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- PDB-4uu3: Ferulic acid decarboxylase from Enterobacter sp. -

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Basic information

Entry
Database: PDB / ID: 4uu3
TitleFerulic acid decarboxylase from Enterobacter sp.
ComponentsFERULIC ACID DECARBOXYLASE
KeywordsLYASE
Function / homologyPhenolic acid decarboxylase / Phenolic acid decarboxylase (PAD) / carboxy-lyase activity / Calycin beta-barrel core domain / Calycin / Lipocalin / Beta Barrel / Mainly Beta / Ferulic acid decarboxylase
Function and homology information
Biological speciesENTEROBACTER SP. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.15 Å
AuthorsHromic, A. / Pavkov-Keller, T. / Steinkellner, G. / Lyskowski, A. / Wuensch, C. / Gross, J. / Fuchs, M. / Fauland, K. / Glueck, S.M. / Faber, K. / Gruber, K.
CitationJournal: Adv. Synth. Catal. / Year: 2015
Title: Regioselective Enzymatic Beta-Carboxylation of Para-Hydroxy-Styrene Derivatives Catalyzed by Phenolic Acid Decarboxylases.
Authors: Wuensch, C. / Pavkov-Keller, T. / Steinkellner, G. / Gross, J. / Fuchs, M. / Hromic, A. / Lyskowski, A. / Fauland, K. / Gruber, K. / Glueck, S.M. / Faber, K.
History
DepositionJul 24, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 10, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2015Group: Database references
Revision 2.0Oct 23, 2019Group: Atomic model / Data collection / Other / Category: atom_site / pdbx_database_status
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 / _pdbx_database_status.status_code_sf
Revision 2.1Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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


Theoretical massNumber of molelcules
Total (without water)38,4272
Polymers38,4272
Non-polymers00
Water9,602533
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2840 Å2
ΔGint-17.1 kcal/mol
Surface area13140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.426, 83.833, 133.278
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein FERULIC ACID DECARBOXYLASE /


Mass: 19213.467 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ENTEROBACTER SP. (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: C6F3U5
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 533 / 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: 2.7 Å3/Da / Density % sol: 54 % / Description: NONE
Crystal growDetails: 0.15 M POTASSIUM BROMIDE AND 30% W/V PEG MONOMETHYL ETHER 2000 20MG/ML PROTEIN (IN 100MM MES, L-MALIC ACID, TRIS PH 7.0 AND 250MM NACL)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97918
DetectorType: DECTRIS PILATUS / Detector: PIXEL / Date: Jul 27, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.13→50 Å / Num. obs: 157334 / % possible obs: 99.7 % / Observed criterion σ(I): 2.2 / Redundancy: 9.1 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 14.2
Reflection shellResolution: 1.13→1.2 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 2.4 / % possible all: 98.4

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3NX2

3nx2


Resolution: 1.15→39.986 Å / SU ML: 0.07 / σ(F): 1.34 / Phase error: 10.31 / Stereochemistry target values: ML
Details: ADDITIONAL SOLVENT IN THE ACTIVE SITE REGION, COULD NOT BE IDENTIFIED WITH 100PROCENT CERTAINTY
RfactorNum. reflection% reflection
Rfree0.133 7878 5 %
Rwork0.1211 --
obs0.1217 157334 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.15→39.986 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2677 0 0 533 3210
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012862
X-RAY DIFFRACTIONf_angle_d1.3493918
X-RAY DIFFRACTIONf_dihedral_angle_d12.6431024
X-RAY DIFFRACTIONf_chiral_restr0.091416
X-RAY DIFFRACTIONf_plane_restr0.008517
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.15-1.16310.20542560.19514930X-RAY DIFFRACTION100
1.1631-1.17680.17542510.15924914X-RAY DIFFRACTION100
1.1768-1.19110.17042800.14714922X-RAY DIFFRACTION100
1.1911-1.20620.17772470.13574901X-RAY DIFFRACTION100
1.2062-1.22210.15052530.13184948X-RAY DIFFRACTION100
1.2221-1.23880.15642880.12984946X-RAY DIFFRACTION100
1.2388-1.25650.15292670.12474866X-RAY DIFFRACTION100
1.2565-1.27530.15392530.12964958X-RAY DIFFRACTION99
1.2753-1.29520.14412640.12134900X-RAY DIFFRACTION100
1.2952-1.31640.14272560.11024945X-RAY DIFFRACTION100
1.3164-1.33910.12122510.10454922X-RAY DIFFRACTION100
1.3391-1.36350.12672530.10565000X-RAY DIFFRACTION100
1.3635-1.38970.12252820.0964876X-RAY DIFFRACTION100
1.3897-1.41810.10812650.09474998X-RAY DIFFRACTION100
1.4181-1.44890.11292550.09224953X-RAY DIFFRACTION100
1.4489-1.48260.12082570.09494911X-RAY DIFFRACTION100
1.4826-1.51970.11922790.09635017X-RAY DIFFRACTION100
1.5197-1.56080.11482340.09464945X-RAY DIFFRACTION100
1.5608-1.60670.11192610.09354971X-RAY DIFFRACTION100
1.6067-1.65860.1262780.09944963X-RAY DIFFRACTION100
1.6586-1.71780.10852810.10164997X-RAY DIFFRACTION100
1.7178-1.78660.10912570.10474982X-RAY DIFFRACTION100
1.7866-1.86790.11812510.10654994X-RAY DIFFRACTION100
1.8679-1.96640.11812580.11015028X-RAY DIFFRACTION100
1.9664-2.08960.1232430.10925024X-RAY DIFFRACTION100
2.0896-2.25090.132730.10945022X-RAY DIFFRACTION100
2.2509-2.47740.12062600.12285058X-RAY DIFFRACTION100
2.4774-2.83580.14012740.14565078X-RAY DIFFRACTION100
2.8358-3.57250.15432820.13825125X-RAY DIFFRACTION100
3.5725-40.00970.13622690.14345362X-RAY DIFFRACTION100

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