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- PDB-3nx2: Enterobacter sp. Px6-4 Ferulic Acid Decarboxylase in complex with... -

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Basic information

Entry
Database: PDB / ID: 3nx2
TitleEnterobacter sp. Px6-4 Ferulic Acid Decarboxylase in complex with substrate analogues
ComponentsFerulic acid decarboxylase
KeywordsLYASE / Ferulic acid / decarboxylase / 4-vinylguaiacol / catalytic mechanism / phenolic acid decarboxylase superfamily
Function / homology
Function and homology information


carboxy-lyase activity
Similarity search - Function
Phenolic acid decarboxylase / Phenolic acid decarboxylase (PAD) / Calycin beta-barrel core domain / Calycin / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
3-(4-HYDROXY-3-METHOXYPHENYL)-2-PROPENOIC ACID / Ferulic acid decarboxylase
Similarity search - Component
Biological speciesEnterobacter sp. Px6-4 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.01 Å
AuthorsGu, W. / Yang, J.K. / Lou, Z.Y. / Meng, Z.H. / Zhang, K.-Q.
CitationJournal: Plos One / Year: 2011
Title: Structural Basis of Enzymatic Activity for the Ferulic Acid Decarboxylase (FADase) from Enterobacter sp. Px6-4
Authors: Gu, W. / Yang, J.K. / Lou, Z.Y. / Liang, L.M. / Sun, Y. / Huang, J.W. / Li, X.M. / Cao, Y. / Meng, Z.H. / Zhang, K.-Q.
History
DepositionJul 12, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 16, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ferulic acid decarboxylase
B: Ferulic acid decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,5293
Polymers38,3352
Non-polymers1941
Water4,504250
1
A: Ferulic acid decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3622
Polymers19,1671
Non-polymers1941
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ferulic acid decarboxylase


Theoretical massNumber of molelcules
Total (without water)19,1671
Polymers19,1671
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2740 Å2
ΔGint-17 kcal/mol
Surface area13290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.334, 88.740, 49.017
Angle α, β, γ (deg.)90.00, 102.30, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Ferulic acid decarboxylase /


Mass: 19167.375 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacter sp. Px6-4 (bacteria) / Plasmid: pET-28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: C6F3U5, Lyases; Carbon-carbon lyases; Carboxy-lyases
#2: Chemical ChemComp-FER / 3-(4-HYDROXY-3-METHOXYPHENYL)-2-PROPENOIC ACID / FERULIC ACID / Ferulic acid


Mass: 194.184 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H10O4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 250 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHERE ARE SEVERAL DISCREPANCIES BETWEEN THE DEPOSITED SEQUENCE AND UNIPROT DATABASE. THE DEPOSITOR ...THERE ARE SEVERAL DISCREPANCIES BETWEEN THE DEPOSITED SEQUENCE AND UNIPROT DATABASE. THE DEPOSITOR STATES THAT THE DEPOSITED SEQUENCE IS CORRECT AND A WRONG SEQUENCE HAS BEEN DEPOSITED ON UNIPROT.

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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: 2.4 Å3/Da / Density % sol: 48.79 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M HEPES pH7.5, 20% (w/v) PEG 10000, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jan 30, 2009
RadiationMonochromator: osmic mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.01→50 Å / Num. all: 23508 / Num. obs: 22288 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3NX1

3nx1


Resolution: 2.01→25.17 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.927 / SU B: 4.691 / SU ML: 0.13 / Cross valid method: THROUGHOUT / ESU R Free: 0.176 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23588 1199 5.1 %RANDOM
Rwork0.18881 ---
obs0.19129 22288 96.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.199 Å2
Baniso -1Baniso -2Baniso -3
1-1.07 Å20 Å20.37 Å2
2---1.71 Å20 Å2
3---0.8 Å2
Refinement stepCycle: LAST / Resolution: 2.01→25.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2620 0 14 250 2884
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0222728
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8981.9313724
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.1855325
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.74324.539141
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.66115407
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.3991512
X-RAY DIFFRACTIONr_chiral_restr0.1290.2396
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022164
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2390.21379
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3110.21828
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.2206
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2060.229
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1530.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8151.51667
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.34922664
X-RAY DIFFRACTIONr_scbond_it2.21731227
X-RAY DIFFRACTIONr_scangle_it3.1514.51060
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.005→2.057 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 63 -
Rwork0.291 1202 -
obs--70.28 %

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