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- PDB-4za4: Structure of A. niger Fdc1 with the prenylated-flavin cofactor in... -

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Basic information

Entry
Database: PDB / ID: 4za4
TitleStructure of A. niger Fdc1 with the prenylated-flavin cofactor in the iminium form.
ComponentsFdc1
KeywordsLYASE / (de)carboxylase / prenylated flavin binding / UbiD-type enzyme
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
Chem-4LU / : / : / Ferulic acid decarboxylase 1
Similarity search - Component
Biological speciesAspergillus niger (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.22 Å
AuthorsPayne, K.A.P. / Leys, D.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council United Kingdom
CitationJournal: Nature / Year: 2015
Title: New cofactor supports alpha , beta-unsaturated acid decarboxylation via 1,3-dipolar cycloaddition.
Authors: Payne, K.A. / White, M.D. / Fisher, K. / Khara, B. / Bailey, S.S. / Parker, D. / Rattray, N.J. / Trivedi, D.K. / Goodacre, R. / Beveridge, R. / Barran, P. / Rigby, S.E. / Scrutton, N.S. / Hay, S. / Leys, D.
History
DepositionApr 13, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 17, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 1, 2015Group: Database references
Revision 1.2Aug 30, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3May 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: Fdc1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,9955
Polymers56,3361
Non-polymers6594
Water8,053447
1
A: Fdc1
hetero molecules

A: Fdc1
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 area33200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.990, 63.930, 87.630
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-854-

HOH

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Components

#1: Protein Fdc1


Mass: 56335.945 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus niger (mold) / Gene: An03g06590 / Production host: Escherichia coli (E. coli)
References: UniProt: A2QHE5, 4-hydroxybenzoate 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.: 447 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.39 Å3/Da / Density % sol: 48.46 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: Initial screening of 0.3 microl 14 mg/ml A. niger Fdc1 in 100 mM NaCl, 25 mM Tris pH 7.5 and 0.3 microl reservoir solution at 4C resulted in a number of hits including PACT condition F4 ...Details: Initial screening of 0.3 microl 14 mg/ml A. niger Fdc1 in 100 mM NaCl, 25 mM Tris pH 7.5 and 0.3 microl reservoir solution at 4C resulted in a number of hits including PACT condition F4 (molecular dimensions). Seed stock produced from these crystals was used in an optimization screen based around 0.2 M potassium thiocyanate, Bis-Tris propane 6.5, 20 % w/v PEG 3350 mixing 0.05 microl seed stock, 0.25 microl protein solution and 0.3 microl reservoir solution at 4C.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.987 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 9, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.22→33.82 Å / Num. obs: 152260 / % possible obs: 99.96 % / Redundancy: 6.1 % / Rpim(I) all: 0.037 / Net I/σ(I): 11.2
Reflection shellResolution: 1.22→1.25 Å / Redundancy: 5.8 % / Mean I/σ(I) obs: 2 / Rpim(I) all: 0.354 / % possible all: 99.99

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.22→33.82 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.966 / SU B: 1.226 / SU ML: 0.025 / Cross valid method: THROUGHOUT / ESU R: 0.037 / ESU R Free: 0.035 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16111 8041 5 %RANDOM
Rwork0.14573 ---
obs0.14652 152260 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 9.809 Å2
Baniso -1Baniso -2Baniso -3
1-1.04 Å2-0 Å20 Å2
2---2.27 Å2-0 Å2
3---1.24 Å2
Refinement stepCycle: 1 / Resolution: 1.22→33.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3847 0 39 447 4333
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0280.0224280
X-RAY DIFFRACTIONr_bond_other_d00.022860
X-RAY DIFFRACTIONr_angle_refined_deg2.3841.9715876
X-RAY DIFFRACTIONr_angle_other_deg4.39337023
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6035563
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.56924.034176
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.31115698
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.0661524
X-RAY DIFFRACTIONr_chiral_restr0.1580.2638
X-RAY DIFFRACTIONr_gen_planes_refined0.0180.0214920
X-RAY DIFFRACTIONr_gen_planes_other0.020.02840
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_it2.3381.52691
X-RAY DIFFRACTIONr_mcbond_other7.5171.51071
X-RAY DIFFRACTIONr_mcangle_it3.09624394
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.87331589
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it6.5694.51482
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr5.0937140
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.22→1.252 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.264 578 -
Rwork0.236 11168 -
obs--99.99 %

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