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- PDB-6ev4: Structure of wild type A. niger Fdc1 purified in the dark with pr... -

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Basic information

Entry
Database: PDB / ID: 6ev4
TitleStructure of wild type A. niger Fdc1 purified in the dark with prFMN in the iminium form
ComponentsFerulic acid decarboxylase 1
KeywordsLYASE
Function / homology
Function and homology information


styrene metabolic process / aromatic amino acid family catabolic process / phenacrylate decarboxylase / 3-octaprenyl-4-hydroxybenzoate carboxy-lyase activity / ferulate metabolic process / cinnamic acid catabolic process / 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
Chem-4LU / : / : / Ferulic acid decarboxylase 1
Similarity search - Component
Biological speciesAspergillus niger (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.14 Å
AuthorsBailey, S.S. / David, L. / Payne, K.A.P.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council United Kingdom
CitationJournal: J. Biol. Chem. / Year: 2018
Title: The role of conserved residues in Fdc decarboxylase in prenylated flavin mononucleotide oxidative maturation, cofactor isomerization, and catalysis.
Authors: Bailey, S.S. / Payne, K.A.P. / Fisher, K. / Marshall, S.A. / Cliff, M.J. / Spiess, R. / Parker, D.A. / Rigby, S.E.J. / Leys, D.
History
DepositionNov 1, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 27, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 3, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 31, 2018Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Feb 28, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year / _citation_author.name
Revision 1.4May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_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

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Assembly

Deposited unit
A: Ferulic acid decarboxylase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,9955
Polymers56,3361
Non-polymers6594
Water15,223845
1
A: Ferulic acid decarboxylase 1
hetero molecules

A: Ferulic acid decarboxylase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,98910
Polymers112,6722
Non-polymers1,3178
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area8370 Å2
ΔGint-48 kcal/mol
Surface area33130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.970, 64.030, 87.630
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#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 (strain CBS 513.88 / FGSC A1513) (mold)
Strain: CBS 513.88 / FGSC A1513 / Gene: fdc1, An03g06590 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A2QHE5, phenacrylate decarboxylase
#2: Chemical ChemComp-4LU / 1-deoxy-5-O-phosphono-1-(3,3,4,5-tetramethyl-9,11-dioxo-2,3,8,9,10,11-hexahydro-7H-quinolino[1,8-fg]pteridin-12-ium-7-y l)-D-ribitol / prenylated-FMN iminium form


Mass: 525.469 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H30N4O9P
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 845 / 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: 2.39 Å3/Da / Density % sol: 48.53 %
Crystal growTemperature: 277 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
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 5, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.14→47.99 Å / Num. obs: 186270 / % possible obs: 94.9 % / Redundancy: 3.6 % / Net I/σ(I): 9.8
Reflection shellResolution: 1.14→1.181 Å / Redundancy: 2.4 % / Num. unique obs: 18286 / Rrim(I) all: 0.807

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
xia2data reduction
xia2data scaling
REFMACphasing
RefinementResolution: 1.14→47.98 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.971 / SU B: 0.526 / SU ML: 0.024 / Cross valid method: THROUGHOUT / ESU R: 0.031 / ESU R Free: 0.033 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16732 9349 5 %RANDOM
Rwork0.14872 ---
obs0.14965 176880 94.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.826 Å2
Baniso -1Baniso -2Baniso -3
1--0.18 Å20 Å20 Å2
2--0.31 Å20 Å2
3----0.13 Å2
Refinement stepCycle: 1 / Resolution: 1.14→47.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3852 0 39 845 4736
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0194303
X-RAY DIFFRACTIONr_bond_other_d0.0030.023893
X-RAY DIFFRACTIONr_angle_refined_deg2.4171.9685877
X-RAY DIFFRACTIONr_angle_other_deg1.24439078
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5955562
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.70624.011177
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.25615699
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6051524
X-RAY DIFFRACTIONr_chiral_restr0.1770.2639
X-RAY DIFFRACTIONr_gen_planes_refined0.0190.0214912
X-RAY DIFFRACTIONr_gen_planes_other0.0090.02857
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_it1.0840.9162159
X-RAY DIFFRACTIONr_mcbond_other1.0840.9172160
X-RAY DIFFRACTIONr_mcangle_it1.5361.3782750
X-RAY DIFFRACTIONr_mcangle_other1.5361.3792751
X-RAY DIFFRACTIONr_scbond_it2.0781.0792141
X-RAY DIFFRACTIONr_scbond_other2.0771.0792142
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.8721.5613128
X-RAY DIFFRACTIONr_long_range_B_refined15.5314.5125468
X-RAY DIFFRACTIONr_long_range_B_other13.03112.7925110
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.14→1.17 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 629 -
Rwork0.29 12865 -
obs--93.91 %

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