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- PDB-1qdt: 2.1 A RESOLUTION STRUCTURE OF ESCHERICHIA COLI LYTIC TRANSGLYCOYS... -

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Basic information

Entry
Database: PDB / ID: 1qdt
Title2.1 A RESOLUTION STRUCTURE OF ESCHERICHIA COLI LYTIC TRANSGLYCOYSLASE SLT35 IN COMPLEX WITH CALCIUM
ComponentsLYTIC MUREIN TRANSGLYCOSYLASE B
KeywordsHYDROLASE / ALPHA-HELICAL PROTEIN WITH AN FIVE-STRANDED ANTIPARALLEL BETA-SHEET / GLYCOSYL TRANSFERASE / EF-HAND
Function / homology
Function and homology information


lytic endotransglycosylase activity / : / 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: 2.1 Å
Authorsvan Asselt, E.J. / Dijkstra, A.J.
Citation
Journal: FEBS Lett. / Year: 1999
Title: Binding of calcium in the EF-hand of Escherichia coli lytic transglycosylase Slt35 is important for stability.
Authors: van Asselt, E.J. / Dijkstra, B.W.
#1: Journal: To be Published / 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.
#2: 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 10, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 24, 2000Provider: 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 3, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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_asym_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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: LYTIC MUREIN TRANSGLYCOSYLASE B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2744
Polymers36,0801
Non-polymers1943
Water5,999333
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.417, 67.788, 99.149
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
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 333 / 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: 2.72 Å3/Da / Density % sol: 54.77 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: PEG 20K, BICINE-NAOH, ISOPROPANOL, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal grow
*PLUS
pH: 7.2
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
17.0 mg/mlprotein1drop
210 mMTris-HCl1drop
31 %isopropanol1drop
41 mMphenylmethylsulfonyl fluoride1drop
5100 mMBicine-NaOH1reservoir
60-6 %PEG20K1reservoir

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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-2030 / Detector: IMAGE PLATE / Date: Nov 21, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→25 Å / Num. obs: 21908 / % possible obs: 92.6 % / Observed criterion σ(I): -3 / Redundancy: 3.3 % / Biso Wilson estimate: 9.4 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 16.5
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.274 / % possible all: 91
Reflection shell
*PLUS
% possible obs: 91 %

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.843refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementResolution: 2.1→20 Å / Rfactor Rfree error: 0.004 / 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
Rfree0.206 2141 10 %RANDOM
Rwork0.159 ---
all0.162 21500 --
obs0.162 21500 91.1 %-
Displacement parametersBiso mean: 17.6 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.22 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2476 0 11 333 2820
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.009
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_deg1.3
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d22.2
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.24
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.731.5
X-RAY DIFFRACTIONx_mcangle_it2.592
X-RAY DIFFRACTIONx_scbond_it32
X-RAY DIFFRACTIONx_scangle_it4.272.5
LS refinement shellResolution: 2.1→2.17 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.288 188 9.3 %
Rwork0.214 1842 -
obs--87.4 %
Software
*PLUS
Name: X-PLOR / Version: 3.843 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg22.2
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.24

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