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- PDB-5o8x: The X-ray Structure of Catenated Lytic Transglycosylase SltB1 fro... -

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Basic information

Entry
Database: PDB / ID: 5o8x
TitleThe X-ray Structure of Catenated Lytic Transglycosylase SltB1 from Pseudomonas aeruginosa
ComponentsSoluble lytic transglycosylase B
KeywordsLYASE / Lytic Transglycosylase
Function / homology
Function and homology information


peptidoglycan lytic transglycosylase activity / peptidoglycan catabolic process / metal 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
CACODYLATE ION / : / Soluble lytic transglycosylase B
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsDominguez-Gil, T. / Molina, R.
CitationJournal: Biochemistry / Year: 2017
Title: X-ray Structure of Catenated Lytic Transglycosylase SltB1.
Authors: Dominguez-Gil, T. / Molina, R. / Dik, D.A. / Spink, E. / Mobashery, S. / Hermoso, J.A.
History
DepositionJun 14, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 29, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 13, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.3May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Soluble lytic transglycosylase B
B: Soluble lytic transglycosylase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,3887
Polymers68,9412
Non-polymers4465
Water1,31573
1
A: Soluble lytic transglycosylase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,7404
Polymers34,4711
Non-polymers2693
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Soluble lytic transglycosylase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6483
Polymers34,4711
Non-polymers1772
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)115.064, 116.358, 54.865
Angle α, β, γ (deg.)90.00, 118.41, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Soluble lytic transglycosylase B


Mass: 34470.645 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria)
Gene: B0B20_29725, BZY57_15515, BZY58_10660, BZY59_02470, BZY60_10655
Production host: Escherichia coli (E. coli) / References: UniProt: A0A1T2V5N0, UniProt: Q9HX24*PLUS
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate


Mass: 136.989 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6AsO2
#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.: 73 / 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: 2.34 Å3/Da / Density % sol: 47.5 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 1M Na-citrate, 0.1M Na-cacodylate pH=6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9796 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2.5→48.26 Å / Num. obs: 21993 / % possible obs: 99.9 % / Redundancy: 6.7 % / Net I/σ(I): 11.4

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→48.258 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.03
RfactorNum. reflection% reflection
Rfree0.2292 1163 5.3 %
Rwork0.177 --
obs0.1798 21953 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.5→48.258 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4832 0 18 73 4923
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034999
X-RAY DIFFRACTIONf_angle_d0.8386770
X-RAY DIFFRACTIONf_dihedral_angle_d17.3752955
X-RAY DIFFRACTIONf_chiral_restr0.07700
X-RAY DIFFRACTIONf_plane_restr0.003895
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5001-2.61390.37171330.28912621X-RAY DIFFRACTION100
2.6139-2.75170.34891610.27332558X-RAY DIFFRACTION100
2.7517-2.92410.33291730.25532565X-RAY DIFFRACTION100
2.9241-3.14980.28371320.21942609X-RAY DIFFRACTION100
3.1498-3.46670.27731320.18392558X-RAY DIFFRACTION100
3.4667-3.96820.22281460.16032608X-RAY DIFFRACTION100
3.9682-4.99860.15681400.13352623X-RAY DIFFRACTION100
4.9986-48.26680.18171460.15192648X-RAY DIFFRACTION100

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