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- PDB-7nf3: Structure of A. niger Fdc T395M variant (AnFdcI) in complex with prFMN -

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Basic information

Entry
Database: PDB / ID: 7nf3
TitleStructure of A. niger Fdc T395M variant (AnFdcI) in complex with prFMN
ComponentsFerulic acid decarboxylase 1
KeywordsLYASE / decarboxylase / prFMN
Function / homology
Function and homology information


styrene metabolic process / aromatic amino acid family catabolic process / phenacrylate decarboxylase / ferulate metabolic process / cinnamic acid catabolic process / carboxy-lyase activity / manganese ion binding / identical protein 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
Chem-4LU / : / : / Ferulic acid decarboxylase 1
Similarity search - Component
Biological speciesAspergillus niger (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,0255
Polymers56,3661
Non-polymers6594
Water8,413467
1
A: Ferulic acid decarboxylase 1
hetero molecules

A: Ferulic acid decarboxylase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,04910
Polymers112,7322
Non-polymers1,3178
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area8430 Å2
ΔGint-47 kcal/mol
Surface area33150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.910, 63.850, 87.820
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Ferulic acid decarboxylase 1 / Phenacrylate decarboxylase


Mass: 56366.039 Da / Num. of mol.: 1 / Mutation: T395M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus niger (strain CBS 513.88 / FGSC A1513) (mold)
Strain: CBS 513.88 / FGSC A1513 / Gene: fdc1, An03g06590 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A2QHE5, phenacrylate decarboxylase
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-4LU / 1-deoxy-5-O-phosphono-1-(3,3,4,5-tetramethyl-9,11-dioxo-2,3,8,9,10,11-hexahydro-7H-quinolino[1,8-fg]pteridin-12-ium-7-y l)-D-ribitol / prenylated-FMN iminium form


Mass: 525.469 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H30N4O9P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 467 / Source method: isolated from a natural source / Formula: H2O
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: 2.44 Å3/Da / Density % sol: 49.52 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: BIS-TRIS propane, potassium thiocyanate, PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 25, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.1→42.09 Å / Num. obs: 213550 / % possible obs: 97.9 % / Redundancy: 4.9 % / CC1/2: 1 / Net I/σ(I): 15.7
Reflection shellResolution: 1.1→1.12 Å / Mean I/σ(I) obs: 2.2 / Num. unique obs: 8943 / CC1/2: 0.3

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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: 1.1→42.09 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.971 / SU B: 0.375 / SU ML: 0.018 / Cross valid method: THROUGHOUT / ESU R: 0.028 / ESU R Free: 0.029 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17163 10735 5 %RANDOM
Rwork0.15818 ---
obs0.15886 202756 97.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.888 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å2-0 Å2
2---0 Å2-0 Å2
3----0 Å2
Refinement stepCycle: 1 / Resolution: 1.1→42.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3867 0 39 467 4373
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0134313
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174022
X-RAY DIFFRACTIONr_angle_refined_deg2.0191.6475912
X-RAY DIFFRACTIONr_angle_other_deg1.5731.589338
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4595563
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.12721.857210
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.06915725
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0411528
X-RAY DIFFRACTIONr_chiral_restr0.1270.2555
X-RAY DIFFRACTIONr_gen_planes_refined0.0180.025021
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02959
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_it1.1011.0392159
X-RAY DIFFRACTIONr_mcbond_other1.0931.0372158
X-RAY DIFFRACTIONr_mcangle_it1.5721.5662753
X-RAY DIFFRACTIONr_mcangle_other1.5751.5672754
X-RAY DIFFRACTIONr_scbond_it2.2311.2742154
X-RAY DIFFRACTIONr_scbond_other2.2331.2752151
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.2831.8223160
X-RAY DIFFRACTIONr_long_range_B_refined3.9513.2644928
X-RAY DIFFRACTIONr_long_range_B_other3.79512.8514843
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.1→1.129 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.397 686 -
Rwork0.39 12849 -
obs--84.77 %

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