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- PDB-5zwq: Structural Basis for the Enantioselectivity of Est-Y29 toward (S)... -

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Basic information

Entry
Database: PDB / ID: 5zwq
TitleStructural Basis for the Enantioselectivity of Est-Y29 toward (S)-ketoprofen
ComponentsEst-Y29
KeywordsHYDROLASE / Est-Y29 / esterase / ketoprofen / 2-(3-benzoylphenyl)-propionic acid
Function / homologyBeta-lactamase / DD-peptidase/beta-lactamase superfamily / 3-Layer(aba) Sandwich / Alpha Beta / Chem-9KF
Function and homology information
Biological speciesmetagenome (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.797 Å
AuthorsNgo, D.T. / Oh, C. / Park, K. / Nguyen, L. / Byun, H.M. / Kim, S. / Yoon, S. / Ryu, Y. / Ryu, B.H. / Kim, T.D. ...Ngo, D.T. / Oh, C. / Park, K. / Nguyen, L. / Byun, H.M. / Kim, S. / Yoon, S. / Ryu, Y. / Ryu, B.H. / Kim, T.D. / Yang, J.W. / Kim, K.K.
CitationJournal: Acs Catalysis / Year: 2019
Title: Structural Basis for the Enantioselectivity of Esterase Est-Y29 toward (S)-Ketoprofen
Authors: Ngo, T.D. / Oh, C. / Mizar, P. / Baek, M. / Park, K. / Nguyen, L. / Byeon, H. / Yoon, S. / Ryu, B.H. / Kim, T.D. / Yang, J.W. / Seok, C. / Lee, S.S. / Kim, K.K.
History
DepositionMay 16, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 13, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Est-Y29
B: Est-Y29
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,3566
Polymers88,6072
Non-polymers7494
Water14,898827
1
A: Est-Y29
B: Est-Y29
hetero molecules

A: Est-Y29
B: Est-Y29
hetero molecules

A: Est-Y29
B: Est-Y29
hetero molecules

A: Est-Y29
B: Est-Y29
hetero molecules


Theoretical massNumber of molelcules
Total (without water)357,42424
Polymers354,4288
Non-polymers2,99516
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-x-1,-y-1,z1
crystal symmetry operation3_455-y-1,x,z1
crystal symmetry operation4_545y,-x-1,z1
Buried area20830 Å2
ΔGint-80 kcal/mol
Surface area106510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.280, 122.280, 155.238
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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Components

#1: Protein Est-Y29


Mass: 44303.516 Da / Num. of mol.: 2 / Mutation: A348V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) metagenome (others) / Plasmid: pQE30 / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-9KF / ethyl (2S)-2-[3-(benzenecarbonyl)phenyl]propanoate


Mass: 282.334 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H18O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 827 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsThe sequence reference of the protein is not available at UNIPROT at the time of data processing. ...The sequence reference of the protein is not available at UNIPROT at the time of data processing. Residue VAL 348 represented mutation (A348V).

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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: 3.38 Å3/Da / Density % sol: 63.63 %
Crystal growTemperature: 295 K / Method: microbatch / pH: 4.6 / Details: 1 M sodium citrate, 100 mM sodium acetate pH 4.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 15, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.797→29.13 Å / Num. obs: 105326 / % possible obs: 99.68 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 24.71
Reflection shellResolution: 1.797→1.861 Å

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.797→29.13 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 0.23 / Phase error: 18.27
RfactorNum. reflection% reflection
Rfree0.1887 5256 4.99 %
Rwork0.1622 --
obs0.1635 105316 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.797→29.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5996 0 54 827 6877
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0126206
X-RAY DIFFRACTIONf_angle_d1.1598428
X-RAY DIFFRACTIONf_dihedral_angle_d18.0562238
X-RAY DIFFRACTIONf_chiral_restr0.072922
X-RAY DIFFRACTIONf_plane_restr0.0071096
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.797-1.81740.2771620.22763180X-RAY DIFFRACTION95
1.8174-1.83880.25841710.21783331X-RAY DIFFRACTION100
1.8388-1.86120.25741700.20893342X-RAY DIFFRACTION100
1.8612-1.88480.24491700.19563325X-RAY DIFFRACTION100
1.8848-1.90960.24431770.18533357X-RAY DIFFRACTION100
1.9096-1.93570.19581780.17333345X-RAY DIFFRACTION100
1.9357-1.96340.19721610.17123342X-RAY DIFFRACTION100
1.9634-1.99270.20891760.16513285X-RAY DIFFRACTION100
1.9927-2.02380.19291700.16043346X-RAY DIFFRACTION100
2.0238-2.0570.18021590.16493351X-RAY DIFFRACTION100
2.057-2.09240.21811740.16393322X-RAY DIFFRACTION100
2.0924-2.13050.18261680.16173360X-RAY DIFFRACTION100
2.1305-2.17140.19072000.16253327X-RAY DIFFRACTION100
2.1714-2.21570.19311580.16883363X-RAY DIFFRACTION100
2.2157-2.26390.20331770.17133332X-RAY DIFFRACTION100
2.2639-2.31650.21341790.16743333X-RAY DIFFRACTION100
2.3165-2.37450.21971880.16753306X-RAY DIFFRACTION100
2.3745-2.43860.20471710.17463362X-RAY DIFFRACTION100
2.4386-2.51030.21071780.17363339X-RAY DIFFRACTION100
2.5103-2.59130.20181700.17663337X-RAY DIFFRACTION100
2.5913-2.68390.19411680.17983337X-RAY DIFFRACTION100
2.6839-2.79130.20751730.17763351X-RAY DIFFRACTION100
2.7913-2.91820.20111700.1713360X-RAY DIFFRACTION100
2.9182-3.07190.18811910.16993326X-RAY DIFFRACTION100
3.0719-3.26410.20561900.1763308X-RAY DIFFRACTION100
3.2641-3.51570.19971660.15873390X-RAY DIFFRACTION100
3.5157-3.86880.17121700.14293360X-RAY DIFFRACTION100
3.8688-4.42690.12621650.12813351X-RAY DIFFRACTION100
4.4269-5.57110.152200.133315X-RAY DIFFRACTION100
5.5711-29.13420.16191860.15063377X-RAY DIFFRACTION99

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