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- PDB-6y9k: Esterase EST8 with transacylase activity -

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Basic information

Entry
Database: PDB / ID: 6y9k
TitleEsterase EST8 with transacylase activity
ComponentsEsterase Est8
KeywordsHYDROLASE / AB Hydrolase / Transacetylase / Transacylase
Biological speciesmetagenome (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.298 Å
AuthorsPalm, G.J. / Lammers, M. / Berndt, L.
Citation
Journal: Angew.Chem.Int.Ed.Engl. / Year: 2020
Title: Sequence-Based Prediction of Promiscuous Acyltransferase Activity in Hydrolases.
Authors: Muller, H. / Becker, A.K. / Palm, G.J. / Berndt, L. / Badenhorst, C.P.S. / Godehard, S.P. / Reisky, L. / Lammers, M. / Bornscheuer, U.T.
#1: Journal: Tetrahedron: Asymmetry / Year: 2008
Title: Asymmetric synthesis of cis-3,5-diacetoxycyclopent-1-ene using metagenome-derived hydrolases
Authors: Bruesehaber, E. / Boettcher, D. / Liebeton, K. / Eck, J. / Naumer, C. / Bornscheuer, U.
#2: Journal: Molecular Microbiology / Year: 2010
Title: Enantioselective kinetic resolution of phenylalkyl carboxylic acids using metagenome-derived esterases.
Authors: Fernandez-Alvaro, E. / Kourist, R. / Winter, J. / Boettcher, D. / Liebeton, K. / Naumer, C. / Eck, J. / Leggewie, C. / Jaeger, K.-E. / Streit, W. / Bornscheuer, U.T.
#3: Journal: Tetrahedron: Asymmetry / Year: 2008
Title: Hydrolase-catalyzed stereoselective preparation of protected a,a-dialkyl-a-hydroxycarboxylic acids
Authors: Kourist, R. / Nguyen, G.-S. / Struebing, D. / Boettcher, D. / Liebeton, K. / Naumer, C. / Eck, J. / Bornscheuer, U.T.
History
DepositionMar 9, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 29, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / refine_hist
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_high

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Esterase Est8
BBB: Esterase Est8
CCC: Esterase Est8
DDD: Esterase Est8


Theoretical massNumber of molelcules
Total (without water)129,8624
Polymers129,8624
Non-polymers00
Water3,225179
1
AAA: Esterase Est8
BBB: Esterase Est8


Theoretical massNumber of molelcules
Total (without water)64,9312
Polymers64,9312
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1460 Å2
ΔGint-14 kcal/mol
Surface area21670 Å2
MethodPISA
2
CCC: Esterase Est8
DDD: Esterase Est8


Theoretical massNumber of molelcules
Total (without water)64,9312
Polymers64,9312
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1440 Å2
ΔGint-15 kcal/mol
Surface area21560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.173, 78.180, 112.664
Angle α, β, γ (deg.)90.000, 100.680, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Esterase Est8


Mass: 32465.414 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) metagenome (others) / Plasmid: pET26 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: hormone-sensitive lipase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 179 / 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: 2.6 Å3/Da / Density % sol: 53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 29% PEG 4000, 0.1 M ammonium sulphate, 0.1 M sodium citrate, pH 5.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Mar 15, 2019
RadiationMonochromator: DCM Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.298→49.5 Å / Num. obs: 59126 / % possible obs: 98.9 % / Observed criterion σ(I): 0 / Redundancy: 7 % / Rsym value: 0.19 / Net I/σ(I): 7.8
Reflection shellResolution: 2.298→2.43 Å / Redundancy: 7.1 % / Mean I/σ(I) obs: 1.4 / Num. unique obs: 9359 / Rsym value: 1.29 / % possible all: 97.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSJan 26, 2018data reduction
XDSJan 26, 2018data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4xvc

4xvc


Resolution: 2.298→49.5 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.938 / SU B: 10.485 / SU ML: 0.221 / Cross valid method: FREE R-VALUE / σ(F): 0 / ESU R: 0.309 / ESU R Free: 0.22
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2389 1491 2.524 %Random selection
Rwork0.2051 ---
all0.206 ---
obs-59075 99.066 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 42.923 Å2
Baniso -1Baniso -2Baniso -3
1--1.953 Å20 Å20.545 Å2
2---2.768 Å20 Å2
3---4.216 Å2
Refinement stepCycle: LAST / Resolution: 2.298→49.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8828 0 0 179 9007
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0139036
X-RAY DIFFRACTIONr_bond_other_d0.0010.0178657
X-RAY DIFFRACTIONr_angle_refined_deg1.631.64212281
X-RAY DIFFRACTIONr_angle_other_deg1.2431.57620071
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.28151190
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.41422380
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.387151471
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.881552
X-RAY DIFFRACTIONr_chiral_restr0.0680.21183
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0210197
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021775
X-RAY DIFFRACTIONr_nbd_refined0.2150.22109
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1950.28085
X-RAY DIFFRACTIONr_nbtor_refined0.1560.24311
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0820.23903
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1840.2267
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1730.25
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1470.212
X-RAY DIFFRACTIONr_nbd_other0.190.268
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.080.26
X-RAY DIFFRACTIONr_mcbond_it3.1174.4184754
X-RAY DIFFRACTIONr_mcbond_other3.1174.4184753
X-RAY DIFFRACTIONr_mcangle_it4.6836.6175937
X-RAY DIFFRACTIONr_mcangle_other4.6836.6175938
X-RAY DIFFRACTIONr_scbond_it3.654.734282
X-RAY DIFFRACTIONr_scbond_other3.654.734282
X-RAY DIFFRACTIONr_scangle_it5.5426.8976341
X-RAY DIFFRACTIONr_scangle_other5.5426.8976341
X-RAY DIFFRACTIONr_lrange_it7.78352.74310032
X-RAY DIFFRACTIONr_lrange_other7.76852.7410018
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.298-2.3580.3921080.34941720.3543260.4520.4798.93670.333
2.358-2.4220.351070.33241270.33242460.5470.5699.71740.314
2.422-2.4920.3431050.3340490.33141680.6530.66699.66410.312
2.492-2.5690.3411010.3139020.31140210.7290.74699.55240.29
2.569-2.6530.337980.2837770.28138970.7750.81399.43550.253
2.653-2.7450.365950.26136840.26438010.7870.83999.42120.232
2.745-2.8490.301920.25735410.25836480.8450.85399.58880.229
2.849-2.9650.24890.22234290.22335380.8860.88599.43470.195
2.965-3.0960.231840.20632600.20633690.9220.91899.25790.181
3.096-3.2460.262790.19930530.232500.9070.93596.36920.18
3.246-3.4210.222760.20529290.20530900.9390.9497.24920.191
3.421-3.6280.24720.227980.20128850.9360.94599.48010.187
3.628-3.8770.208690.17426770.17527560.950.95999.63720.165
3.877-4.1850.182650.15824930.15925640.9580.96399.7660.153
4.185-4.5810.154600.14223030.14223700.970.96899.70460.141
4.581-5.1160.202530.15520760.15621380.960.96899.5790.157
5.116-5.8970.179480.15118340.15219010.9750.97199.00050.15
5.897-7.1970.211380.14614940.14716120.9480.97295.03720.147
7.197-10.0730.169330.1312440.13112770.9620.9771000.143
10.073-49.4690.277190.2747290.2747490.9510.93999.86650.354

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