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- PDB-8y64: Crystal structure of open state ferulic acid decarboxylase from S... -

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Basic information

Entry
Database: PDB / ID: 8y64
TitleCrystal structure of open state ferulic acid decarboxylase from Saccharomyces cerevisiae, F397V/I398L/T438P/P441V mutant
ComponentsFerulic acid decarboxylase 1
KeywordsLYASE / ferulic acid decarboxylase
Function / homology
Function and homology information


ferulate catabolic process / phenacrylate decarboxylase / ferulate metabolic process / cinnamic acid catabolic process / carboxy-lyase activity / metal ion binding / cytoplasm
Similarity search - Function
UbiD-like decarboxylase/ferulic acid decarboxylase 1 / : / : / : / 3-octaprenyl-4-hydroxybenzoate carboxy-lyase N-terminal domain / 3-octaprenyl-4-hydroxybenzoate carboxy-lyase C-terminal domain / UbiD decarboxylyase family / 3-octaprenyl-4-hydroxybenzoate carboxy-lyase Rift-related domain
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Ferulic acid decarboxylase 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsFeng, Y.B. / Song, X. / Zhu, X.N.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Biochem Eng J / Year: 2025
Title: Integrated strategies for engineering ferulic acid decarboxylase with tunnel conformation and substrate pocket for adapting non-natural substrates.
Authors: Zhu, X.N. / Feng, Y.B. / Wang, M.D. / Li, S. / Li, H.F. / Liu, L. / Xue, S.
History
DepositionFeb 1, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 1, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ferulic acid decarboxylase 1
B: Ferulic acid decarboxylase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,0229
Polymers112,3632
Non-polymers6597
Water19,0781059
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, homodimer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8640 Å2
ΔGint-45 kcal/mol
Surface area36600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.778, 81.830, 166.321
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Ferulic acid decarboxylase 1 / Phenacrylate decarboxylase


Mass: 56181.660 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: F397V,I398L,T438P,P441V
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: FDC1, YDR539W, D3703.2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q03034, phenacrylate decarboxylase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1059 / 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: 2.46 Å3/Da / Density % sol: 50 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 0.1 M Bis-Tris, pH5.5, 25% w/v PEG 3350 / PH range: 5-8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9799 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 8, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9799 Å / Relative weight: 1
ReflectionResolution: 1.97→30.81 Å / Num. obs: 79148 / % possible obs: 98.34 % / Redundancy: 11.8 % / Biso Wilson estimate: 23.96 Å2 / CC1/2: 0.968 / Rmerge(I) obs: 0.1316 / Rpim(I) all: 0.03941 / Rrim(I) all: 0.1375 / Net I/σ(I): 12.87
Reflection shellResolution: 1.97→2.04 Å / Redundancy: 11.7 % / Rmerge(I) obs: 0.6737 / Mean I/σ(I) obs: 4.4 / Num. unique obs: 7273 / CC1/2: 0.868 / % possible all: 92.47

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
HKL-3000version 723data reduction
HKL-3000version 723data scaling
PHENIX1.20.1_4487phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.97→30.81 Å / SU ML: 0.1647 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.3072
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1841 3810 4.87 %
Rwork0.1506 74353 -
obs0.1522 78163 98.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.65 Å2
Refinement stepCycle: LAST / Resolution: 1.97→30.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7859 0 43 1059 8961
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00828112
X-RAY DIFFRACTIONf_angle_d0.982911016
X-RAY DIFFRACTIONf_chiral_restr0.06251241
X-RAY DIFFRACTIONf_plane_restr0.00921401
X-RAY DIFFRACTIONf_dihedral_angle_d6.95951084
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.97-20.25841040.19722496X-RAY DIFFRACTION87.96
2-2.020.24061250.1812586X-RAY DIFFRACTION95.26
2.02-2.050.19571250.16532674X-RAY DIFFRACTION95.07
2.05-2.080.19691440.1712630X-RAY DIFFRACTION96.76
2.08-2.110.19921400.16962689X-RAY DIFFRACTION96.39
2.11-2.140.2611540.16212676X-RAY DIFFRACTION97.86
2.14-2.180.18481490.1562714X-RAY DIFFRACTION98.05
2.18-2.220.19281080.16162752X-RAY DIFFRACTION98.65
2.22-2.260.1941380.14912727X-RAY DIFFRACTION98.83
2.26-2.30.18671740.15522685X-RAY DIFFRACTION98.28
2.3-2.350.17271410.15312775X-RAY DIFFRACTION99.05
2.35-2.40.20821140.15592771X-RAY DIFFRACTION99.14
2.4-2.450.1911550.15862751X-RAY DIFFRACTION99.35
2.45-2.510.2011480.15962731X-RAY DIFFRACTION99.31
2.51-2.580.21891570.15952775X-RAY DIFFRACTION99.59
2.58-2.660.23411440.15842764X-RAY DIFFRACTION99.55
2.66-2.740.22241650.15722770X-RAY DIFFRACTION99.39
2.74-2.840.18921340.15652768X-RAY DIFFRACTION99.42
2.84-2.960.19161330.16462798X-RAY DIFFRACTION99.83
2.96-3.090.19411710.16182767X-RAY DIFFRACTION99.63
3.09-3.250.20281480.15462809X-RAY DIFFRACTION99.76
3.25-3.460.19691610.14942780X-RAY DIFFRACTION99.86
3.46-3.720.16021380.14412844X-RAY DIFFRACTION99.97
3.72-4.10.16381210.1312857X-RAY DIFFRACTION100
4.1-4.690.12911430.11432854X-RAY DIFFRACTION100
4.69-5.90.13351240.13782914X-RAY DIFFRACTION99.93
5.9-30.810.17641520.16112996X-RAY DIFFRACTION99.27

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