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- PDB-6tib: Structure of A. niger Fdc I327S variant in complex with 2 naphtho... -

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Basic information

Entry
Database: PDB / ID: 6tib
TitleStructure of A. niger Fdc I327S variant in complex with 2 naphthoic 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 / naphthalene-2-carboxylic acid / : / : / DI(HYDROXYETHYL)ETHER / Ferulic acid decarboxylase 1
Similarity search - Component
Biological speciesAspergillus niger (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.07 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)57,2647
Polymers56,3101
Non-polymers9546
Water13,241735
1
AAA: Ferulic acid decarboxylase 1
hetero molecules

AAA: Ferulic acid decarboxylase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,52814
Polymers112,6202
Non-polymers1,90812
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area9030 Å2
ΔGint-38 kcal/mol
Surface area32810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.642, 63.592, 87.741
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-1085-

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: 56309.867 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 , 6 types, 741 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-FIV / naphthalene-2-carboxylic acid / 2-naphthoic acid


Mass: 172.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H8O2 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 735 / 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: 2.37 Å3/Da / Density % sol: 48.08 %
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: 0.9159 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: 0.9159 Å / Relative weight: 1
ReflectionResolution: 1.07→87.74 Å / Num. obs: 169880 / % possible obs: 95.6 % / Redundancy: 6.5 % / CC1/2: 1 / Rrim(I) all: 0.158 / Net I/σ(I): 6.5
Reflection shellResolution: 1.07→1.17 Å / Mean I/σ(I) obs: 1.6 / Num. unique obs: 638 / CC1/2: 0.7 / Rrim(I) all: 1.127 / % possible all: 73.9

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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: 1.07→87.74 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.974 / SU B: 1.267 / SU ML: 0.025 / Cross valid method: FREE R-VALUE / ESU R: 0.031 / ESU R Free: 0.032
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1519 8543 5.029 %
Rwork0.1243 --
all0.126 --
obs-169880 72.058 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 12.67 Å2
Baniso -1Baniso -2Baniso -3
1-0.363 Å20 Å20 Å2
2---0.335 Å20 Å2
3----0.028 Å2
Refinement stepCycle: LAST / Resolution: 1.07→87.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3850 0 60 735 4645
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0134316
X-RAY DIFFRACTIONr_bond_other_d0.0030.0173913
X-RAY DIFFRACTIONr_angle_refined_deg2.1481.6585920
X-RAY DIFFRACTIONr_angle_other_deg1.6761.5829131
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7745564
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.92922.376202
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.82215701
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.2311524
X-RAY DIFFRACTIONr_chiral_restr0.1420.2560
X-RAY DIFFRACTIONr_gen_planes_refined0.0230.024975
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02887
X-RAY DIFFRACTIONr_nbd_refined0.2650.2986
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2050.23812
X-RAY DIFFRACTIONr_nbtor_refined0.180.22087
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0880.21897
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2290.2478
X-RAY DIFFRACTIONr_metal_ion_refined0.0970.26
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.330.227
X-RAY DIFFRACTIONr_nbd_other0.2920.2110
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.290.239
X-RAY DIFFRACTIONr_mcbond_it2.0461.0452167
X-RAY DIFFRACTIONr_mcbond_other1.9681.0452167
X-RAY DIFFRACTIONr_mcangle_it2.091.5772760
X-RAY DIFFRACTIONr_mcangle_other2.1221.5792761
X-RAY DIFFRACTIONr_scbond_it4.0711.2932149
X-RAY DIFFRACTIONr_scbond_other4.0721.2952150
X-RAY DIFFRACTIONr_scangle_it4.5311.8473160
X-RAY DIFFRACTIONr_scangle_other4.531.8483161
X-RAY DIFFRACTIONr_lrange_it3.88815.0125339
X-RAY DIFFRACTIONr_lrange_other3.44313.5945114
X-RAY DIFFRACTIONr_rigid_bond_restr5.29338229
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
1.069-1.0970.305370.2386380.241173520.7780.8363.890.242
1.097-1.1270.2571070.23921720.24168260.8720.88313.54450.24
1.127-1.1590.2462240.23141300.232163780.8910.88826.58440.229
1.159-1.1950.2473220.22562790.226159280.8770.8941.44270.224
1.195-1.2340.2344070.21882170.219154830.9010.90355.69980.214
1.234-1.2770.2085210.205101790.205149350.920.92171.64380.2
1.277-1.3260.2076430.177121200.178144810.9230.93388.13620.172
1.326-1.380.186360.153128240.154138790.9460.95196.9810.147
1.38-1.4410.1686820.136126210.137133390.9540.96199.73010.128
1.441-1.5110.1576480.116121430.118127930.9650.97199.98440.109
1.511-1.5930.1416650.102115300.104121990.9730.97999.96720.095
1.593-1.690.1255750.089109180.091114940.9790.98499.99130.085
1.69-1.8060.1275430.085103240.088108670.9790.9851000.083
1.806-1.9510.1245140.09295950.093101120.9820.98599.97030.092
1.951-2.1370.1314910.09988530.10193490.980.98599.94650.105
2.137-2.3890.1234480.09180210.09384720.9820.98699.96460.102
2.389-2.7580.1323690.10371650.10475380.9790.98399.94690.119
2.758-3.3780.1393160.12460820.12464010.9760.97899.95310.148
3.378-4.7730.142540.12147640.12250210.9810.98399.94030.156
4.773-87.7410.2131410.18727620.18829090.9660.96999.79370.244

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