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- PDB-3nad: Crystal Structure of Phenolic Acid Decarboxylase from Bacillus pu... -

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Basic information

Entry
Database: PDB / ID: 3nad
TitleCrystal Structure of Phenolic Acid Decarboxylase from Bacillus pumilus UI-670
ComponentsFerulate decarboxylase
KeywordsLYASE / beta barrel / lipocalin / biocatalysis / decarboxylase
Function / homology
Function and homology information


Lyases; Carbon-carbon lyases; Carboxy-lyases / 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
Ferulate decarboxylase
Similarity search - Component
Biological speciesBacillus pumilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.69 Å
AuthorsMatte, A. / Grosse, S. / Bergeron, H. / Abokitse, K. / Lau, P.C.K.
Citation
Journal: Acta Crystallogr.,Sect.F / Year: 2010
Title: Structural analysis of Bacillus pumilus phenolic acid decarboxylase, a lipocalin-fold enzyme.
Authors: Matte, A. / Grosse, S. / Bergeron, H. / Abokitse, K. / Lau, P.C.
#1: Journal: Proteins: Struct.,Funct.,Genet. / Year: 2010
Title: p-Coumaric acid decarboxylase from Lactobacillus plantarum: Structural insights into the active site and decarboxylation catalytic mechanism
Authors: Rodriguez, H. / Angulo, I. / de las Rivas, B. / Campillo, N. / Paez, J.A. / Munoz, R. / Mancheno, J.M.
#2: Journal: Protein Sci. / Year: 1993
Title: Structure and sequence relationships in the lipcalins and related proteins
Authors: Flower, D.R. / North, A.C.T. / Attwood, T.K.
#3: Journal: Biochim.Biophys.Acta / Year: 2000
Title: The bacterial lipocalins.
Authors: Bishop, R.E.
#4: Journal: J.Bacteriol. / Year: 2008
Title: Phenolic-acid mediated regulation of the padC gene encoding the phenolic acid decarboxylase of Bacillus subtilus
Authors: Tran, N.P. / Gury, J. / Dartois, V. / Nguyen, T.K.C. / Seraut, H. / Barthelmebs, L. / Gervais, P. / Cavin, J.-F.
#5: Journal: Appl.Environ.Microbiol. / Year: 1995
Title: Cloning, sequencing and expression in Escherichia coli of the Bacillus pumilus gene for ferulic acid decarboxylase
Authors: Zago, A. / Degrassi, G. / Bruschi, C.V.
History
DepositionJun 1, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 10, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 11, 2012Group: Database references
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software
Revision 1.4Sep 6, 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: Ferulate decarboxylase
B: Ferulate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,3093
Polymers38,2132
Non-polymers961
Water6,630368
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2660 Å2
ΔGint-30 kcal/mol
Surface area13530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.107, 109.964, 45.428
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Ferulate decarboxylase / Ferulic acid decarboxylase


Mass: 19106.564 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus pumilus (bacteria) / Strain: UI-670 / Gene: fdc, padC / Plasmid: pKK223-3 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: Q45361
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 368 / Source method: isolated from a natural source / Formula: H2O

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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: 3.01 Å3/Da / Density % sol: 59.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 5.6
Details: 0.2 M Na/K tartarate, 0.1 M tri-sodium citrate, 0.5 M ammonium sulfate, pH 5.6, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 Å
DetectorType: Rayonix 225 HE / Detector: CCD / Date: Jun 4, 2008
RadiationMonochromator: Kohzu HLD-4 double crystal Diamond(111) / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.69→50 Å / Num. obs: 52226 / % possible obs: 99.1 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.095 / Χ2: 0.976 / Net I/σ(I): 10.5
Reflection shellResolution: 1.69→1.75 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.603 / Num. unique all: 4990 / Χ2: 0.876 / % possible all: 95.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2P8G

2p8g


Resolution: 1.69→50 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.949 / WRfactor Rfree: 0.242 / WRfactor Rwork: 0.244 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.876 / SU B: 3.445 / SU ML: 0.056 / SU R Cruickshank DPI: 0.118 / SU Rfree: 0.103 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.087 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.204 2653 5.1 %RANDOM
Rwork0.185 ---
obs0.186 52132 98.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 116.32 Å2 / Biso mean: 19.448 Å2 / Biso min: 9.34 Å2
Baniso -1Baniso -2Baniso -3
1-0.78 Å20 Å20 Å2
2---0.86 Å20 Å2
3---0.09 Å2
Refinement stepCycle: LAST / Resolution: 1.69→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2666 0 5 368 3039
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0222768
X-RAY DIFFRACTIONr_angle_refined_deg1.0591.933766
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1825326
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.52423.931145
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.28915464
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.7951515
X-RAY DIFFRACTIONr_chiral_restr0.080.2391
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212149
X-RAY DIFFRACTIONr_mcbond_it0.5221.51602
X-RAY DIFFRACTIONr_mcangle_it1.04622624
X-RAY DIFFRACTIONr_scbond_it1.78231166
X-RAY DIFFRACTIONr_scangle_it3.0474.51138
LS refinement shellResolution: 1.69→1.731 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 162 -
Rwork0.258 3316 -
all-3478 -
obs--90.98 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.5932-0.4989-0.28820.73710.09860.8742-0.0165-0.0229-0.03910.03910.038-0.0207-0.031-0.0163-0.0215-0.0239-0.0001-0.006-0.0394-0.0019-0.0248-15.3567-31.2526-18.374
20.3871-0.2385-0.16820.7270.04330.64370.0021-0.01250.0376-0.0843-0.00850.0644-0.0054-0.0170.0064-0.0180.0157-0.0099-0.027-0.0017-0.0097-28.7673-10.6977-27.0182
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 161
2X-RAY DIFFRACTION2B1 - 159

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