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- PDB-8v16: Esterase with a monomeric cooperative, hysteresis or allokairy -

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Basic information

Entry
Database: PDB / ID: 8v16
TitleEsterase with a monomeric cooperative, hysteresis or allokairy
ComponentsEsterase 1
KeywordsHYDROLASE / esterase / hysteresis/allokairy / metagenomic / alpha/beta-Hydrolases
Function / homology: / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold / Esterase 1
Function and homology information
Biological speciesuncultured proteobacterium (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsGuzzo, C.R. / Vinces, T.G.C. / Visnardi, A.B.
Funding support Brazil, 2items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2022/08730-7; 2019/00195-2; 2020/04680-0; 2021/05262-0; 2021/10577-0; 2017/17303-7 Brazil
Coordination for the Improvement of Higher Education Personnel01 Brazil
CitationJournal: Biochemistry / Year: 2024
Title: Monomeric Esterase: Insights into Cooperative Behavior, Hysteresis/Allokairy.
Authors: Vinces, T.C. / de Souza, A.S. / Carvalho, C.F. / Visnardi, A.B. / Teixeira, R.D. / Llontop, E.E. / Bismara, B.A.P. / Vicente, E.J. / Pereira, J.O. / de Souza, R.F. / Yonamine, M. / Marana, S. ...Authors: Vinces, T.C. / de Souza, A.S. / Carvalho, C.F. / Visnardi, A.B. / Teixeira, R.D. / Llontop, E.E. / Bismara, B.A.P. / Vicente, E.J. / Pereira, J.O. / de Souza, R.F. / Yonamine, M. / Marana, S.R. / Farah, C.S. / Guzzo, C.R.
History
DepositionNov 19, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 23, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: Esterase 1
A: Esterase 1
B: Esterase 1
D: Esterase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,2838
Polymers119,9144
Non-polymers3684
Water6,431357
1
C: Esterase 1


Theoretical massNumber of molelcules
Total (without water)29,9791
Polymers29,9791
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: Esterase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1633
Polymers29,9791
Non-polymers1842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Esterase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1633
Polymers29,9791
Non-polymers1842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Esterase 1


Theoretical massNumber of molelcules
Total (without water)29,9791
Polymers29,9791
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)72.076, 105.891, 145.371
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Esterase 1


Mass: 29978.604 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: Amazonian Dark Soil
Source: (gene. exp.) uncultured proteobacterium (environmental samples)
Gene: ade1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RP / References: UniProt: A0A8E4UR43
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 357 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.35 Å3/Da / Density % sol: 47.67 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M Ammonium sulfate, 0.1 M Sodium cacodylate trihydrate pH 6.5 and, 30% w/v Polyethylene glycol 8,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: LNLS SIRIUS / Beamline: MANACA / Wavelength: 0.9772 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 19, 2021
Details: vertical focusing mirror (side-bounce sagittal cylindrical mirror)
RadiationMonochromator: horizontal Double-Crystal Monochromator (DCM) equipped with two pairs of Si crystals (111 and 311)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9772 Å / Relative weight: 1
ReflectionResolution: 1.77→30 Å / % possible obs: 99.7 % / Redundancy: 6.8 % / Biso Wilson estimate: 36 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.11 / Net I/σ(I): 11.1
Reflection shellResolution: 1.77→1.87 Å / Num. unique obs: 33449 / CC1/2: 0.37

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→30 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.95 / SU B: 3.469 / SU ML: 0.101 / Cross valid method: FREE R-VALUE / ESU R: 0.145 / ESU R Free: 0.134
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2171 4413 5 %
Rwork0.1797 83854 -
all0.182 --
obs-88267 99.959 %
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: 33.727 Å2
Baniso -1Baniso -2Baniso -3
1-1.215 Å2-0 Å20 Å2
2--0.256 Å2-0 Å2
3----1.471 Å2
Refinement stepCycle: LAST / Resolution: 1.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8190 0 24 357 8571
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0128434
X-RAY DIFFRACTIONr_bond_other_d0.0010.0167930
X-RAY DIFFRACTIONr_angle_refined_deg1.4841.64911455
X-RAY DIFFRACTIONr_angle_other_deg0.491.55718466
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.13451063
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.908551
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.326101397
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.79510352
X-RAY DIFFRACTIONr_chiral_restr0.0710.21299
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.029532
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021608
X-RAY DIFFRACTIONr_nbd_refined0.2210.21685
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1870.27125
X-RAY DIFFRACTIONr_nbtor_refined0.1760.24049
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.24365
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1360.2337
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0450.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.20.218
X-RAY DIFFRACTIONr_nbd_other0.2020.259
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2920.27
X-RAY DIFFRACTIONr_mcbond_it2.9673.2614246
X-RAY DIFFRACTIONr_mcbond_other2.9673.2614246
X-RAY DIFFRACTIONr_mcangle_it3.9534.8715299
X-RAY DIFFRACTIONr_mcangle_other3.9534.8715300
X-RAY DIFFRACTIONr_scbond_it4.2083.824188
X-RAY DIFFRACTIONr_scbond_other4.2073.824189
X-RAY DIFFRACTIONr_scangle_it6.2685.5096152
X-RAY DIFFRACTIONr_scangle_other6.2675.516153
X-RAY DIFFRACTIONr_lrange_it7.88964.76835562
X-RAY DIFFRACTIONr_lrange_other7.88864.7335399
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.9490.2663210.2416098X-RAY DIFFRACTION100
1.949-2.0020.2823140.2245971X-RAY DIFFRACTION100
2.002-2.060.2713040.2155769X-RAY DIFFRACTION100
2.06-2.1230.252970.2025634X-RAY DIFFRACTION100
2.123-2.1920.2352870.1945469X-RAY DIFFRACTION100
2.192-2.2690.2362780.185274X-RAY DIFFRACTION100
2.269-2.3540.2162700.1875128X-RAY DIFFRACTION100
2.354-2.450.2372580.1864913X-RAY DIFFRACTION100
2.45-2.5580.2262500.1844743X-RAY DIFFRACTION100
2.558-2.6820.252390.1854533X-RAY DIFFRACTION100
2.682-2.8250.2372260.2024303X-RAY DIFFRACTION99.9779
2.825-2.9950.2642180.1944133X-RAY DIFFRACTION100
2.995-3.20.2432030.1923856X-RAY DIFFRACTION100
3.2-3.4530.2161900.1853608X-RAY DIFFRACTION100
3.453-3.7770.1981760.1743351X-RAY DIFFRACTION100
3.777-4.2150.1961590.1513028X-RAY DIFFRACTION100
4.215-4.8510.1671430.1392712X-RAY DIFFRACTION99.965
4.851-5.9030.1931220.1632314X-RAY DIFFRACTION100
5.903-8.1910.18970.1741849X-RAY DIFFRACTION99.9486
8.191-300.169600.171145X-RAY DIFFRACTION100

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