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- PDB-6tio: Structure of A. niger Fdc Wt in complex with FMN and benzothiophe... -

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Basic information

Entry
Database: PDB / ID: 6tio
TitleStructure of A. niger Fdc Wt in complex with FMN and benzothiophene 2 carboxylic acid
ComponentsFerulic acid decarboxylase 1
KeywordsLIGASE / (de)carboxylase / UbiD / aromatic acid / 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 / 3-octaprenyl-4-hydroxybenzoate carboxy-lyase activity / ubiquinone biosynthetic process / manganese ion binding / identical protein 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
FLAVIN MONONUCLEOTIDE / : / : / benzothiophene 2 carboxylic acid / Ferulic acid decarboxylase 1
Similarity search - Component
Biological speciesAspergillus niger (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.54 Å
AuthorsLeys, D.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/K017802 United Kingdom
European Research Councilpre-FAB 695013 United Kingdom
CitationJournal: Nat.Chem.Biol. / Year: 2020
Title: Enzymatic C-H activation of aromatic compounds through CO 2 fixation.
Authors: Aleku, G.A. / Saaret, A. / Bradshaw-Allen, R.T. / Derrington, S.R. / Titchiner, G.R. / Gostimskaya, I. / Gahloth, D. / Parker, D.A. / Hay, S. / Leys, D.
History
DepositionNov 22, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 24, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 12, 2020Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_struct_conn_angle / struct_conn
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Revision 1.2Sep 30, 2020Group: Database references / Category: citation / Item: _citation.title
Revision 1.3Oct 28, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.4Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _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
AAA: Ferulic acid decarboxylase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,1046
Polymers56,3361
Non-polymers7685
Water8,341463
1
AAA: Ferulic acid decarboxylase 1
hetero molecules

AAA: Ferulic acid decarboxylase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,20712
Polymers112,6722
Non-polymers1,53510
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area10650 Å2
ΔGint-68 kcal/mol
Surface area31350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.390, 63.283, 87.501
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 1 types, 1 molecules AAA

#1: Protein Ferulic acid decarboxylase 1 / Phenacrylate decarboxylase


Mass: 56335.945 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus niger (mold) / Gene: fdc1, An03g06590 / Production host: Escherichia coli (E. coli) / References: UniProt: A2QHE5, phenacrylate decarboxylase

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Non-polymers , 5 types, 468 molecules

#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-ND8 / benzothiophene 2 carboxylic acid


Mass: 178.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H6O2S / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 463 / 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: 2.34 Å3/Da / Density % sol: 47.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M potassium thiocyanate, Bis-Tris propane pH 6.5, 20% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 22, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.54→95.57 Å / Num. obs: 78889 / % possible obs: 99.8 % / Redundancy: 5 % / CC1/2: 1 / Rrim(I) all: 0.136 / Net I/σ(I): 6.9
Reflection shellResolution: 1.54→1.57 Å / Mean I/σ(I) obs: 1.7 / Num. unique obs: 19027 / CC1/2: 0.5 / Rrim(I) all: 0.816

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
DIALSdata reduction
DIALSdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 4ZAA

4zaa


Resolution: 1.54→64.482 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.957 / SU B: 4.656 / SU ML: 0.067 / Cross valid method: FREE R-VALUE / ESU R: 0.085 / ESU R Free: 0.075
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1951 3869 4.908 %
Rwork0.1479 --
all0.15 --
obs-78838 99.736 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 18.2 Å2
Baniso -1Baniso -2Baniso -3
1-0.328 Å20 Å20 Å2
2---0.449 Å20 Å2
3---0.121 Å2
Refinement stepCycle: LAST / Resolution: 1.54→64.482 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3807 0 46 463 4316
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0134224
X-RAY DIFFRACTIONr_bond_other_d0.0020.0173834
X-RAY DIFFRACTIONr_angle_refined_deg1.981.6595793
X-RAY DIFFRACTIONr_angle_other_deg1.591.5818935
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7885556
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.5421.929197
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.43715682
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.3441526
X-RAY DIFFRACTIONr_chiral_restr0.1130.2550
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.024886
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02882
X-RAY DIFFRACTIONr_nbd_refined0.2390.2924
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1940.23667
X-RAY DIFFRACTIONr_nbtor_refined0.1710.22017
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0850.21715
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1970.2336
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0380.21
X-RAY DIFFRACTIONr_metal_ion_refined0.1020.26
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2450.221
X-RAY DIFFRACTIONr_nbd_other0.2220.295
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2380.242
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0760.22
X-RAY DIFFRACTIONr_mcbond_it2.8411.7392139
X-RAY DIFFRACTIONr_mcbond_other2.8351.7382138
X-RAY DIFFRACTIONr_mcangle_it3.4042.6172723
X-RAY DIFFRACTIONr_mcangle_other3.4052.6182724
X-RAY DIFFRACTIONr_scbond_it3.2911.9382085
X-RAY DIFFRACTIONr_scbond_other3.2911.9382086
X-RAY DIFFRACTIONr_scangle_it3.7452.8273070
X-RAY DIFFRACTIONr_scangle_other3.7422.8263070
X-RAY DIFFRACTIONr_lrange_it4.66322.1175007
X-RAY DIFFRACTIONr_lrange_other4.66222.1155008
X-RAY DIFFRACTIONr_rigid_bond_restr3.83838057
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.54-1.580.382310.34454370.34557510.560.57898.55680.318
1.58-1.6230.3232700.30953630.30956350.7030.7299.96450.28
1.623-1.670.322730.28351730.28554470.730.76199.98160.259
1.67-1.7210.322650.24650710.2553430.7750.82399.8690.224
1.721-1.7780.252370.21349340.21551770.8650.87899.88410.192
1.778-1.840.2422650.17447020.17849670.910.9241000.154
1.84-1.9090.2062360.1546370.15348750.9260.94299.9590.131
1.909-1.9870.2112080.13844330.14246530.9350.95199.74210.12
1.987-2.0760.1692310.1242250.12244590.9570.96499.93270.105
2.076-2.1770.1782240.11140480.11442860.9560.9799.67340.099
2.177-2.2940.1822030.10238770.10640850.9580.97599.87760.091
2.294-2.4330.1541680.09937160.10138840.9670.9781000.09
2.433-2.6010.161710.09834410.10136160.9680.97999.88940.089
2.601-2.8090.1711950.10932000.11334070.9660.97599.64780.101
2.809-3.0770.1661500.12429680.12631430.9680.97499.20460.116
3.077-3.4390.1781540.13927010.14128550.9670.9751000.132
3.439-3.9690.1661400.12724160.12925560.9710.9791000.119
3.969-4.8560.1451210.11120410.11321690.9810.98499.67730.1
4.856-6.8490.188780.15816280.15917190.9760.97999.24380.148
6.849-64.4820.207490.1799580.1810190.9570.96798.82240.163

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