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- PDB-6h0a: Serum paraoxonase-1 by directed evolution with the L69G/H115W/H13... -

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Basic information

Entry
Database: PDB / ID: 6h0a
TitleSerum paraoxonase-1 by directed evolution with the L69G/H115W/H134R/F222S/T332S mutations
ComponentsSerum Paraoxonase-1 by directed evolution with the L69G/H115W/H134R/F222S/T332S mutations
KeywordsHYDROLASE / beta-propeller / Lactonase / HDL / Organophosphate-hydrolase
Function / homologyTolB, C-terminal domain / 6 Propeller / Neuraminidase / Mainly Beta / BROMIDE ION / DI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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
DepositionJul 7, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 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 1.3Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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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/H115W/H134R/F222S/T332S mutations
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,6007
Polymers39,5411
Non-polymers1,0596
Water3,711206
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1330 Å2
ΔGint-17 kcal/mol
Surface area14200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.457, 94.457, 141.604
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein Serum Paraoxonase-1 by directed evolution with the L69G/H115W/H134R/F222S/T332S mutations


Mass: 39540.836 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 16 aa at the N-term are ...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 16 aa at the N-term are missing due to lack of electron density.
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#4: Sugar ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM

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Non-polymers , 5 types, 211 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: 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: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Br
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 206 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 4 Å3/Da / Density meas: 69.23 Mg/m3 / 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: ID14-4 / Wavelength: 0.9393 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 4, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9393 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 38094 / % possible obs: 99.95 % / Redundancy: 14.4 % / Rmerge(I) obs: 0.114 / Rpim(I) all: 0.031 / Rrim(I) all: 0.118 / Net I/σ(I): 28.467
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 14.6 % / Rmerge(I) obs: 0.888 / Mean I/σ(I) obs: 3 / Num. unique obs: 1853 / CC1/2: 0.867 / Rpim(I) all: 0.238 / Rrim(I) all: 0.92 / % 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 / Resolution: 2.1→47.228 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.24
RfactorNum. reflection% reflection
Rfree0.2055 2000 5.25 %
Rwork0.1878 --
obs0.1887 38094 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.1→47.228 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2582 0 58 206 2846
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072711
X-RAY DIFFRACTIONf_angle_d0.8473704
X-RAY DIFFRACTIONf_dihedral_angle_d3.6882145
X-RAY DIFFRACTIONf_chiral_restr0.061431
X-RAY DIFFRACTIONf_plane_restr0.005470
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0997-2.15220.22371390.21052519X-RAY DIFFRACTION100
2.1522-2.21040.23491410.19852532X-RAY DIFFRACTION100
2.2104-2.27540.23351390.20032517X-RAY DIFFRACTION100
2.2754-2.34890.21541410.19772552X-RAY DIFFRACTION100
2.3489-2.43280.21921420.22557X-RAY DIFFRACTION100
2.4328-2.53020.26141410.20492533X-RAY DIFFRACTION100
2.5302-2.64540.25191400.19772540X-RAY DIFFRACTION100
2.6454-2.78480.21211430.19922583X-RAY DIFFRACTION100
2.7848-2.95930.20351420.18712556X-RAY DIFFRACTION100
2.9593-3.18770.1911420.18962573X-RAY DIFFRACTION100
3.1877-3.50840.20881450.18012600X-RAY DIFFRACTION100
3.5084-4.01590.20981430.17812598X-RAY DIFFRACTION100
4.0159-5.05860.14511480.15782650X-RAY DIFFRACTION100
5.0586-47.24020.22911540.20772784X-RAY DIFFRACTION99

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