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- PDB-6igb: the structure of Pseudomonas aeruginosa Periplasmic gluconolacton... -

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Basic information

Entry
Database: PDB / ID: 6igb
Titlethe structure of Pseudomonas aeruginosa Periplasmic gluconolactonase, PpgL
ComponentsPeriplasmic gluconolactonase, PpgL
KeywordsHYDROLASE / 6-phosphogluconolactonase activity
Function / homology
Function and homology information


6-phosphogluconolactonase activity / cytosol
Similarity search - Function
: / Lactonase, 7-bladed beta propeller / Lactonase, 7-bladed beta-propeller / Nitrous oxide reductase, N-terminal / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / WD40/YVTN repeat-like-containing domain superfamily / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / Periplasmic gluconolactonase, PpgL
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.651 Å
AuthorsSong, Y.J. / Shen, Y.L. / Wang, K.L. / Li, T. / Zhu, Y.B. / Li, C.C. / He, L.H. / Zhao, N.L. / Zhao, C. / Yang, J. ...Song, Y.J. / Shen, Y.L. / Wang, K.L. / Li, T. / Zhu, Y.B. / Li, C.C. / He, L.H. / Zhao, N.L. / Zhao, C. / Yang, J. / Huang, Q. / Mu, X.Y.
CitationJournal: Infect.Immun. / Year: 2019
Title: Structural and Functional Insights into PpgL, a Metal-Independent beta-Propeller Gluconolactonase That Contributes toPseudomonas aeruginosaVirulence.
Authors: Song, Y.J. / Wang, K.L. / Shen, Y.L. / Gao, J. / Li, T. / Zhu, Y.B. / Li, C.C. / He, L.H. / Zhou, Q.X. / Zhao, N.L. / Zhao, C. / Yang, J. / Huang, Q. / Mu, X.Y. / Li, H. / Dou, D.F. / Liu, C. ...Authors: Song, Y.J. / Wang, K.L. / Shen, Y.L. / Gao, J. / Li, T. / Zhu, Y.B. / Li, C.C. / He, L.H. / Zhou, Q.X. / Zhao, N.L. / Zhao, C. / Yang, J. / Huang, Q. / Mu, X.Y. / Li, H. / Dou, D.F. / Liu, C. / He, J.H. / Sun, B. / Bao, R.
History
DepositionSep 25, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 21, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 28, 2018Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.year
Revision 1.2Jun 5, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Nov 22, 2023Group: 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: Periplasmic gluconolactonase, PpgL
B: Periplasmic gluconolactonase, PpgL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,6556
Polymers78,3452
Non-polymers3104
Water5,495305
1
A: Periplasmic gluconolactonase, PpgL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,3283
Polymers39,1721
Non-polymers1552
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area160 Å2
ΔGint-12 kcal/mol
Surface area14110 Å2
MethodPISA
2
B: Periplasmic gluconolactonase, PpgL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,3283
Polymers39,1721
Non-polymers1552
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area170 Å2
ΔGint-12 kcal/mol
Surface area14190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.763, 91.763, 170.708
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Periplasmic gluconolactonase, PpgL


Mass: 39172.441 Da / Num. of mol.: 2 / Fragment: UNP residues 25-388
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Strain: PAO1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9HWH7
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 305 / 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: 2.29 Å3/Da / Density % sol: 46.37 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.2M Ammonium sulphate, 0.1M Sodium acetate pH 4.6,30% PEG 2000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jan 24, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 1.651→39.9 Å / Num. obs: 88173 / % possible obs: 99.98 % / Redundancy: 17.6 % / Rmerge(I) obs: 0.178 / Net I/σ(I): 18.692
Reflection shellResolution: 1.651→1.71 Å / Rmerge(I) obs: 0.807 / Num. unique obs: 8687

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
HKL-2000data reduction
PHENIXmodel building
PHENIXphasing
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4qrj

4qrj


Resolution: 1.651→38.697 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.42 / Phase error: 21.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2215 2000 2.27 %
Rwork0.1957 --
obs0.1963 88037 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.651→38.697 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5530 0 18 305 5853
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0185678
X-RAY DIFFRACTIONf_angle_d1.5427722
X-RAY DIFFRACTIONf_dihedral_angle_d23.9962056
X-RAY DIFFRACTIONf_chiral_restr0.197832
X-RAY DIFFRACTIONf_plane_restr0.0091052
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.651-1.69230.34391410.34456058X-RAY DIFFRACTION100
1.6923-1.7380.33211410.3196053X-RAY DIFFRACTION100
1.738-1.78920.31241410.29336054X-RAY DIFFRACTION100
1.7892-1.84690.29561410.26336076X-RAY DIFFRACTION100
1.8469-1.91290.27961410.23186083X-RAY DIFFRACTION100
1.9129-1.98950.24591420.20736079X-RAY DIFFRACTION100
1.9895-2.08010.23541410.19126079X-RAY DIFFRACTION100
2.0801-2.18970.23161420.17856098X-RAY DIFFRACTION100
2.1897-2.32690.20621420.16726118X-RAY DIFFRACTION100
2.3269-2.50650.19381430.16816135X-RAY DIFFRACTION100
2.5065-2.75870.19891430.1786163X-RAY DIFFRACTION100
2.7587-3.15780.2461440.17476217X-RAY DIFFRACTION100
3.1578-3.97780.18181450.16456270X-RAY DIFFRACTION100
3.9778-38.70730.18171530.18336554X-RAY DIFFRACTION100

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