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- PDB-6tij: Structure of A. niger Fdc WT in complex with indol-2-carboxylic acid -

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Basic information

Entry
Database: PDB / ID: 6tij
TitleStructure of A. niger Fdc WT in complex with indol-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 / 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
hydroxylated prenyl-FMN / 1H-indole-2-carboxylic acid / : / : / Ferulic acid decarboxylase 1
Similarity search - Component
Biological speciesAspergillus niger (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.12 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)57,3347
Polymers56,3361
Non-polymers9986
Water11,818656
1
AAA: Ferulic acid decarboxylase 1
hetero molecules

AAA: Ferulic acid decarboxylase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,66814
Polymers112,6722
Non-polymers1,99612
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area8380 Å2
ΔGint-49 kcal/mol
Surface area33010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.781, 63.725, 87.707
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11AAA-1009-

HOH

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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, 662 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-BYN / hydroxylated prenyl-FMN


Mass: 542.476 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C22H31N4O10P / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-ICB / 1H-indole-2-carboxylic acid


Mass: 161.157 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H7NO2 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 656 / 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: 2.42 Å3/Da / Density % sol: 49.07 %
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: 1.12→64.79 Å / Num. obs: 204931 / % possible obs: 99.5 % / Redundancy: 6 % / CC1/2: 1 / Rrim(I) all: 0.093 / Net I/σ(I): 9.3
Reflection shellResolution: 1.12→1.14 Å / Mean I/σ(I) obs: 1.5 / Num. unique obs: 31550 / CC1/2: 0.5 / Rrim(I) all: 0.739 / % possible all: 91.9

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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: 1.12→64.685 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.974 / SU B: 1.214 / SU ML: 0.024 / Cross valid method: FREE R-VALUE / ESU R: 0.029 / ESU R Free: 0.031
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1686 10012 4.937 %
Rwork0.1397 --
all0.141 --
obs-202805 98.513 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 12.659 Å2
Baniso -1Baniso -2Baniso -3
1--0.022 Å20 Å20 Å2
2---0.149 Å20 Å2
3---0.171 Å2
Refinement stepCycle: LAST / Resolution: 1.12→64.685 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3852 0 64 656 4572
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0134323
X-RAY DIFFRACTIONr_bond_other_d0.0020.0173913
X-RAY DIFFRACTIONr_angle_refined_deg2.2241.6635937
X-RAY DIFFRACTIONr_angle_other_deg1.6861.5859129
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7835565
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.40522.376202
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.80315698
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.991524
X-RAY DIFFRACTIONr_chiral_restr0.1490.2560
X-RAY DIFFRACTIONr_gen_planes_refined0.0240.024996
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02892
X-RAY DIFFRACTIONr_nbd_refined0.2540.2966
X-RAY DIFFRACTIONr_symmetry_nbd_other0.20.23757
X-RAY DIFFRACTIONr_nbtor_refined0.1810.22077
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.090.21870
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.220.2407
X-RAY DIFFRACTIONr_metal_ion_refined0.0920.26
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2120.227
X-RAY DIFFRACTIONr_nbd_other0.2250.2103
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.3020.243
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.2310.21
X-RAY DIFFRACTIONr_mcbond_it2.0141.0472168
X-RAY DIFFRACTIONr_mcbond_other2.0041.0472168
X-RAY DIFFRACTIONr_mcangle_it2.1911.5782763
X-RAY DIFFRACTIONr_mcangle_other2.1941.5812764
X-RAY DIFFRACTIONr_scbond_it3.1171.2992155
X-RAY DIFFRACTIONr_scbond_other3.1171.32156
X-RAY DIFFRACTIONr_scangle_it3.6321.8593174
X-RAY DIFFRACTIONr_scangle_other3.6331.8593174
X-RAY DIFFRACTIONr_lrange_it4.18314.865254
X-RAY DIFFRACTIONr_lrange_other4.18314.865255
X-RAY DIFFRACTIONr_rigid_bond_restr5.22738236
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
1.12-1.1490.3576890.35130130.35150440.7320.7391.07950.332
1.149-1.180.3097100.301136390.301147580.830.82997.22860.28
1.18-1.2150.36930.262133480.263142860.8580.87298.2850.237
1.215-1.2520.2617040.243129900.244139110.8830.89298.44010.216
1.252-1.2930.2646580.228126350.229134850.890.90498.57620.199
1.293-1.3380.2486320.203123020.205130890.9090.92398.81580.176
1.338-1.3890.2186010.175118930.177126200.9360.94599.00160.149
1.389-1.4460.1945920.156114510.158121400.9420.95499.2010.132
1.446-1.510.1676030.129109440.131116390.9620.96899.20960.11
1.51-1.5830.1395140.106105630.108111460.9730.97999.38090.091
1.583-1.6690.1395580.095100540.097106520.9750.98299.62450.083
1.669-1.770.1274480.0995970.091100690.9790.98499.76170.08
1.77-1.8920.1194960.08589410.08794510.9830.98799.85190.079
1.892-2.0440.1284460.09284170.09488770.980.98699.84230.088
2.044-2.2390.1243810.09777560.09881420.9820.98599.93860.095
2.239-2.5030.1173680.09170450.09374180.9840.98799.93260.092
2.503-2.8890.1343180.10362680.10565900.9790.98499.93930.105
2.889-3.5360.1532600.13153290.13255920.9710.97799.94640.139
3.536-4.9940.1292070.11841940.11944030.9840.98599.95460.132
4.994-64.6850.1941340.18124150.18125540.9640.9799.80420.201

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