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- PDB-7e7l: The crystal structure of arylacetate decarboxylase from Olsenella... -

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Basic information

Entry
Database: PDB / ID: 7e7l
TitleThe crystal structure of arylacetate decarboxylase from Olsenella scatoligenes.
ComponentsHydroxyphenylacetic acid decarboxylase
KeywordsLYASE / Decarboxylase
Function / homology
Function and homology information


lyase activity / cytosol
Similarity search - Function
: / Formate C-acetyltransferase glycine radical, conserved site / Glycine radical domain signature. / Pyruvate formate lyase domain / Pyruvate formate lyase-like / Pyruvate formate-lyase domain profile. / Glycine radical / Glycine radical domain / Glycine radical domain profile.
Similarity search - Domain/homology
4-HYDROXYPHENYLACETATE / Formate C-acetyltransferase
Similarity search - Component
Biological speciesOlsenella scatoligenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.53 Å
AuthorsLu, Q. / Duan, Y. / Zhang, Y. / Yuchi, Z.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)31870049 China
CitationJournal: Acs Catalysis / Year: 2021
Title: The Glycyl Radical Enzyme Arylacetate Decarboxylase from Olsenella scatoligenes
Authors: Lu, Q. / Wei, Y. / Lin, L. / Liu, J. / Duan, Y. / Li, Y. / Zhai, W. / Liu, Y. / Ang, E.L. / Zhao, H. / Yuchi, Z. / Zhang, Y.
History
DepositionFeb 26, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 28, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hydroxyphenylacetic acid decarboxylase
B: Hydroxyphenylacetic acid decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)185,0234
Polymers184,7192
Non-polymers3042
Water00
1
A: Hydroxyphenylacetic acid decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,5122
Polymers92,3591
Non-polymers1521
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Hydroxyphenylacetic acid decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,5122
Polymers92,3591
Non-polymers1521
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.946, 225.548, 234.679
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Hydroxyphenylacetic acid decarboxylase


Mass: 92359.406 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Olsenella scatoligenes (bacteria) / Gene: AUL39_01475 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A100YWM3
#2: Chemical ChemComp-4HP / 4-HYDROXYPHENYLACETATE


Mass: 152.147 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H8O3 / Feature type: SUBJECT OF INVESTIGATION
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: 3.08 Å3/Da / Density % sol: 60.05 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.1M MES pH 6.0, 0.2M Sodium chloride, 20% w/v PEG 2000 MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 19, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.498→50 Å / Num. obs: 28962 / % possible obs: 99.9 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.221 / Rpim(I) all: 0.092 / Rrim(I) all: 0.239 / Χ2: 0.453 / Net I/σ(I): 2.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.53-3.5970.78614640.7850.3180.8480.429100
3.59-3.6670.62313840.8260.2510.6720.427100
3.66-3.736.90.55914330.8560.2270.6040.452100
3.73-3.86.90.52114370.8720.2120.5630.431100
3.8-3.896.90.45814080.9140.1870.4960.43100
3.89-3.986.80.42914340.9090.1760.4650.458100
3.98-4.076.80.36214400.950.1490.3920.449100
4.07-4.186.80.31414180.9560.130.340.439100
4.18-4.316.60.27414600.9670.1150.2980.463100
4.31-4.456.30.23514050.970.1010.2570.474100
4.45-4.615.90.20114300.970.0920.2210.468100
4.61-4.7960.18714730.9780.0840.2050.465100
4.79-5.016.30.17914290.9810.0780.1950.472100
5.01-5.2770.18814400.9810.0760.2030.462100
5.27-5.66.90.18514580.9830.0750.20.457100
5.6-6.036.90.17914480.9810.0730.1940.45100
6.03-6.646.80.16214840.9850.0660.1750.452100
6.64-7.66.40.12514680.9910.0530.1360.452100
7.6-9.565.80.06914940.9960.0310.0760.446100
9.56-506.20.05715550.9970.0250.0630.48798.9

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Processing

Software
NameVersionClassification
PHENIX1.14_3247refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5FAU

5fau


Resolution: 3.53→37.591 Å / SU ML: 0.56 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 35.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3584 1879 6.87 %
Rwork0.29 25464 -
obs0.2946 27343 93.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 118.5 Å2 / Biso mean: 53.8351 Å2 / Biso min: 18.46 Å2
Refinement stepCycle: final / Resolution: 3.53→37.591 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11317 0 22 0 11339
Biso mean--50.2 --
Num. residues----1536
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.53-3.59280.44861130.3655155575
3.5928-3.69840.42241400.3339186891
3.6984-3.81770.3931360.3186190992
3.8177-3.9540.41881420.3175189392
3.954-4.11210.38421420.3033195093
4.1121-4.2990.3721460.2884196794
4.299-4.52530.34031480.2697199596
4.5253-4.80830.3431470.2635199096
4.8083-5.17870.31571450.2735201496
5.1787-5.69820.33911510.2965203097
5.6982-6.5190.35941510.3029204297
6.519-8.19920.33391560.288210198
8.1992-37.5910.31911620.2523215096

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