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- PDB-7nf2: Structure of T. atroviride Fdc variant TaFdcV in complex with prF... -

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Basic information

Entry
Database: PDB / ID: 7nf2
TitleStructure of T. atroviride Fdc variant TaFdcV in complex with prFMN crotonic acid adduct
ComponentsFerulic acid decarboxylase 1
KeywordsLYASE / decarboxylase / prFMN
Function / homology
Function and homology information


phenacrylate decarboxylase / 3-octaprenyl-4-hydroxybenzoate carboxy-lyase activity / ferulate metabolic process / cinnamic acid catabolic process / ubiquinone biosynthetic process / metal ion binding / cytosol
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
ACETATE ION / prFMN cofactor and crotonic acid adduct / : / : / Ferulic acid decarboxylase 1
Similarity search - Component
Biological speciesHypocrea atroviridis (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.33 Å
AuthorsSaaret, A. / Leys, D.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
European Research Council (ERC)695013 United Kingdom
CitationJournal: Nat Commun / Year: 2021
Title: Directed evolution of prenylated FMN-dependent Fdc supports efficient in vivo isobutene production.
Authors: Saaret, A. / Villiers, B. / Stricher, F. / Anissimova, M. / Cadillon, M. / Spiess, R. / Hay, S. / Leys, D.
History
DepositionFeb 5, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 4, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 6, 2021Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_2 / diffrn_source / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / diffrn_source / pdbx_initial_refinement_model
Item: _diffrn_source.pdbx_synchrotron_site

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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)115,79316
Polymers114,0402
Non-polymers1,75414
Water19,0061055
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10030 Å2
ΔGint-46 kcal/mol
Surface area31780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.540, 74.540, 345.360
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-1757-

HOH

21A-1775-

HOH

31A-1803-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Ferulic acid decarboxylase 1 / Phenacrylate decarboxylase


Mass: 57019.812 Da / Num. of mol.: 2
Mutation: E25N N31G G305A D351R K377H P402V F404Y T405M T429A V445P Q448W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hypocrea atroviridis (strain ATCC 20476 / IMI 206040) (fungus)
Strain: ATCC 20476 / IMI 206040 / Gene: FDC1, TRIATDRAFT_53567 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: G9NLP8, phenacrylate decarboxylase

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Non-polymers , 5 types, 1069 molecules

#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-JRH / prFMN cofactor and crotonic acid adduct


Mass: 566.541 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H35N4O9P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#5: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1055 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.55 Å3/Da / Density % sol: 51.76 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Potassium thiocyanate, sodium bromide, MES, PEG smear high (BCS screen from Molecular Dimensions)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9159 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9159 Å / Relative weight: 1
ReflectionResolution: 1.33→115.12 Å / Num. obs: 256349 / % possible obs: 100 % / Redundancy: 9.2 % / CC1/2: 1 / Net I/σ(I): 6.7
Reflection shellResolution: 1.33→1.35 Å / Num. unique obs: 12523 / CC1/2: 0.5 / % possible all: 99.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6EV4

6ev4


Resolution: 1.33→115.12 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.971 / SU B: 0.944 / SU ML: 0.037 / Cross valid method: THROUGHOUT / ESU R: 0.046 / ESU R Free: 0.047 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18081 12653 4.9 %RANDOM
Rwork0.16229 ---
obs0.16321 243405 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.037 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å20 Å2
2---0 Å2-0 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.33→115.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7634 0 108 1055 8797
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0138141
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177717
X-RAY DIFFRACTIONr_angle_refined_deg1.8251.64911128
X-RAY DIFFRACTIONr_angle_other_deg1.5261.57817833
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.69651034
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.05622.031389
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.064151326
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7571552
X-RAY DIFFRACTIONr_chiral_restr0.1010.21077
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.029281
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021779
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.261.5014085
X-RAY DIFFRACTIONr_mcbond_other1.2211.54082
X-RAY DIFFRACTIONr_mcangle_it1.6282.2495132
X-RAY DIFFRACTIONr_mcangle_other1.6292.2495133
X-RAY DIFFRACTIONr_scbond_it2.1241.6834056
X-RAY DIFFRACTIONr_scbond_other2.1241.6834057
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.0392.455997
X-RAY DIFFRACTIONr_long_range_B_refined4.17719.3919497
X-RAY DIFFRACTIONr_long_range_B_other3.93618.6639214
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.33→1.365 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.279 909 -
Rwork0.295 17605 -
obs--99.36 %

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