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- PDB-6r3l: Aspergillus niger ferulic acid decarboxylase (Fdc) in complex wit... -

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Basic information

Entry
Database: PDB / ID: 6r3l
TitleAspergillus niger ferulic acid decarboxylase (Fdc) in complex with the covalent adduct formed between prFMN cofactor and cinnamic acid following decarboxylation (Int3)
ComponentsFerulic acid decarboxylase 1
KeywordsLYASE / (de)carboxylase / UbiD / prFMN binding
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 / prFMN cofactor and cinnamic acid adduct / : / : / ethenylbenzene / Ferulic acid decarboxylase 1
Similarity search - Component
Biological speciesAspergillus niger (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.24 Å
AuthorsBailey, S.S. / Leys, D.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
European Research CouncilpreFAB 695013 United Kingdom
Biotechnology and Biological Sciences Research CouncilBB/K017802 United Kingdom
CitationJournal: To be published
Title: Atomic description of an enzyme reaction dependent on reversible 1,3-dipolar cycloaddition
Authors: Bailey, S.S. / Payne, K.A.P. / Saaret, A. / Marshall, S.A. / Gostimskaya, I. / Kosov, I. / Fisher, K. / Hay, S. / Leys, D.
History
DepositionMar 20, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 28, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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_alt_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.pdbx_ptnr2_label_alt_id / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ferulic acid decarboxylase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,7447
Polymers56,3361
Non-polymers1,4086
Water12,592699
1
A: Ferulic acid decarboxylase 1
hetero molecules

A: Ferulic acid decarboxylase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,48914
Polymers112,6722
Non-polymers2,81712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area8380 Å2
ΔGint-49 kcal/mol
Surface area33190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.923, 64.219, 87.773
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-1038-

HOH

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Components

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Protein , 1 types, 1 molecules A

#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 , 6 types, 705 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-JSH / prFMN cofactor and cinnamic acid adduct


Mass: 628.610 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H37N4O9P
#5: Chemical ChemComp-BYN / hydroxylated prenyl-FMN


Mass: 542.476 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H31N4O10P
#6: Chemical ChemComp-SYN / ethenylbenzene / styrene


Mass: 104.149 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H8
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 699 / Source method: isolated from a natural source / Formula: H2O

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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: 2.4 Å3/Da / Density % sol: 48.74 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.2 M POTASSIUM THIOCYANATE, BIS-TRIS PROPANE 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 300K / 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: 1.24→87.77 Å / Num. obs: 153420 / % possible obs: 99.8 % / Redundancy: 4.3 % / Net I/σ(I): 7.41
Reflection shellResolution: 1.24→1.28 Å / Mean I/σ(I) obs: 1.76 / Num. unique obs: 15174

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
xia2data reduction
xia2data scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 4ZA9

4za9


Resolution: 1.24→87.77 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.973 / SU B: 1.699 / SU ML: 0.031 / Cross valid method: THROUGHOUT / ESU R: 0.036 / ESU R Free: 0.039 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.167 7551 4.9 %RANDOM
Rwork0.13 ---
obs0.132 145843 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 12.99 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2---0.15 Å20 Å2
3---0.13 Å2
Refinement stepCycle: LAST / Resolution: 1.24→87.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3852 0 92 699 4643
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0194344
X-RAY DIFFRACTIONr_bond_other_d0.0020.023931
X-RAY DIFFRACTIONr_angle_refined_deg2.3571.9585972
X-RAY DIFFRACTIONr_angle_other_deg1.292.989169
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5855563
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.44623.778180
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.73815699
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.5171524
X-RAY DIFFRACTIONr_chiral_restr0.4520.2644
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.0214982
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02867
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4741.0592163
X-RAY DIFFRACTIONr_mcbond_other1.4741.062164
X-RAY DIFFRACTIONr_mcangle_it1.7331.5952755
X-RAY DIFFRACTIONr_mcangle_other1.7371.5962756
X-RAY DIFFRACTIONr_scbond_it2.561.252181
X-RAY DIFFRACTIONr_scbond_other2.561.252182
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.7711.8013218
X-RAY DIFFRACTIONr_long_range_B_refined3.90615.3945217
X-RAY DIFFRACTIONr_long_range_B_other3.90615.3945218
X-RAY DIFFRACTIONr_rigid_bond_restr5.26538274
X-RAY DIFFRACTIONr_sphericity_free24.2075425
X-RAY DIFFRACTIONr_sphericity_bonded7.29958410
LS refinement shellResolution: 1.24→1.27 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 552 -
Rwork0.269 10681 -
obs--99.87 %

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