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- PDB-1d0l: THE ESCHERICHIA COLI LYTIC TRANSGLYCOSYLASE SLT35 IN COMPLEX WITH... -

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Basic information

Entry
Database: PDB / ID: 1d0l
TitleTHE ESCHERICHIA COLI LYTIC TRANSGLYCOSYLASE SLT35 IN COMPLEX WITH BULGECIN A
Components35KD SOLUBLE LYTIC TRANSGLYCOSYLASE
KeywordsTRANSFERASE / ALPHA-HELICAL PROTEIN WITH A FIVE STRANDED ANTI-PARALLEL 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
Chem-BLG / Membrane-bound lytic murein transglycosylase B
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.97 Å
Authorsvan Asselt, E.J. / Kalk, K.H. / Dijkstra, B.W.
CitationJournal: Biochemistry / Year: 2000
Title: Crystallographic studies of the interactions of Escherichia coli lytic transglycosylase Slt35 with peptidoglycan.
Authors: van Asselt, E.J. / Kalk, K.H. / Dijkstra, B.W.
History
DepositionSep 12, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 6, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / diffrn_source ...database_2 / diffrn_source / 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 / _diffrn_source.pdbx_synchrotron_site / _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 7, 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: 35KD SOLUBLE LYTIC TRANSGLYCOSYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,6723
Polymers36,0801
Non-polymers5932
Water5,152286
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.395, 67.785, 97.735
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 35KD SOLUBLE LYTIC TRANSGLYCOSYLASE / SLT35


Mass: 36079.660 Da / Num. of mol.: 1 / Mutation: L40M, L41V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / 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-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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 286 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHREE DOMAIN STRUCTURE: ALPHA DOMAIN WITH RESIDUES 40-98, 170-215, BETA DOMAIN WITH RESIDUES 270- ...THREE DOMAIN STRUCTURE: ALPHA DOMAIN WITH RESIDUES 40-98, 170-215, BETA DOMAIN WITH RESIDUES 270-329, CORE DOMAIN WITH RESIDUES 109-169, 216-269, 330-361.

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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: 2.68 Å3/Da / Density % sol: 54.09 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: BICINE-NAOH, ISOPRAPANOL, PEG20K, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal grow
*PLUS
Components of the solutions
*PLUS
Conc.: 0.1 M / Common name: bicine-NaOH

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.9057
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 29, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9057 Å / Relative weight: 1
ReflectionResolution: 1.97→32.8 Å / Num. all: 205843 / Num. obs: 27987 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 7.3 % / Biso Wilson estimate: 12 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 33.4
Reflection shellResolution: 1.97→2 Å / Redundancy: 6 % / Rmerge(I) obs: 0.249 / % possible all: 85
Reflection
*PLUS
Num. measured all: 205843
Reflection shell
*PLUS
% possible obs: 85 %

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.843refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementResolution: 1.97→20 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.0001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.2 2763 10.1 %RANDOM
Rwork0.168 ---
obs0.17 27351 97.4 %-
all-27351 --
Displacement parametersBiso mean: 23.5 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.13 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 1.97→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2535 0 36 286 2857
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_d21.7
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_it1.511.5
X-RAY DIFFRACTIONx_mcangle_it2.32
X-RAY DIFFRACTIONx_scbond_it2.722
X-RAY DIFFRACTIONx_scangle_it4.152.5
LS refinement shellResolution: 1.97→2.03 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 12
RfactorNum. reflection% reflection
Rfree0.235 204 10.1 %
Rwork0.198 1817 -
obs--87.2 %
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_deg21.7
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.05

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