reflection% reflectionSelection details
Rfree0.191 9733 10 %RANDOM
Rwork0.168 ---
obs0.169 97005 88.4 %-
Displacement parametersBiso mean: 20.3 Å2
Baniso -1Baniso -2Baniso -3
1-6.25 Å20 Å20 Å2
2---3.79 Å20 Å2
3----2.46 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.18 Å0.15 Å
Luzzati d res low-5 Å
Luzzati sigma a0.16 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 1.65→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4964 0 111 989 6064
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.008
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_d20
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.32
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.151.5
X-RAY DIFFRACTIONx_mcangle_it1.622
X-RAY DIFFRACTIONx_scbond_it2.192
X-RAY DIFFRACTIONx_scangle_it3.442.5
LS refinement shellResolution: 1.65→1.7 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 12
RfactorNum. reflection% reflection
Rfree0.254 623 10.8 %
Rwork0.217 5145 -
obs--63.7 %
Software
*PLUS
Name: X-PLOR / Version: 3.843 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / σ(F): 0
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 20.3 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_deg20
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.32
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: 0.254 / % reflection Rfree: 10.8 % / Rfactor Rwork: 0.217

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