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- PDB-4uu2: Ferulic acid decarboxylase from Enterobacter sp., single mutant -

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Basic information

Entry
Database: PDB / ID: 4uu2
TitleFerulic acid decarboxylase from Enterobacter sp., single mutant
ComponentsFERULIC ACID DECARBOXYLASE
KeywordsLYASE
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
GLYCINE / PHOSPHATE ION / Ferulic acid decarboxylase
Similarity search - Component
Biological speciesENTEROBACTER SP. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 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 1.2Sep 27, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.type
Revision 1.3May 1, 2024Group: 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: FERULIC ACID DECARBOXYLASE
B: FERULIC ACID DECARBOXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,7687
Polymers38,3112
Non-polymers4575
Water8,611478
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3900 Å2
ΔGint-55.4 kcal/mol
Surface area13060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.210, 83.880, 132.020
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: 19155.430 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ENTEROBACTER SP. (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: C6F3U5
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-GLY / GLYCINE


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H5NO2
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 478 / 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: 0.2 M AMMONIUM SULFATE, 0.1 M BIS-TRIS PH 5.5 AND 25 % W/V PEG 3350 20MG/ML PROTEIN (IN 100 MM SUCCINIC ACID, SODIUM DIHYDROGEN PHOSPHATE MONOHYDRATE AND GLYCINE, PH 7.0)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97939
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 13, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97939 Å / Relative weight: 1
ReflectionResolution: 1.49→41.9 Å / Num. obs: 71286 / % possible obs: 98.7 % / Observed criterion σ(I): 2.4 / Redundancy: 8.4 % / Biso Wilson estimate: 16.14 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 11.8
Reflection shellResolution: 1.49→1.59 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 2.4 / % possible all: 93.2

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: NATIVE STRUCTURE OF THE SAME PROTEIN

Resolution: 1.49→41.94 Å / SU ML: 0.15 / σ(F): 1.36 / Phase error: 17.72 / Stereochemistry target values: ML
Details: THERE ARE BOTH, PO4 AND SO4 IONS, PRESENT IN CRYSTALLIZATION SETUP. BOTH COULD BE FITTED AS SOLVENT MOLECULES BUT WE CAN NOT BE SURE WHETHER PO4 OR SO4 IS CORRECT
RfactorNum. reflection% reflection
Rfree0.1765 3608 5.1 %
Rwork0.1582 --
obs0.1592 71216 98.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.49→41.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2684 0 25 478 3187
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062904
X-RAY DIFFRACTIONf_angle_d1.033982
X-RAY DIFFRACTIONf_dihedral_angle_d12.7511031
X-RAY DIFFRACTIONf_chiral_restr0.08424
X-RAY DIFFRACTIONf_plane_restr0.005523
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.49-1.50960.32191250.30412151X-RAY DIFFRACTION82
1.5096-1.53030.33551420.28742297X-RAY DIFFRACTION90
1.5303-1.55220.28851580.25732499X-RAY DIFFRACTION96
1.5522-1.57530.28631330.23162588X-RAY DIFFRACTION100
1.5753-1.59990.24131310.21932581X-RAY DIFFRACTION100
1.5999-1.62620.25691450.20972625X-RAY DIFFRACTION100
1.6262-1.65420.23741290.20212603X-RAY DIFFRACTION100
1.6542-1.68430.20191450.19432595X-RAY DIFFRACTION100
1.6843-1.71670.24031160.18482647X-RAY DIFFRACTION100
1.7167-1.75170.2171250.18092568X-RAY DIFFRACTION99
1.7517-1.78980.19381460.17482610X-RAY DIFFRACTION99
1.7898-1.83150.20871400.16712602X-RAY DIFFRACTION100
1.8315-1.87730.18661340.16192620X-RAY DIFFRACTION100
1.8773-1.9280.17781310.16242616X-RAY DIFFRACTION100
1.928-1.98480.18181410.14962618X-RAY DIFFRACTION100
1.9848-2.04880.19841380.15322643X-RAY DIFFRACTION100
2.0488-2.1220.16291370.15362595X-RAY DIFFRACTION100
2.122-2.2070.1711320.14462656X-RAY DIFFRACTION100
2.207-2.30740.17981570.14742621X-RAY DIFFRACTION100
2.3074-2.42910.2051260.15592641X-RAY DIFFRACTION100
2.4291-2.58120.18161380.15422642X-RAY DIFFRACTION100
2.5812-2.78050.17241230.15762689X-RAY DIFFRACTION100
2.7805-3.06020.18191410.1622670X-RAY DIFFRACTION100
3.0602-3.50290.15461590.15032674X-RAY DIFFRACTION100
3.5029-4.41250.12791600.12322711X-RAY DIFFRACTION100
4.4125-41.95660.13771560.13622846X-RAY DIFFRACTION100

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