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- PDB-4alb: Structure of Phenolic Acid Decarboxylase from Bacillus subtilis: ... -

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Basic information

Entry
Database: PDB / ID: 4alb
TitleStructure of Phenolic Acid Decarboxylase from Bacillus subtilis: Tyr19Ala mutant in complex with coumaric acid
ComponentsPHENOLIC ACID DECARBOXYLASE PADC
KeywordsLYASE / LIPOCALIN OLD / CINNAMATE
Function / homology
Function and homology information


phenacrylate decarboxylase / carboxy-lyase activity / catabolic process / response to toxic substance
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
4'-HYDROXYCINNAMIC ACID / Phenolic acid decarboxylase PadC
Similarity search - Component
Biological speciesBACILLUS SUBTILIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.03 Å
AuthorsFrank, A. / Eborall, W. / Hyde, R. / Hart, S. / Turkenburg, J.P. / Grogan, G.
CitationJournal: Catal.Sci.Technol. / Year: 2012
Title: Mutational Analysis of Phenolic Acid Decarboxylase from Bacillus Subtilis (Bspad), which Converts Bio-Derived Phenolic Acids to Styrene Derivatives
Authors: Frank, A. / Eborall, W. / Hyde, R. / Hart, S. / Turkenburg, J.P. / Grogan, G.
History
DepositionMar 2, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 22, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _pdbx_database_status.status_code_sf / _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: PHENOLIC ACID DECARBOXYLASE PADC
B: PHENOLIC ACID DECARBOXYLASE PADC
C: PHENOLIC ACID DECARBOXYLASE PADC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,5186
Polymers57,0253
Non-polymers4923
Water23413
1
A: PHENOLIC ACID DECARBOXYLASE PADC
B: PHENOLIC ACID DECARBOXYLASE PADC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,3454
Polymers38,0172
Non-polymers3282
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3270 Å2
ΔGint-9.3 kcal/mol
Surface area12940 Å2
MethodPISA
2
C: PHENOLIC ACID DECARBOXYLASE PADC
hetero molecules

C: PHENOLIC ACID DECARBOXYLASE PADC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,3454
Polymers38,0172
Non-polymers3282
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area3180 Å2
ΔGint-12.2 kcal/mol
Surface area12680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.210, 107.210, 92.800
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.2676, -0.9635, 0.004203), (-0.9635, 0.2676, 0.006662), (-0.005294, 0.005833, -1)38.14, 29.15, -29.16
2given(-0.9928, -0.1193, 0.009776), (-0.1192, 0.9928, 0.006168), (-0.01044, 0.004958, -0.9999)53.52, -30.98, -14.73

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Components

#1: Protein PHENOLIC ACID DECARBOXYLASE PADC / PAD


Mass: 19008.393 Da / Num. of mol.: 3 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACILLUS SUBTILIS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: O07006, Lyases; Carbon-carbon lyases; Carboxy-lyases
#2: Chemical ChemComp-HC4 / 4'-HYDROXYCINNAMIC ACID / PARA-COUMARIC ACID


Mass: 164.158 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C9H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 2.8 Å3/Da / Density % sol: 55 % / Description: NONE
Crystal growpH: 9
Details: 0.2 M KSCN, 17% (W/V) PEG 1000, 17% (W/V) PEG 8000, IN 0.1 M TRIS/HCL BUFFER AT PH 9. 15 MM COUMARIC ACID. PROTEIN AT 20 MG PER ML

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9763
DetectorType: ADSC CCD / Detector: CCD / Date: Oct 23, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 3.02→53.6 Å / Num. obs: 12362 / % possible obs: 99.5 % / Observed criterion σ(I): 2 / Redundancy: 10.8 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 21.4
Reflection shellResolution: 3.02→3.1 Å / Redundancy: 11 % / Rmerge(I) obs: 0.86 / Mean I/σ(I) obs: 3.3 / % possible all: 98.6

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Processing

Software
NameVersionClassification
REFMAC5.6.0119refinement
xia2data reduction
xia2data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB MODEL 2P8G

2p8g


Resolution: 3.03→92.85 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.9 / SU B: 17.885 / SU ML: 0.317 / Cross valid method: THROUGHOUT / ESU R Free: 0.469 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2632 595 4.8 %RANDOM
Rwork0.20151 ---
obs0.20436 11708 99.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.643 Å2
Baniso -1Baniso -2Baniso -3
1-2.89 Å21.45 Å20 Å2
2--2.89 Å20 Å2
3----4.34 Å2
Refinement stepCycle: LAST / Resolution: 3.03→92.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3852 0 36 13 3901
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.023999
X-RAY DIFFRACTIONr_bond_other_d0.0050.022609
X-RAY DIFFRACTIONr_angle_refined_deg1.441.9115438
X-RAY DIFFRACTIONr_angle_other_deg1.23436328
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5165472
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.65324.32206
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.82415626
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8311518
X-RAY DIFFRACTIONr_chiral_restr0.0810.2566
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024497
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02865
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.025→3.104 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.337 50 -
Rwork0.329 778 -
obs--98.22 %

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