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

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Basic information

Entry
Database: PDB / ID: 5zwv
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
Function and homology information
Biological speciesmetagenome (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.099 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. / Yang, J.W.
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 17, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 13, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)88,6292
Polymers88,6292
Non-polymers00
Water13,872770
1
B: Est-Y29
A: Est-Y29

B: Est-Y29
A: Est-Y29

B: Est-Y29
A: Est-Y29

B: Est-Y29
A: Est-Y29


Theoretical massNumber of molelcules
Total (without water)354,5168
Polymers354,5168
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Buried area19800 Å2
ΔGint-84 kcal/mol
Surface area105350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.815, 121.815, 155.365
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: 44314.500 Da / Num. of mol.: 2 / Mutation: F125W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) metagenome (others) / Production host: Escherichia coli (E. coli)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 770 / 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 TRP 125 represented mutation (F125W).

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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: 3.25 Å3/Da / Density % sol: 62.17 %
Crystal growTemperature: 287 K / Method: microbatch / pH: 4.6
Details: 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: Jul 23, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.099→39.285 Å / Num. obs: 65894 / % possible obs: 99.92 % / Redundancy: 7.5 % / Net I/σ(I): 34.53
Reflection shellResolution: 2.099→2.174 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: 2.099→39.285 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.17
RfactorNum. reflection% reflection
Rfree0.1901 1994 3.03 %
Rwork0.1501 --
obs0.1513 65894 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.099→39.285 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6022 0 0 770 6792
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076201
X-RAY DIFFRACTIONf_angle_d0.8338433
X-RAY DIFFRACTIONf_dihedral_angle_d2.4525065
X-RAY DIFFRACTIONf_chiral_restr0.05923
X-RAY DIFFRACTIONf_plane_restr0.0051100
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0987-2.15120.20111420.15734498X-RAY DIFFRACTION99
2.1512-2.20940.21181390.15714573X-RAY DIFFRACTION100
2.2094-2.27440.19471390.154549X-RAY DIFFRACTION100
2.2744-2.34780.19891430.15154539X-RAY DIFFRACTION100
2.3478-2.43170.19961430.15544547X-RAY DIFFRACTION100
2.4317-2.5290.2311420.15994572X-RAY DIFFRACTION100
2.529-2.64410.19991430.16584562X-RAY DIFFRACTION100
2.6441-2.78350.22371450.16814553X-RAY DIFFRACTION100
2.7835-2.95780.21231430.16614566X-RAY DIFFRACTION100
2.9578-3.18610.2031410.16854577X-RAY DIFFRACTION100
3.1861-3.50650.21151420.15644573X-RAY DIFFRACTION100
3.5065-4.01350.17011420.13454591X-RAY DIFFRACTION100
4.0135-5.05490.1481430.11664584X-RAY DIFFRACTION100
5.0549-39.29230.16361470.15074616X-RAY DIFFRACTION100

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