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- PDB-4hhq: Serum paraoxonase-1 by directed evolution with the H115Q and H134... -

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Basic information

Entry
Database: PDB / ID: 4hhq
TitleSerum paraoxonase-1 by directed evolution with the H115Q and H134Q mutations
ComponentsSERUM PARAOXONASE BY DIRECTED EVOLUTION
KeywordsHYDROLASE / 6-blades -propeller fold
Function / homologyTolB, C-terminal domain / 6 Propeller / Neuraminidase / Mainly Beta / BROMIDE ION
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsMoshe, B.-D. / Grzegorz, W. / Mikael, E. / Israel, S. / Joel, L.S. / Dan, S.T.
CitationJournal: J.Mol.Biol. / Year: 2013
Title: Catalytic metal ion rearrangements underline promiscuity and evolvability of a metalloenzyme.
Authors: Ben-David, M. / Wieczorek, G. / Elias, M. / Silman, I. / Sussman, J.L. / Tawfik, D.S.
History
DepositionOct 10, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SERUM PARAOXONASE BY DIRECTED EVOLUTION
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,4147
Polymers39,5841
Non-polymers8306
Water2,648147
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)93.789, 93.789, 144.602
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 BY DIRECTED EVOLUTION


Mass: 39583.914 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others)
Gene: Homo sapiens, oryctolagus cuniculus, mus musculus, rattus rattus
Plasmid details: FROM SHUFFLED GENES OF HOMO SAPIENS, ORYCTOLAGUS CUNICULUS, MUS MUSCULUS, AND RATTUS
Plasmid: PET32 / Production host: Escherichia coli (E. coli) / Strain (production host): Origami DE3
References: arylesterase, aryldialkylphosphatase, 1,4-lactonase
#2: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 79.904 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Br
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 147 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsCRYSTALLIZED SEQUENCE REPRESENTS A CHIMERIC CONSTRUCT OF PARAOXONASE-1 FROM FOUR DIFFERENCE SOURCES

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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: 4.02 Å3/Da / Density % sol: 69.38 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 20% PEG 3350, 0.2M NaBr, 0.1M 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: ID14-1 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 14, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.3→39.34 Å / Num. all: 27832 / Num. obs: 27832 / % possible obs: 100 % / Redundancy: 13.5 % / Biso Wilson estimate: 30.187 Å2 / Rmerge(I) obs: 0.062 / Rsym value: 0.086 / Net I/σ(I): 30.93
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 8.7 % / Rmerge(I) obs: 0.483 / Mean I/σ(I) obs: 4.2 / Num. unique all: 2860 / Rsym value: 0.519 / % 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 / Resolution: 2.3→39.34 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.922 / SU B: 3.66 / SU ML: 0.091 / Cross valid method: THROUGHOUT / ESU R: 0.165 / ESU R Free: 0.159 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2181 1491 5.1 %RANDOM
Rwork0.1766 ---
all0.17871 27832 --
obs0.17871 27832 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.187 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2---0.01 Å2-0 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.3→39.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2519 0 29 147 2695
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0290.0222615
X-RAY DIFFRACTIONr_angle_refined_deg2.1911.9633576
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3855323
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.24125.043117
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.75915401
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.6157
X-RAY DIFFRACTIONr_chiral_restr0.1710.2417
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0211981
LS refinement shellResolution: 2.301→2.361 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 101 -
Rwork0.231 1832 -
obs--99.95 %

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