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- PDB-7dq9: Crystal structure of a type-A feruloyl esterase from gut Alistipe... -

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Basic information

Entry
Database: PDB / ID: 7dq9
TitleCrystal structure of a type-A feruloyl esterase from gut Alistipes shahii
ComponentsPredicted hydrolases or acyltransferases (Alpha/beta hydrolase superfamily)
KeywordsHYDROLASE / gut microorganisms / Alistipes shahii / esterase / ester bond
Function / homology: / Alpha/beta hydrolase family / Epoxide hydrolase-like / acyltransferase activity / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold / hydrolase activity / Predicted hydrolases or acyltransferases (Alpha/beta hydrolase superfamily)
Function and homology information
Biological speciesAlistipes shahii WAL 8301 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.702 Å
AuthorsWei, X. / Gu, T.Y. / Xin, F.J. / Wang, Y.L.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31801475 China
CitationJournal: J.Agric.Food Chem. / Year: 2021
Title: The alpha-Helical Cap Domain of a Novel Esterase from Gut Alistipes shahii Shaping the Substrate-Binding Pocket.
Authors: Wei, X. / Wang, Y.L. / Wen, B.T. / Liu, S.J. / Wang, L. / Sun, L. / Gu, T.Y. / Li, Z. / Bao, Y. / Fan, S.L. / Zhou, H. / Wang, F. / Xin, F.
History
DepositionDec 22, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 22, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 6, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: 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: Predicted hydrolases or acyltransferases (Alpha/beta hydrolase superfamily)
B: Predicted hydrolases or acyltransferases (Alpha/beta hydrolase superfamily)
C: Predicted hydrolases or acyltransferases (Alpha/beta hydrolase superfamily)
D: Predicted hydrolases or acyltransferases (Alpha/beta hydrolase superfamily)


Theoretical massNumber of molelcules
Total (without water)118,1684
Polymers118,1684
Non-polymers00
Water26,5361473
1
A: Predicted hydrolases or acyltransferases (Alpha/beta hydrolase superfamily)


Theoretical massNumber of molelcules
Total (without water)29,5421
Polymers29,5421
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Predicted hydrolases or acyltransferases (Alpha/beta hydrolase superfamily)


Theoretical massNumber of molelcules
Total (without water)29,5421
Polymers29,5421
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Predicted hydrolases or acyltransferases (Alpha/beta hydrolase superfamily)


Theoretical massNumber of molelcules
Total (without water)29,5421
Polymers29,5421
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Predicted hydrolases or acyltransferases (Alpha/beta hydrolase superfamily)


Theoretical massNumber of molelcules
Total (without water)29,5421
Polymers29,5421
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.469, 75.545, 161.021
Angle α, β, γ (deg.)90.000, 92.340, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Predicted hydrolases or acyltransferases (Alpha/beta hydrolase superfamily) / feruloyl esterase


Mass: 29542.016 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Alistipes shahii WAL 8301 (bacteria) / Gene: AL1_21970 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: D4INH0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1473 / 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: 2.36 Å3/Da / Density % sol: 47.82 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7.42
Details: 0.1 M Bistris propane (pH 7.42), 22% PEG3350, 0.2M Potassium thiocyanate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 30, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 116510 / % possible obs: 97.9 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.023 / Rrim(I) all: 0.059 / Χ2: 0.486 / Net I/σ(I): 7.1 / Num. measured all: 737979
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.7-1.765.60.274119020.9460.1260.3030.35799.9
1.76-1.836.60.22118110.9720.0920.2390.38199.9
1.83-1.916.40.175118040.980.0740.1910.40299.7
1.91-2.026.40.124118210.990.0530.1350.425100
2.02-2.146.90.096119050.9950.0390.1040.448100
2.14-2.315.70.077102340.9950.0340.0840.48586.3
2.31-2.546.80.061118770.9980.0250.0660.599.9
2.54-2.916.40.048118940.9980.020.0520.53899.9
2.91-3.666.20.036115080.9990.0150.0390.63996.2
1.7-1.766.20.03117540.9990.0130.0330.69696.8

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
HKL-2000data collection
HKL-20003.27data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4UHH

4uhh


Resolution: 1.702→45.431 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 18.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2024 5785 4.97 %
Rwork0.1663 110642 -
obs0.1681 116427 97.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 56.77 Å2 / Biso mean: 19.2872 Å2 / Biso min: 4.33 Å2
Refinement stepCycle: final / Resolution: 1.702→45.431 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8198 0 0 1473 9671
Biso mean---28.34 -
Num. residues----1056
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.702-1.72110.25531830.2051335589
1.7211-1.74130.24312160.20013784100
1.7413-1.76260.22312210.18793758100
1.7626-1.78490.23741620.18363715100
1.7849-1.80840.21542270.18453778100
1.8084-1.83310.24972210.17763748100
1.8331-1.85930.21571830.18063748100
1.8593-1.88710.2292160.1773757100
1.8871-1.91660.23812040.1788373799
1.9166-1.9480.22921980.17943769100
1.948-1.98160.21611780.17573785100
1.9816-2.01760.23351720.17563770100
2.0176-2.05640.21891910.17613795100
2.0564-2.09840.21872050.17333777100
2.0984-2.1440.20131940.16843747100
2.144-2.19390.20611750.16493811100
2.1939-2.24880.18841520.1719300680
2.2488-2.30960.19931670.1741297379
2.3096-2.37750.19981850.16813813100
2.3775-2.45430.19322220.17133722100
2.4543-2.5420.22181840.17183812100
2.542-2.64370.2022200.17123761100
2.6437-2.76410.20771960.17043773100
2.7641-2.90980.20341890.16543799100
2.9098-3.0920.21171650.16483814100
3.092-3.33070.18962230.16583753100
3.3307-3.66570.1761650.1533341589
3.6657-4.19590.16651760.1467349991
4.1959-5.28510.17891850.13973812100
5.2851-45.430.20122100.1649385698

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