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- PDB-7atl: EstCE1, a hydrolase with promiscuous acyltransferase activity -

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Basic information

Entry
Database: PDB / ID: 7atl
TitleEstCE1, a hydrolase with promiscuous acyltransferase activity
ComponentsEsterase
KeywordsHYDROLASE / esterase / acyltransferase / transacylase
Function / homology: / Beta-lactamase-related / Beta-lactamase / Beta-lactamase/transpeptidase-like / DI(HYDROXYETHYL)ETHER / Esterase
Function and homology information
Biological speciesuncultured bacterium pCosCE1 (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.478 Å
AuthorsPalm, G.J. / Lammers, M. / Berndt, L.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2021
Title: Discovery and Design of Family VIII Carboxylesterases as Highly Efficient Acyltransferases.
Authors: Muller, H. / Godehard, S.P. / Palm, G.J. / Berndt, L. / Badenhorst, C.P.S. / Becker, A.K. / Lammers, M. / Bornscheuer, U.T.
History
DepositionOct 30, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 18, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.name
Revision 1.2Jan 31, 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
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,9697
Polymers43,0681
Non-polymers9016
Water3,117173
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1930 Å2
ΔGint10 kcal/mol
Surface area14990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.433, 99.433, 228.132
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11AAA-402-

PG4

21AAA-403-

PG4

31AAA-515-

HOH

41AAA-667-

HOH

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Components

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Protein , 1 types, 1 molecules AAA

#1: Protein Esterase


Mass: 43068.367 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) uncultured bacterium pCosCE1 (environmental samples)
Gene: estCE / Plasmid: pET24c / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q1I192

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Non-polymers , 5 types, 179 molecules

#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 173 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 3.78 Å3/Da / Density % sol: 68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 2 ul (17 mg/ml protein, 50 mM Na-phophate, pH 7.5) + 2 ul (10% PEG8000, 200 mM Mg(OAc)2), cryo buffer: 10% PEG8000, 12% PEG400, 200 mM Mg(OAc)2

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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 20, 2020
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: 2.478→50 Å / Num. obs: 44454 / % possible obs: 99.1 % / Redundancy: 10.5 % / Biso Wilson estimate: 36 Å2 / CC1/2: 0.978 / Rsym value: 0.406 / Net I/σ(I): 7.1
Reflection shellResolution: 2.478→2.63 Å / Redundancy: 10.5 % / Rmerge(I) obs: 2.092 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 7167 / CC1/2: 0.442 / % possible all: 99

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSVERSION Mar 15, 2019data reduction
XSCALEVERSION Mar 15, 2019data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ci8

1ci8


Resolution: 2.478→48.624 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.933 / Cross valid method: FREE R-VALUE / ESU R: 0.283 / ESU R Free: 0.2
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2355 1209 4.974 %
Rwork0.2038 23097 -
all0.204 --
obs-24306 98.978 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 32.464 Å2
Baniso -1Baniso -2Baniso -3
1-0.145 Å20.073 Å20 Å2
2--0.145 Å20 Å2
3----0.471 Å2
Refinement stepCycle: LAST / Resolution: 2.478→48.624 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2911 0 60 173 3144
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0133048
X-RAY DIFFRACTIONr_bond_other_d0.0350.0172826
X-RAY DIFFRACTIONr_angle_refined_deg1.5671.6434126
X-RAY DIFFRACTIONr_angle_other_deg2.3291.5786548
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1495384
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.97721.887159
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.78415467
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7131522
X-RAY DIFFRACTIONr_chiral_restr0.0670.2380
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023431
X-RAY DIFFRACTIONr_gen_planes_other0.0090.02635
X-RAY DIFFRACTIONr_nbd_refined0.2020.2620
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2140.22747
X-RAY DIFFRACTIONr_nbtor_refined0.1640.21433
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.070.21285
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1410.2157
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2030.29
X-RAY DIFFRACTIONr_nbd_other0.1880.223
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1380.211
X-RAY DIFFRACTIONr_mcbond_it2.4553.3031527
X-RAY DIFFRACTIONr_mcbond_other2.4553.3021525
X-RAY DIFFRACTIONr_mcangle_it3.8494.9481908
X-RAY DIFFRACTIONr_mcangle_other3.8494.9481908
X-RAY DIFFRACTIONr_scbond_it3.2083.6911521
X-RAY DIFFRACTIONr_scbond_other3.2073.6941522
X-RAY DIFFRACTIONr_scangle_it5.0335.3662216
X-RAY DIFFRACTIONr_scangle_other5.0325.372217
X-RAY DIFFRACTIONr_lrange_it6.61138.6143332
X-RAY DIFFRACTIONr_lrange_other6.66238.6173307
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.478-2.5420.34860.31653X-RAY DIFFRACTION98.0271
2.542-2.6120.31910.291619X-RAY DIFFRACTION99.1879
2.612-2.6880.36830.351584X-RAY DIFFRACTION98.9905
2.688-2.770.37770.291513X-RAY DIFFRACTION97.546
2.77-2.8610.31940.251468X-RAY DIFFRACTION98.4868
2.861-2.9620.28630.221459X-RAY DIFFRACTION99.3473
2.962-3.0730.23700.211410X-RAY DIFFRACTION99.5293
3.073-3.1990.25650.221368X-RAY DIFFRACTION99.307
3.199-3.3410.22650.221305X-RAY DIFFRACTION99.7089
3.341-3.5040.27710.221251X-RAY DIFFRACTION99.6232
3.504-3.6940.24700.211177X-RAY DIFFRACTION98.1117
3.694-3.9180.2560.191143X-RAY DIFFRACTION99.5847
3.918-4.1880.2460.161084X-RAY DIFFRACTION99.8233
4.188-4.5230.17560.131023X-RAY DIFFRACTION99.9074
4.523-4.9550.19540.12923X-RAY DIFFRACTION99.8978
4.955-5.5390.23510.16831X-RAY DIFFRACTION97.4586
5.539-6.3960.2260.16771X-RAY DIFFRACTION99.8747
6.396-7.8320.19370.17668X-RAY DIFFRACTION100
7.832-11.0690.15240.14525X-RAY DIFFRACTION97.1681
11.069-48.60.2240.25322X-RAY DIFFRACTION98.2955

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