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

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Basic information

Entry
Database: PDB / ID: 5zwr
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 / (2S)-2-[3-(benzenecarbonyl)phenyl]propanoic acid
Function and homology information
Biological speciesmetagenome (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.69 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. / 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 1.1Dec 11, 2019Group: Structure summary / Category: chem_comp / Item: _chem_comp.pdbx_synonyms
Revision 1.2Nov 22, 2023Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)89,1106
Polymers88,4172
Non-polymers6934
Water20,6631147
1
B: Est-Y29
A: Est-Y29
hetero molecules

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

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

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


Theoretical massNumber of molelcules
Total (without water)356,43824
Polymers353,6678
Non-polymers2,77116
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation4_565y,-x+1,z1
Buried area20620 Å2
ΔGint-85 kcal/mol
Surface area106080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.251, 122.251, 155.824
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: 44208.398 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) metagenome (others) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


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


Mass: 254.281 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H14O3 / Comment: antiinflammatory*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1147 / Source method: isolated from a natural source / Formula: H2O

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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: 3.29 Å3/Da / Density % sol: 62.58 %
Crystal growTemperature: 295 K / Method: microbatch / pH: 4.6
Details: containing 1 M sodium citrate and 100 mM sodium acetate pH 4.6

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Data collection

DiffractionMean temperature: 100 K
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: 1.69→28.94 Å / Num. obs: 127327 / % possible obs: 99.68 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 49.85
Reflection shellResolution: 1.69→1.75 Å

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998)refinement
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4P6B

4p6b


Resolution: 1.69→28.94 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.05 / Phase error: 16.74
RfactorNum. reflection% reflection
Rfree0.1777 2006 1.58 %
Rwork0.1557 --
obs0.156 127320 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.69→28.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5994 0 50 1147 7191
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066198
X-RAY DIFFRACTIONf_angle_d0.8298418
X-RAY DIFFRACTIONf_dihedral_angle_d12.1423653
X-RAY DIFFRACTIONf_chiral_restr0.052921
X-RAY DIFFRACTIONf_plane_restr0.0061097
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6897-1.73190.19041420.17678946X-RAY DIFFRACTION100
1.7319-1.77870.20141430.17098885X-RAY DIFFRACTION100
1.7787-1.83110.20511440.16578941X-RAY DIFFRACTION100
1.8311-1.89020.1931440.16278929X-RAY DIFFRACTION100
1.8902-1.95770.18371450.16418929X-RAY DIFFRACTION100
1.9577-2.03610.18031420.16288951X-RAY DIFFRACTION100
2.0361-2.12870.18521470.16118926X-RAY DIFFRACTION100
2.1287-2.24090.20491400.168976X-RAY DIFFRACTION100
2.2409-2.38120.20681380.16228912X-RAY DIFFRACTION100
2.3812-2.5650.19921440.17038947X-RAY DIFFRACTION100
2.565-2.82290.21251430.1778987X-RAY DIFFRACTION100
2.8229-3.23090.1971470.16638976X-RAY DIFFRACTION100
3.2309-4.06890.13681450.13558979X-RAY DIFFRACTION100
4.0689-28.94140.13261420.12949030X-RAY DIFFRACTION100

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