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- PDB-4za5: Structure of A. niger Fdc1 with the prenylated-flavin cofactor in... -

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Basic information

Entry
Database: PDB / ID: 4za5
TitleStructure of A. niger Fdc1 with the prenylated-flavin cofactor in the iminium and ketimine forms.
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 / 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 / Chem-FZZ / : / : / Ferulic acid decarboxylase 1
Similarity search - Component
Biological speciesAspergillus niger (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å
AuthorsPayne, K.A.P. / Leys, D.
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 1.2May 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.pdbx_ptnr1_label_alt_id / _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)57,5196
Polymers56,3361
Non-polymers1,1835
Water8,485471
1
A: Fdc1
hetero molecules

A: Fdc1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,03812
Polymers112,6722
Non-polymers2,36610
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area8370 Å2
ΔGint-48 kcal/mol
Surface area32700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.020, 63.790, 87.720
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-936-

HOH

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Components

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Protein , 1 types, 1 molecules A

#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

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Non-polymers , 5 types, 476 molecules

#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-FZZ / 1-deoxy-5-O-phosphono-1-[(10aR)-2,2,3,4-tetramethyl-8,10-dioxo-1,2,8,9,10,10a-hexahydro-6H-indeno[1,7-ef]pyrimido[4,5-b][1,4]diazepin-6-yl]-D-ribitol


Mass: 524.461 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H29N4O9P
#4: Chemical ChemComp-MN / MANGANESE (II) ION


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


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


Mass: 18.015 Da / Num. of mol.: 471 / 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: 2.38 Å3/Da / Density % sol: 48.41 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging 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
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.987 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Aug 13, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.1→48.01 Å / Num. obs: 206025 / % possible obs: 99.97 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.032 / Net I/σ(I): 12.6
Reflection shellResolution: 1.1→1.13 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.378 / Mean I/σ(I) obs: 2.1 / % 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: 1.1→48.01 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.975 / SU B: 0.963 / SU ML: 0.021 / Cross valid method: THROUGHOUT / ESU R: 0.027 / ESU R Free: 0.026 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.15613 10689 4.9 %RANDOM
Rwork0.14442 ---
obs0.145 206025 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 10.711 Å2
Baniso -1Baniso -2Baniso -3
1-0.99 Å20 Å2-0 Å2
2---2.26 Å2-0 Å2
3---1.28 Å2
Refinement stepCycle: 1 / Resolution: 1.1→48.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3834 0 75 471 4380
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0280.0224356
X-RAY DIFFRACTIONr_bond_other_d00.022898
X-RAY DIFFRACTIONr_angle_refined_deg2.4851.9835991
X-RAY DIFFRACTIONr_angle_other_deg4.42737122
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3885571
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.44824.023174
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.23415706
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.4361524
X-RAY DIFFRACTIONr_chiral_restr0.2020.2650
X-RAY DIFFRACTIONr_gen_planes_refined0.0180.0214997
X-RAY DIFFRACTIONr_gen_planes_other0.0230.02848
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_it2.4521.52724
X-RAY DIFFRACTIONr_mcbond_other7.6821.51082
X-RAY DIFFRACTIONr_mcangle_it3.19824451
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.88331632
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it6.6234.51540
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr5.15837254
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.1→1.129 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 729 -
Rwork0.259 14820 -
obs--99.99 %

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