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- PDB-4q1u: Serum paraoxonase-1 by directed evolution with the K192Q mutation -

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Basic information

Entry
Database: PDB / ID: 4q1u
TitleSerum paraoxonase-1 by directed evolution with the K192Q mutation
ComponentsSerum paraoxonase/arylesterase 1
KeywordsHYDROLASE / 6-blades-propeller fold / lactonase
Function / homologyTolB, C-terminal domain / 6 Propeller / Neuraminidase / Mainly Beta / BROMIDE ION / PHOSPHATE ION
Function and homology information
Biological specieshybrid (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.302 Å
AuthorsBen-David, M. / Sussman, J.L. / Tawfik, D.S.
CitationJournal: J.Mol.Biol. / Year: 2015
Title: Catalytic stimulation by restrained active-site floppiness-the case of high density lipoprotein-bound serum paraoxonase-1.
Authors: Ben-David, M. / Sussman, J.L. / Maxwell, C.I. / Szeler, K. / Kamerlin, S.C. / Tawfik, D.S.
History
DepositionApr 4, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 18, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2015Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serum paraoxonase/arylesterase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,3767
Polymers39,5751
Non-polymers8016
Water2,396133
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)93.514, 93.514, 144.007
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/arylesterase 1 / Aromatic esterase 1 / A-esterase 1 / Serum aryldialkylphosphatase 1


Mass: 39574.883 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) hybrid (others) / Plasmid: pET32 / Production host: Escherichia coli (E. coli) / Strain (production host): Origami DE3
References: arylesterase, quorum-quenching N-acyl-homoserine lactonase, aryldialkylphosphatase
#3: 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, 138 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#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.: 133 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsTHE PROTEIN SEQUENCE IS A CHIMERIC MIXTURE OF THE PARAOXONASE-1 GENES OF HOMO SAPIENS, ORYCTOLAGUS ...THE PROTEIN SEQUENCE IS A CHIMERIC MIXTURE OF THE PARAOXONASE-1 GENES OF HOMO SAPIENS, ORYCTOLAGUS CUNICULUS, MUS MUSCULUS, AND RATTUS RATTUS WITH AN ADDITIONAL K192Q MUTATION.

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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: 3.98 Å3/Da / Density % sol: 69.1 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 20% PEG3350, 0.2 M sodium bromide, 0.1 M Bis-tris propane, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 27, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.302→44.472 Å / Num. all: 29105 / Num. obs: 29105 / % possible obs: 100 % / Observed criterion σ(F): 2.3 / Observed criterion σ(I): 2.3 / Redundancy: 14.1 % / Biso Wilson estimate: 34.38 Å2 / Rmerge(I) obs: 0.11 / Rsym value: 0.125 / Net I/σ(I): 27.7
Reflection shellResolution: 2.302→2.34 Å / Redundancy: 13.9 % / Rmerge(I) obs: 0.706 / Mean I/σ(I) obs: 4.3 / Num. unique all: 1424 / Rsym value: 0.684 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.6.0111refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3SRE

3sre


Resolution: 2.302→44.47 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.936 / SU B: 3.648 / SU ML: 0.091 / Cross valid method: THROUGHOUT / σ(F): 2.3 / ESU R: 0.165 / ESU R Free: 0.155 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.21191 1477 5.1 %RANDOM
Rwork0.17583 ---
obs0.17773 27542 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.401 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å2-0 Å2-0 Å2
2--0 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.302→44.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2529 0 33 133 2695
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0280.0222623
X-RAY DIFFRACTIONr_angle_refined_deg2.1751.9623592
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5365326
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.07924.912114
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.31315386
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.309156
X-RAY DIFFRACTIONr_chiral_restr0.1620.2422
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0211988
LS refinement shellResolution: 2.302→2.361 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.252 84 -
Rwork0.209 1804 -
obs--99.79 %

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