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- PDB-7yc0: Acetylesterase (LgEstI) W.T. -

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Basic information

Entry
Database: PDB / ID: 7yc0
TitleAcetylesterase (LgEstI) W.T.
ComponentsAlpha/beta hydrolaseAlpha/beta hydrolase superfamily
KeywordsHYDROLASE / Esterase / Lipase / pathogen bacteria
Function / homologyACETATE ION / :
Function and homology information
Biological speciesLactococcus garvieae subsp. garvieae (lactic acid bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsDo, H. / Lee, J.H.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)NRF-2021M1A5A1075524 Korea, Republic Of
CitationJournal: Plos One / Year: 2023
Title: Crystal structure and biochemical analysis of acetylesterase (LgEstI) from Lactococcus garvieae.
Authors: Do, H. / Yoo, W. / Wang, Y. / Nam, Y. / Shin, S.C. / Kim, H.W. / Kim, K.K. / Lee, J.H.
History
DepositionJun 30, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 7, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alpha/beta hydrolase
B: Alpha/beta hydrolase
C: Alpha/beta hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,1996
Polymers109,0463
Non-polymers1543
Water8,935496
1
A: Alpha/beta hydrolase
B: Alpha/beta hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,7924
Polymers72,6972
Non-polymers942
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Alpha/beta hydrolase
hetero molecules

C: Alpha/beta hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,8154
Polymers72,6972
Non-polymers1182
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Unit cell
Length a, b, c (Å)54.410, 92.770, 218.111
Angle α, β, γ (deg.)90.000, 96.615, 90.000
Int Tables number5
Space group name H-MI121

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Components

#1: Protein Alpha/beta hydrolase / Alpha/beta hydrolase superfamily


Mass: 36348.645 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactococcus garvieae subsp. garvieae (lactic acid bacteria)
Gene: F4V47_03290 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A5M9R5N4
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 496 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.51 Å3/Da / Density % sol: 50.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1M Tris-HCl, pH 7.0, 0.2M calcium acetate hydrate, 20% (w/v) PEG 3000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.97949 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 16, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2→28.49 Å / Num. obs: 71847 / % possible obs: 98.7 % / Redundancy: 6.9 % / CC1/2: 0.999 / Net I/σ(I): 16.1
Reflection shellResolution: 2→2.04 Å / Rmerge(I) obs: 0.54 / Num. unique obs: 4652 / CC1/2: 0.961

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: model

Resolution: 2→28.49 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.941 / SU B: 5.646 / SU ML: 0.143 / Cross valid method: FREE R-VALUE / ESU R: 0.186 / ESU R Free: 0.165
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2349 3591 4.998 %
Rwork0.1917 68254 -
all0.194 --
obs-71845 98.718 %
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: 40.693 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å20 Å2-0.012 Å2
2--0 Å2-0 Å2
3---0.003 Å2
Refinement stepCycle: LAST / Resolution: 2→28.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7572 0 9 496 8077
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0137737
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177194
X-RAY DIFFRACTIONr_angle_refined_deg1.5651.64210506
X-RAY DIFFRACTIONr_angle_other_deg1.3191.57916533
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1725942
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.68323.245453
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.459151308
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9711548
X-RAY DIFFRACTIONr_chiral_restr0.0730.21014
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.028882
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021806
X-RAY DIFFRACTIONr_nbd_refined0.2040.21658
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1830.26962
X-RAY DIFFRACTIONr_nbtor_refined0.1620.23729
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.23529
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1570.2488
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1840.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3830.221
X-RAY DIFFRACTIONr_nbd_other0.2360.248
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1160.217
X-RAY DIFFRACTIONr_mcbond_it2.9884.1333779
X-RAY DIFFRACTIONr_mcbond_other2.9884.1313777
X-RAY DIFFRACTIONr_mcangle_it4.0016.1894716
X-RAY DIFFRACTIONr_mcangle_other4.0016.194717
X-RAY DIFFRACTIONr_scbond_it3.6424.4713958
X-RAY DIFFRACTIONr_scbond_other3.6424.4713959
X-RAY DIFFRACTIONr_scangle_it5.4356.5755790
X-RAY DIFFRACTIONr_scangle_other5.4356.5755791
X-RAY DIFFRACTIONr_lrange_it6.56148.5268834
X-RAY DIFFRACTIONr_lrange_other6.53848.3688736
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.0520.3512490.3275106X-RAY DIFFRACTION99.795
2.052-2.1080.3642970.3234958X-RAY DIFFRACTION99.7343
2.108-2.1690.3112400.2654814X-RAY DIFFRACTION99.9209
2.169-2.2360.2992390.2914411X-RAY DIFFRACTION94.493
2.236-2.3090.5062100.4794013X-RAY DIFFRACTION88.2919
2.309-2.390.2442360.1994412X-RAY DIFFRACTION99.8711
2.39-2.480.2632230.1914246X-RAY DIFFRACTION99.9553
2.48-2.5820.2862450.1914049X-RAY DIFFRACTION99.9767
2.582-2.6960.2671880.23943X-RAY DIFFRACTION100
2.696-2.8280.2741840.1863751X-RAY DIFFRACTION99.9746
2.828-2.9810.2381760.1893579X-RAY DIFFRACTION100
2.981-3.1610.2531810.2013382X-RAY DIFFRACTION100
3.161-3.380.2611660.1973167X-RAY DIFFRACTION100
3.38-3.650.2241640.1932943X-RAY DIFFRACTION99.8073
3.65-3.9980.181480.1732701X-RAY DIFFRACTION99.1646
3.998-4.4690.161310.1272486X-RAY DIFFRACTION99.9236
4.469-5.1590.1811140.1242172X-RAY DIFFRACTION99.8689
5.159-6.3150.186790.1471879X-RAY DIFFRACTION100
6.315-8.9150.141800.1181451X-RAY DIFFRACTION100
8.915-28.490.176410.152791X-RAY DIFFRACTION96.7442

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