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- PDB-6gmu: Serum paraoxonase-1 by directed evolution with the L69G/H134R/F22... -

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Basic information

Entry
Database: PDB / ID: 6gmu
TitleSerum paraoxonase-1 by directed evolution with the L69G/H134R/F222S/T332S mutations
ComponentsSerum Paraoxonase-1 by directed evolution with the L69G/H134R/F222S/T332S mutations
KeywordsHYDROLASE / beta-propeller / Lactonase / HDL / Organophosphate-hydrolase
Function / homologyTolB, C-terminal domain / 6 Propeller / Neuraminidase / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsBen-David, M. / Sussman, J.L. / Tawfik, D.S.
CitationJournal: Mol.Biol.Evol. / Year: 2020
Title: Enzyme Evolution: An Epistatic Ratchet versus a Smooth Reversible Transition.
Authors: Ben-David, M. / Soskine, M. / Dubovetskyi, A. / Cherukuri, K.P. / Dym, O. / Sussman, J.L. / Liao, Q. / Szeler, K. / Kamerlin, S.C.L. / Tawfik, D.S.
History
DepositionMay 28, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 17, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2020Group: 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Apr 8, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year
Revision 1.3Jan 17, 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
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serum Paraoxonase-1 by directed evolution with the L69G/H134R/F222S/T332S mutations
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,9627
Polymers39,4931
Non-polymers4696
Water1,18966
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area940 Å2
ΔGint-52 kcal/mol
Surface area14140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.318, 94.318, 142.410
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Serum Paraoxonase-1 by directed evolution with the L69G/H134R/F222S/T332S mutations


Mass: 39492.773 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: 1. There is no entry for this protein in the Uniprot, since the protein is a chimera (recombinant protein) of four genes (human, rabbit, mouse and rat). 2. The first 17 aa at the N-term is ...Details: 1. There is no entry for this protein in the Uniprot, since the protein is a chimera (recombinant protein) of four genes (human, rabbit, mouse and rat). 2. The first 17 aa at the N-term is missing due to lack of electron density.
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-B3P / 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL


Mass: 282.334 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H26N2O6 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 66 / 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: 3.99 Å3/Da / Density % sol: 69.2 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.1M Bis-Tris Propane pH 6.5, 0.2M Sodium Bromide and 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9724 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 14, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9724 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 18335 / % possible obs: 99.9 % / Redundancy: 13.5 % / Rmerge(I) obs: 0.157 / Rpim(I) all: 0.045 / Rrim(I) all: 0.163 / Net I/σ(I): 16.53
Reflection shellResolution: 2.7→2.75 Å / Redundancy: 13.7 % / Rmerge(I) obs: 0.853 / Mean I/σ(I) obs: 2.96 / Num. unique obs: 881 / CC1/2: 0.927 / Rpim(I) all: 0.238 / Rrim(I) all: 0.886 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3SRG

3srg


Resolution: 2.7→33.308 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.38
RfactorNum. reflection% reflection
Rfree0.2285 1829 10 %
Rwork0.1788 --
obs0.1839 18284 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.7→33.308 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2603 0 24 66 2693
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082689
X-RAY DIFFRACTIONf_angle_d0.8993675
X-RAY DIFFRACTIONf_dihedral_angle_d7.5561579
X-RAY DIFFRACTIONf_chiral_restr0.057419
X-RAY DIFFRACTIONf_plane_restr0.006473
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.77240.30831380.21551238X-RAY DIFFRACTION100
2.7724-2.85390.25111370.19161236X-RAY DIFFRACTION100
2.8539-2.9460.24491390.18041245X-RAY DIFFRACTION100
2.946-3.05120.22041370.17231239X-RAY DIFFRACTION100
3.0512-3.17330.22261370.17861233X-RAY DIFFRACTION100
3.1733-3.31760.23751390.17591249X-RAY DIFFRACTION100
3.3176-3.49230.23531390.17391260X-RAY DIFFRACTION100
3.4923-3.71090.24971390.17381250X-RAY DIFFRACTION100
3.7109-3.99690.21671410.16911259X-RAY DIFFRACTION100
3.9969-4.39840.20731410.15021269X-RAY DIFFRACTION100
4.3984-5.03290.16141420.1431285X-RAY DIFFRACTION100
5.0329-6.33380.22311460.1871310X-RAY DIFFRACTION100
6.3338-330.27261540.23091382X-RAY DIFFRACTION100

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