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- PDB-8crd: Aspergillus niger ferulic acid decarboxylase (Fdc) T40C-S315C (DB... -

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Basic information

Entry
Database: PDB / ID: 8crd
TitleAspergillus niger ferulic acid decarboxylase (Fdc) T40C-S315C (DB1) variant in complex with prenylated flavin hydroxylated at the C1 prime position
ComponentsFerulic acid decarboxylase 1
KeywordsLYASE / Decarboxylase / prFMN
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 / : / : / THIOCYANATE ION / Ferulic acid decarboxylase 1
Similarity search - Component
Biological speciesAspergillus niger CBS 513.88 (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsRoberts, G.W. / Leys, D.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC) United Kingdom
CitationJournal: To Be Published
Title: Aspergillus niger ferulic acid decarboxylase (Fdc) T40C-S315C (DB1) variant in complex with prenylated flavin hydroxylated at the C1 prime position
Authors: Roberts, G.W. / Leys, D.
History
DepositionMar 8, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 6, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)57,2629
Polymers56,3541
Non-polymers9088
Water9,944552
1
A: Ferulic acid decarboxylase 1
hetero molecules

A: Ferulic acid decarboxylase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,52418
Polymers112,7082
Non-polymers1,81616
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area9790 Å2
ΔGint-72 kcal/mol
Surface area33280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.780, 64.030, 87.590
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-1015-

HOH

21A-1104-

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: 56354.047 Da / Num. of mol.: 1 / Mutation: T40C S315C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus niger CBS 513.88 (mold) / Gene: fdc1, An03g06590 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A2QHE5, phenacrylate decarboxylase

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Non-polymers , 5 types, 560 molecules

#2: Chemical ChemComp-BYN / hydroxylated prenyl-FMN


Mass: 542.476 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C22H31N4O10P / Feature type: SUBJECT OF INVESTIGATION
#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: Chemical
ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: CNS
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 552 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 48.48 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: BIS-TRIS propane, potassium thiocyanate, PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Sep 11, 2021
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.35→53.29 Å / Num. obs: 110958 / % possible obs: 93.5 % / Redundancy: 13.3 % / CC1/2: 1 / Net I/σ(I): 13.7
Reflection shellResolution: 1.35→1.37 Å / Redundancy: 10.6 % / Num. unique obs: 3493 / CC1/2: 0.3 / % possible all: 59.6

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Processing

Software
NameVersionClassification
REFMAC5.5.0026refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.35→53.29 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.968 / SU B: 0.958 / SU ML: 0.037 / Cross valid method: THROUGHOUT / ESU R: 0.05 / ESU R Free: 0.052 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17596 5601 5 %RANDOM
Rwork0.15206 ---
obs0.15325 105313 93.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.14 Å2
Baniso -1Baniso -2Baniso -3
1--0.9 Å20 Å20 Å2
2--1.09 Å20 Å2
3----0.19 Å2
Refinement stepCycle: 1 / Resolution: 1.35→53.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3854 0 52 552 4458
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0124235
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163887
X-RAY DIFFRACTIONr_angle_refined_deg1.781.6555802
X-RAY DIFFRACTIONr_angle_other_deg0.6151.5739020
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5595550
X-RAY DIFFRACTIONr_dihedral_angle_2_deg11.31527
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.4310668
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0990.2632
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.025035
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02920
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_it1.5361.7862133
X-RAY DIFFRACTIONr_mcbond_other1.5071.7842130
X-RAY DIFFRACTIONr_mcangle_it2.1033.1992702
X-RAY DIFFRACTIONr_mcangle_other2.1023.2012703
X-RAY DIFFRACTIONr_scbond_it2.3841.9632102
X-RAY DIFFRACTIONr_scbond_other2.381.9612095
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.2763.5193097
X-RAY DIFFRACTIONr_long_range_B_refined4.62620.684962
X-RAY DIFFRACTIONr_long_range_B_other4.62620.684963
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.35→1.385 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.375 284 -
Rwork0.374 5027 -
obs--61.28 %

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