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- PDB-5k1r: Structure of Burkholderia pseudomallei K96243 sphingosine-1-phosp... -

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Basic information

Entry
Database: PDB / ID: 5k1r
TitleStructure of Burkholderia pseudomallei K96243 sphingosine-1-phosphate lyase Bpss2021
ComponentsBurkholderia pseudomallei sphingosine-1-phosphate lyase Bpss2021
KeywordsLYASE / Sphingosine-1-phosphate Sphingosine-1-phosphate lyase Burkholderia pseudomallei PLP
Function / homology
Function and homology information


carboxy-lyase activity / carboxylic acid metabolic process / pyridoxal phosphate binding
Similarity search - Function
Pyridoxal phosphate-dependent decarboxylase / Pyridoxal-dependent decarboxylase conserved domain / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
PYRIDOXAL-5'-PHOSPHATE / Putative decarboxylase
Similarity search - Component
Biological speciesBurkholderia pseudomallei K96243 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.104 Å
AuthorsMclean, C.J. / Campopiano, D.J. / Marles-Wright, J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/M010996/1 United Kingdom
CitationJournal: J. Lipid Res. / Year: 2017
Title: Characterization of homologous sphingosine-1-phosphate lyase isoforms in the bacterial pathogen Burkholderia pseudomallei.
Authors: McLean, C.J. / Marles-Wright, J. / Custodio, R. / Lowther, J. / Kennedy, A.J. / Pollock, J. / Clarke, D.J. / Brown, A.R. / Campopiano, D.J.
History
DepositionMay 18, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Nov 2, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Dec 6, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Burkholderia pseudomallei sphingosine-1-phosphate lyase Bpss2021
B: Burkholderia pseudomallei sphingosine-1-phosphate lyase Bpss2021
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,0954
Polymers106,6002
Non-polymers4942
Water5,405300
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13920 Å2
ΔGint-78 kcal/mol
Surface area29540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.600, 126.776, 59.725
Angle α, β, γ (deg.)90.00, 97.51, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Burkholderia pseudomallei sphingosine-1-phosphate lyase Bpss2021


Mass: 53300.129 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia pseudomallei K96243 (bacteria)
Gene: BPSS2021 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q63IP8
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate / Pyridoxal phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 300 / 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: 2.16 Å3/Da / Density % sol: 43.16 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: Midas B11 20 % v/v polypropylene glycol 400 10 % 1-propanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 5, 2016
RadiationMonochromator: Single Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.104→43.27 Å / Num. obs: 101458 / % possible obs: 100 % / Redundancy: 5.5 % / Biso Wilson estimate: 27.8 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.1336 / Rsym value: 0.1475 / Net I/σ(I): 8.57
Reflection shellHighest resolution: 2.104 Å

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XDSdata scaling
Aimlessdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3MAD

3mad


Resolution: 2.104→43.271 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2298 5148 5.21 %
Rwork0.1736 --
obs0.1765 98845 98.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.104→43.271 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6860 0 30 300 7190
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0137082
X-RAY DIFFRACTIONf_angle_d1.2179609
X-RAY DIFFRACTIONf_dihedral_angle_d12.4344119
X-RAY DIFFRACTIONf_chiral_restr0.06993
X-RAY DIFFRACTIONf_plane_restr0.0081266
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1039-2.12780.30062000.28132946X-RAY DIFFRACTION90
2.1278-2.15290.34971420.273037X-RAY DIFFRACTION99
2.1529-2.17910.32111800.26823151X-RAY DIFFRACTION99
2.1791-2.20670.33022380.28863082X-RAY DIFFRACTION99
2.2067-2.23570.33791470.313106X-RAY DIFFRACTION99
2.2357-2.26640.41231710.35433118X-RAY DIFFRACTION97
2.2664-2.29870.34371650.30653241X-RAY DIFFRACTION99
2.2987-2.3330.2861580.25983046X-RAY DIFFRACTION99
2.333-2.36950.33411850.2443132X-RAY DIFFRACTION99
2.3695-2.40830.29571820.24773096X-RAY DIFFRACTION98
2.4083-2.44990.27851670.23683149X-RAY DIFFRACTION99
2.4499-2.49440.30081920.23243158X-RAY DIFFRACTION99
2.4944-2.54240.26491780.19813109X-RAY DIFFRACTION99
2.5424-2.59430.2311680.17613255X-RAY DIFFRACTION100
2.5943-2.65070.26611660.17873071X-RAY DIFFRACTION100
2.6507-2.71230.24421820.17883237X-RAY DIFFRACTION98
2.7123-2.78010.24561610.16783053X-RAY DIFFRACTION99
2.7801-2.85530.24281760.16723214X-RAY DIFFRACTION100
2.8553-2.93930.25361800.16673123X-RAY DIFFRACTION99
2.9393-3.03420.23431760.15113195X-RAY DIFFRACTION100
3.0342-3.14260.19981710.15153196X-RAY DIFFRACTION99
3.1426-3.26830.23071550.15983106X-RAY DIFFRACTION99
3.2683-3.4170.21541400.14193214X-RAY DIFFRACTION99
3.417-3.59710.18541650.14683108X-RAY DIFFRACTION98
3.5971-3.82240.16691450.13913069X-RAY DIFFRACTION97
3.8224-4.11730.17921740.13033106X-RAY DIFFRACTION97
4.1173-4.53120.1842230.12413034X-RAY DIFFRACTION97
4.5312-5.18590.20641600.13393096X-RAY DIFFRACTION97
5.1859-6.53010.20671470.16273143X-RAY DIFFRACTION98
6.5301-43.27980.1951540.1623106X-RAY DIFFRACTION97

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