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- PDB-6tie: Structure of A. niger Fdc I327S variant in complex with indol-2-c... -

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Basic information

Entry
Database: PDB / ID: 6tie
TitleStructure of A. niger Fdc I327S variant in complex with indol-2-carboxylic acid
ComponentsFerulic acid decarboxylase 1
KeywordsLIGASE / (de)carboxylase / UbiD / aromatic acid / prFMN
Function / homology
Function and homology information


phenacrylate decarboxylase / ferulate metabolic process / cinnamic acid catabolic process / carboxy-lyase activity / metal ion 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: 1.06 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 / Refinement description
Category: citation / citation_author ...citation / citation_author / pdbx_struct_conn_angle / software / 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 / _software.name / _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)57,1777
Polymers56,1791
Non-polymers9986
Water11,007611
1
AAA: Ferulic acid decarboxylase 1
hetero molecules

AAA: Ferulic acid decarboxylase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,35314
Polymers112,3572
Non-polymers1,99612
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area8370 Å2
ΔGint-48 kcal/mol
Surface area33030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.703, 63.798, 87.700
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-975-

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: 56178.676 Da / Num. of mol.: 1 / Mutation: I327S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus niger (mold) / Gene: FDC1, ATCC64974_75990, CAN33_0036860 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A3F3RNU4, phenacrylate decarboxylase

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Non-polymers , 5 types, 617 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.: 611 / 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: 49.11 %
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: I04-1 / Wavelength: 0.916 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 14, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.916 Å / Relative weight: 1
ReflectionResolution: 1.06→87.7 Å / Num. obs: 196014 / % possible obs: 95.9 % / Redundancy: 6.6 % / CC1/2: 1 / Rrim(I) all: 0.172 / Net I/σ(I): 6
Reflection shellResolution: 1.06→1.12 Å / Mean I/σ(I) obs: 1.5 / Num. unique obs: 1093 / CC1/2: 0.7 / Rrim(I) all: 1.016 / % possible all: 75.9

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Processing

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

4zaa


Resolution: 1.06→87.7 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.971 / SU B: 1.06 / SU ML: 0.022 / Cross valid method: FREE R-VALUE / ESU R: 0.029 / ESU R Free: 0.029
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1581 9773 4.986 %
Rwork0.1346 --
all0.136 --
obs-196014 78.833 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 12.073 Å2
Baniso -1Baniso -2Baniso -3
1-0.171 Å20 Å20 Å2
2---0.743 Å20 Å2
3---0.571 Å2
Refinement stepCycle: LAST / Resolution: 1.06→87.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3850 0 64 611 4525
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0134335
X-RAY DIFFRACTIONr_bond_other_d0.0030.0173920
X-RAY DIFFRACTIONr_angle_refined_deg2.2271.6635952
X-RAY DIFFRACTIONr_angle_other_deg1.6931.5859147
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8095567
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.15822.376202
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.76815701
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.8981524
X-RAY DIFFRACTIONr_chiral_restr0.1420.2561
X-RAY DIFFRACTIONr_gen_planes_refined0.0250.025010
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02895
X-RAY DIFFRACTIONr_nbd_refined0.2720.2973
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1980.23789
X-RAY DIFFRACTIONr_nbtor_refined0.1810.22091
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0910.21877
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1860.2398
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1490.21
X-RAY DIFFRACTIONr_metal_ion_refined0.0840.27
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1920.230
X-RAY DIFFRACTIONr_nbd_other0.2310.2112
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2460.243
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1560.21
X-RAY DIFFRACTIONr_mcbond_it2.0930.9932176
X-RAY DIFFRACTIONr_mcbond_other2.0930.9932176
X-RAY DIFFRACTIONr_mcangle_it2.2771.4972773
X-RAY DIFFRACTIONr_mcangle_other2.2791.52774
X-RAY DIFFRACTIONr_scbond_it3.6881.2512159
X-RAY DIFFRACTIONr_scbond_other3.6881.2532160
X-RAY DIFFRACTIONr_scangle_it3.9051.7913179
X-RAY DIFFRACTIONr_scangle_other3.9041.7913179
X-RAY DIFFRACTIONr_lrange_it4.17114.0075258
X-RAY DIFFRACTIONr_lrange_other4.17114.0095259
X-RAY DIFFRACTIONr_rigid_bond_restr9.1238255
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
1.051-1.0780.351610.29910930.302182600.8530.8496.31980.297
1.078-1.1080.2862910.2754210.271177700.8790.87232.14410.27
1.108-1.140.2474770.23986960.24173310.8840.88852.92830.237
1.14-1.1750.2185210.204101190.205167380.9140.91963.56790.199
1.175-1.2140.1975340.185110020.185163150.9290.93370.70790.176
1.214-1.2560.2085830.18119170.181157760.9230.93579.23430.169
1.256-1.3040.1997380.173134530.174152260.9330.94293.20240.158
1.304-1.3570.1727340.151139170.152146630.9540.95599.91820.136
1.357-1.4170.1547230.13133630.132140860.9620.9661000.119
1.417-1.4860.1556580.116128230.118134830.9650.97399.98520.108
1.486-1.5670.1346500.106121690.108128200.9740.97899.99220.102
1.567-1.6620.146110.102115480.104121590.9750.981000.102
1.662-1.7770.1315870.104108570.105114440.9780.9811000.106
1.777-1.9190.1415210.109101360.11106580.9760.98199.99060.117
1.919-2.1020.1435380.1293160.12198570.9740.97999.96960.134
2.102-2.350.1434540.11584940.11789510.9750.98199.96650.136
2.35-2.7130.1453740.11475400.11679150.9730.9899.98740.141
2.713-3.3220.1463160.13664260.13667460.9730.97599.94070.167
3.322-4.6940.1562560.13550450.13653080.9730.97799.86810.178
4.694-87.70.1921470.19429060.19430610.9710.96899.73860.261

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