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- PDB-4zab: Structure of A. niger Fdc1 in complex with alpha-fluoro cinnamic acid -

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Basic information

Entry
Database: PDB / ID: 4zab
TitleStructure of A. niger Fdc1 in complex with alpha-fluoro cinnamic acid
ComponentsA niger Fdc1
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 / (2Z)-2-fluoro-3-phenylprop-2-enoic acid / Chem-FZZ / : / : / Ferulic acid decarboxylase 1
Similarity search - Component
Biological speciesAspergillus niger (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.16 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 2.0Jun 14, 2017Group: Advisory / Atomic model / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / pdbx_struct_conn_angle / pdbx_validate_close_contact / pdbx_validate_symm_contact / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.label_alt_id / _atom_site.occupancy / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_label_alt_id / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _pdbx_validate_symm_contact.auth_seq_id_1 / _pdbx_validate_symm_contact.auth_seq_id_2
Revision 2.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model / 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: A niger Fdc1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,6857
Polymers56,3361
Non-polymers1,3496
Water8,737485
1
A: A niger Fdc1
hetero molecules

A: A niger Fdc1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,37014
Polymers112,6722
Non-polymers2,69812
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area8390 Å2
ΔGint-48 kcal/mol
Surface area32930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.910, 64.200, 87.790
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-929-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein A niger Fdc1


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: An03g06590 / Production host: Escherichia coli (E. coli)
References: UniProt: A2QHE5, 4-hydroxybenzoate decarboxylase

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Non-polymers , 6 types, 491 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: Chemical ChemComp-4LW / (2Z)-2-fluoro-3-phenylprop-2-enoic acid


Mass: 166.149 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H7FO2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 485 / 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: 2.4 Å3/Da / Density % sol: 48.72 %
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: 0.98 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: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.16→32.28 Å / Num. obs: 175535 / % possible obs: 98.7 % / Redundancy: 4.2 % / Net I/σ(I): 12
Reflection shellResolution: 1.16→1.19 Å / Rmerge(I) obs: 0.361 / Mean I/σ(I) obs: 2.3 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZA4

4za4


Resolution: 1.16→32.28 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.971 / SU B: 1.041 / SU ML: 0.021 / Cross valid method: THROUGHOUT / ESU R: 0.032 / ESU R Free: 0.03 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.15388 9183 5 %RANDOM
Rwork0.14623 ---
obs0.14661 175535 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: 9.837 Å2
Baniso -1Baniso -2Baniso -3
1-0.17 Å2-0 Å20 Å2
2---0.43 Å2-0 Å2
3---0.26 Å2
Refinement stepCycle: 1 / Resolution: 1.16→32.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3843 0 87 485 4415
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0310.0214344
X-RAY DIFFRACTIONr_bond_other_d00.022885
X-RAY DIFFRACTIONr_angle_refined_deg2.6221.9835970
X-RAY DIFFRACTIONr_angle_other_deg4.46637082
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4355566
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.95424175
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.20115699
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6741524
X-RAY DIFFRACTIONr_chiral_restr0.20.2645
X-RAY DIFFRACTIONr_gen_planes_refined0.0190.0214983
X-RAY DIFFRACTIONr_gen_planes_other0.0260.02853
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_it2.4931.52710
X-RAY DIFFRACTIONr_mcbond_other7.5231.51078
X-RAY DIFFRACTIONr_mcangle_it3.32924419
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.13831634
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it6.7274.51551
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr5.20337229
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.16→1.19 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.235 612 -
Rwork0.23 12481 -
obs--99.98 %

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