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- PDB-5ohu: The X-ray Structure of Lytic Transglycosylase Slt from Pseudomona... -

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Basic information

Entry
Database: PDB / ID: 5ohu
TitleThe X-ray Structure of Lytic Transglycosylase Slt from Pseudomonas aeruginosa
ComponentsSoluble lytic murein transglycosylase
KeywordsLYASE / Lytic Transglycosylase
Function / homology
Function and homology information


hydrolase activity, hydrolyzing O-glycosyl compounds / periplasmic space
Similarity search - Function
Lytic transglycosylase, superhelical linker / Soluble lytic murein transglycosylase L domain / Lytic transglycosylase, superhelical U-shaped / Lytic transglycosylase, superhelical linker domain superfamily / Transglycosylase SLT domain 1 / Transglycosylase SLT domain / Lysozyme-like domain superfamily
Similarity search - Domain/homology
PHOSPHATE ION / Transglycosylase SLT domain-containing protein / Probable soluble lytic transglycosylase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 2.2 Å
AuthorsBatuecas, M.T. / Dominguez-Gil, T. / Hermoso, J.A.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Exolytic and endolytic turnover of peptidoglycan by lytic transglycosylase Slt ofPseudomonas aeruginosa.
Authors: Lee, M. / Batuecas, M.T. / Tomoshige, S. / Dominguez-Gil, T. / Mahasenan, K.V. / Dik, D.A. / Hesek, D. / Millan, C. / Uson, I. / Lastochkin, E. / Hermoso, J.A. / Mobashery, S.
History
DepositionJul 18, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 18, 2018Provider: repository / Type: Initial release
Revision 1.1May 2, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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 murein transglycosylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,1539
Polymers73,3931
Non-polymers7608
Water6,539363
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1410 Å2
ΔGint-41 kcal/mol
Surface area29030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)163.981, 163.981, 56.706
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

#1: Protein Soluble lytic murein transglycosylase


Mass: 73393.273 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: slt, AOY09_04369, PAMH19_2049 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A069QJX4, UniProt: Q9HZI6*PLUS, Lyases; Carbon-oxygen lyases; Acting on polysaccharides
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 363 / 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 Å3/Da / Density % sol: 58.98 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: K/Na phosphate 1M

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→47.34 Å / Num. obs: 44540 / % possible obs: 99.98 % / Redundancy: 19.4 % / CC1/2: 0.99 / Rpim(I) all: 0.05 / Net I/σ(I): 14.8
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 19.3 % / Mean I/σ(I) obs: 1.35 / Num. unique all: 3846 / CC1/2: 0.72 / Rpim(I) all: 0.86 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 2.2→47.337 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.64
RfactorNum. reflection% reflection
Rfree0.2378 1995 4.48 %
Rwork0.1818 --
obs0.1843 44540 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.2→47.337 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4969 0 40 363 5372
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075173
X-RAY DIFFRACTIONf_angle_d0.8777027
X-RAY DIFFRACTIONf_dihedral_angle_d17.0943099
X-RAY DIFFRACTIONf_chiral_restr0.05731
X-RAY DIFFRACTIONf_plane_restr0.006913
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.2550.39211420.33323020X-RAY DIFFRACTION100
2.255-2.3160.35871410.27843018X-RAY DIFFRACTION100
2.316-2.38410.2861430.25292989X-RAY DIFFRACTION100
2.3841-2.46110.30831430.23253022X-RAY DIFFRACTION100
2.4611-2.5490.29631410.20943021X-RAY DIFFRACTION100
2.549-2.65110.23791380.19683002X-RAY DIFFRACTION100
2.6511-2.77170.25361480.18923040X-RAY DIFFRACTION100
2.7717-2.91790.22961400.17683013X-RAY DIFFRACTION100
2.9179-3.10060.23841420.17953048X-RAY DIFFRACTION100
3.1006-3.340.23831420.16983056X-RAY DIFFRACTION100
3.34-3.6760.21291410.15773020X-RAY DIFFRACTION100
3.676-4.20760.181420.13263061X-RAY DIFFRACTION100
4.2076-5.30.19471400.13493075X-RAY DIFFRACTION100
5.3-47.34820.20011520.17223160X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 38.2679 Å / Origin y: 89.8571 Å / Origin z: 19.5337 Å
111213212223313233
T0.147 Å20.0067 Å2-0.018 Å2-0.1846 Å2-0.0037 Å2--0.1593 Å2
L0.5229 °2-0.4088 °20.0381 °2-0.3098 °20.0429 °2--0.13 °2
S-0.0069 Å °-0.0217 Å °0.1241 Å °0.0151 Å °0.0214 Å °-0.1674 Å °-0.0129 Å °0.0573 Å °-0.0124 Å °
Refinement TLS groupSelection details: all

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