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- PDB-6tin: Structure of A. niger Fdc WT in complex with FMN and indole 2 car... -

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Basic information

Entry
Database: PDB / ID: 6tin
TitleStructure of A. niger Fdc WT in complex with FMN and indole 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 / 1H-indole-2-carboxylic acid / : / : / Ferulic acid decarboxylase 1
Similarity search - Component
Biological speciesAspergillus niger (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.28 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

Downloads & links

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Assembly

Deposited unit
AAA: Ferulic acid decarboxylase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,0876
Polymers56,3361
Non-polymers7515
Water8,359464
1
AAA: Ferulic acid decarboxylase 1
hetero molecules

AAA: Ferulic acid decarboxylase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,17312
Polymers112,6722
Non-polymers1,50110
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area10680 Å2
ΔGint-65 kcal/mol
Surface area31610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.894, 63.934, 87.668
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, 469 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-ICB / 1H-indole-2-carboxylic acid


Mass: 161.157 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H7NO2 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 464 / 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: 2.39 Å3/Da / Density % sol: 48.43 %
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: I04 / Wavelength: 0.975 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 25, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.975 Å / Relative weight: 1
ReflectionResolution: 1.28→64.79 Å / Num. obs: 139040 / % possible obs: 100 % / Redundancy: 6.4 % / CC1/2: 1 / Rrim(I) all: 0.12 / Net I/σ(I): 8.5
Reflection shellResolution: 1.28→1.3 Å / Mean I/σ(I) obs: 1.8 / Num. unique obs: 39655 / CC1/2: 0.5 / Rrim(I) all: 0.818 / % possible all: 98.9

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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: 1.28→64.704 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.961 / SU B: 2.216 / SU ML: 0.039 / Cross valid method: FREE R-VALUE / ESU R: 0.048 / ESU R Free: 0.048
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1976 6826 4.972 %
Rwork0.1604 --
all0.162 --
obs-137282 98.717 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 11.866 Å2
Baniso -1Baniso -2Baniso -3
1-0.117 Å20 Å20 Å2
2---0.174 Å20 Å2
3---0.057 Å2
Refinement stepCycle: LAST / Resolution: 1.28→64.704 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3807 0 46 464 4317
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0134244
X-RAY DIFFRACTIONr_bond_other_d0.0030.0173854
X-RAY DIFFRACTIONr_angle_refined_deg2.2231.6625819
X-RAY DIFFRACTIONr_angle_other_deg1.6811.5838976
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7765556
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.621.929197
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.34115684
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.7531526
X-RAY DIFFRACTIONr_chiral_restr0.1290.2551
X-RAY DIFFRACTIONr_gen_planes_refined0.0170.024900
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02891
X-RAY DIFFRACTIONr_nbd_refined0.2470.2904
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1930.23657
X-RAY DIFFRACTIONr_nbtor_refined0.1760.22023
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0880.21783
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1660.2310
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0390.21
X-RAY DIFFRACTIONr_metal_ion_refined0.1190.25
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2150.220
X-RAY DIFFRACTIONr_nbd_other0.2250.286
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.240.230
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0220.21
X-RAY DIFFRACTIONr_mcbond_it2.0651.0612142
X-RAY DIFFRACTIONr_mcbond_other2.0651.062141
X-RAY DIFFRACTIONr_mcangle_it2.4151.6022725
X-RAY DIFFRACTIONr_mcangle_other2.4141.6032726
X-RAY DIFFRACTIONr_scbond_it2.9311.2662102
X-RAY DIFFRACTIONr_scbond_other2.9311.2662103
X-RAY DIFFRACTIONr_scangle_it3.331.8173094
X-RAY DIFFRACTIONr_scangle_other3.3291.8163093
X-RAY DIFFRACTIONr_lrange_it3.99913.7914992
X-RAY DIFFRACTIONr_lrange_other3.99913.794993
X-RAY DIFFRACTIONr_rigid_bond_restr4.98138097
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
1.28-1.3130.364730.33393350.334101480.7380.76696.64960.324
1.313-1.3490.3585550.32591140.32799010.7630.77897.65680.311
1.349-1.3880.364610.30190010.30397020.7970.81897.52630.283
1.388-1.4310.2984280.26587420.26693800.8550.86597.76120.244
1.431-1.4780.3164350.24684890.24991010.8620.88498.05520.222
1.478-1.5290.2554500.20482260.20788050.9020.91998.53490.179
1.529-1.5870.2574410.19179430.19484970.910.92798.67010.166
1.587-1.6520.2133950.16177350.16482150.9380.94898.96530.138
1.652-1.7250.2223910.14874200.15178740.9350.95499.19990.126
1.725-1.8090.23300.13671520.13975400.9510.96199.23080.117
1.809-1.9070.1763570.11967850.12171770.9620.97299.51230.103
1.907-2.0230.1613370.1264470.12268030.9660.97699.72070.107
2.023-2.1620.1463100.11760690.11964010.9760.97899.65630.107
2.162-2.3350.1422930.11256640.11459750.9760.9899.69870.103
2.335-2.5580.1582780.10852360.1155240.9720.97999.8190.1
2.558-2.8590.1442430.11547660.11650270.9760.9899.64190.108
2.859-3.3010.1572160.14442370.14444560.9710.97499.93270.14
3.301-4.040.1521980.14735900.14737930.9750.97599.86820.147
4.04-5.7020.1671430.12928490.13129930.9790.98699.96660.133
5.702-64.7040.175920.19516550.19417520.9510.9699.71460.194

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