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- PDB-2wtb: Arabidopsis thaliana multifuctional protein, MFP2 -

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Basic information

Entry
Database: PDB / ID: 2wtb
TitleArabidopsis thaliana multifuctional protein, MFP2
ComponentsFATTY ACID MULTIFUNCTIONAL PROTEIN (ATMFP2)
KeywordsOXIDOREDUCTASE / PEROXISOMES / BETA-OXIDATION / FATTY ACID OXIDATION / FATTY ACID DEGRADATION
Function / homology
Function and homology information


glyoxysome / 3-hydroxybutyryl-CoA epimerase / 3-hydroxybutyryl-CoA epimerase activity / 3-hydroxyacyl-CoA dehydratase activity / Delta3-Delta2-enoyl-CoA isomerase / delta(3)-delta(2)-enoyl-CoA isomerase activity / enoyl-CoA hydratase / plant-type cell wall / 3-hydroxyacyl-CoA dehydrogenase / 3-hydroxyacyl-CoA dehydrogenase activity ...glyoxysome / 3-hydroxybutyryl-CoA epimerase / 3-hydroxybutyryl-CoA epimerase activity / 3-hydroxyacyl-CoA dehydratase activity / Delta3-Delta2-enoyl-CoA isomerase / delta(3)-delta(2)-enoyl-CoA isomerase activity / enoyl-CoA hydratase / plant-type cell wall / 3-hydroxyacyl-CoA dehydrogenase / 3-hydroxyacyl-CoA dehydrogenase activity / plasmodesma / fatty acid beta-oxidation / NAD+ binding / peroxisome / nucleolus / cytosol
Similarity search - Function
N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 - #50 / 3-hydroxyacyl-CoA dehydrogenase, conserved site / 3-hydroxyacyl-CoA dehydrogenase signature. / 3-hydroxyacyl-CoA dehydrogenase, C-terminal / 3-hydroxyacyl-CoA dehydrogenase, NAD binding / 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain / 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain / Enoyl-CoA hydratase/isomerase, conserved site / Enoyl-CoA hydratase/isomerase signature. / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 ...N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 - #50 / 3-hydroxyacyl-CoA dehydrogenase, conserved site / 3-hydroxyacyl-CoA dehydrogenase signature. / 3-hydroxyacyl-CoA dehydrogenase, C-terminal / 3-hydroxyacyl-CoA dehydrogenase, NAD binding / 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain / 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain / Enoyl-CoA hydratase/isomerase, conserved site / Enoyl-CoA hydratase/isomerase signature. / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / Enoyl-CoA hydratase/isomerase / Enoyl-CoA hydratase/isomerase / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / ClpP/crotonase-like domain superfamily / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Peroxisomal fatty acid beta-oxidation multifunctional protein MFP2
Similarity search - Component
Biological speciesARABIDOPSIS THALIANA (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsArent, S. / Pye, V.E. / Christensen, C.E. / Norgaard, A. / Henriksen, A.
Citation
Journal: J.Biol.Chem. / Year: 2010
Title: The Multi-Functional Protein in Peroxisomal Beta-Oxidation. Structure and Substrate Specificity of the Arabidopsis Thaliana Protein, Mfp2
Authors: Arent, S. / Pye, V.E. / Christen, C.E. / Norgaard, A. / Henriksen, A.
#1: Journal: Plant J. / Year: 2006
Title: The Arabidopsis Thaliana Multifunctional Protein Gene (Mfp2) of Peroxisomal Beta-Oxidation is Essential for Seedling Establishment.
Authors: Rylott, E.L. / Eastmond, P.J. / Gilday, A.D. / Slocombe, S.P. / Larson, T.R. / Baker, A. / Graham, I.A.
History
DepositionSep 15, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 12, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 9, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_status / reflns
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp ..._exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.status_code_sf / _reflns.pdbx_Rmerge_I_obs
Revision 1.4Dec 20, 2023Group: 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

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Assembly

Deposited unit
A: FATTY ACID MULTIFUNCTIONAL PROTEIN (ATMFP2)


Theoretical massNumber of molelcules
Total (without water)78,9441
Polymers78,9441
Non-polymers00
Water45025
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)110.480, 110.480, 125.470
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein FATTY ACID MULTIFUNCTIONAL PROTEIN (ATMFP2) / MFP2


Mass: 78944.008 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ARABIDOPSIS THALIANA (thale cress) / Plasmid: PET24B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9ZPI5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsRESIDUES 1-6,71-82, 365-368, 576-596 AND 720-725 HAVE HAVE POORLY DEFINED ELECTRON DENSITY AND HAVE ...RESIDUES 1-6,71-82, 365-368, 576-596 AND 720-725 HAVE HAVE POORLY DEFINED ELECTRON DENSITY AND HAVE NOT BEEN INCLUDED IN THE MODEL

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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: 56 % / Description: NONE
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.5
Details: 4.2M NACHO2, 2(V/V)% GLYCEROL, 40(V/V)% POLYPROPYLENE GLYCOL, pH 7.5

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Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9537
DetectorType: MARRESEARCH / Detector: CCD / Date: May 15, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.5→25.3 Å / Num. obs: 34691 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 51.03 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 6
Reflection shellResolution: 2.5→2.67 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD
Starting model: PDB ENTRY 1WDK

1wdk


Resolution: 2.5→25.279 Å / SU ML: 1.95 / σ(F): 0.01 / Phase error: 30.46 / Stereochemistry target values: ML
Details: RESIDUES 71-82,365-368 AND 576- -596 ARE DISORDERED. DISORDERED REGIONS WERE OMITTED FROM THE MODEL
RfactorNum. reflection% reflection
Rfree0.2688 2490 5 %
Rwork0.2157 --
obs0.2183 27626 84.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.538 Å2 / ksol: 0.335 e/Å3
Displacement parametersBiso mean: 77.1 Å2
Baniso -1Baniso -2Baniso -3
1-5.3204 Å2-0 Å2-0 Å2
2--5.3204 Å2-0 Å2
3----10.6409 Å2
Refinement stepCycle: LAST / Resolution: 2.5→25.279 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4999 0 0 25 5024
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025089
X-RAY DIFFRACTIONf_angle_d0.5816891
X-RAY DIFFRACTIONf_dihedral_angle_d11.5451836
X-RAY DIFFRACTIONf_chiral_restr0.04805
X-RAY DIFFRACTIONf_plane_restr0.003886
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.58930.39751720.33023635X-RAY DIFFRACTION64
2.5893-2.69280.33912060.3093977X-RAY DIFFRACTION70
2.6928-2.81520.37462240.30874156X-RAY DIFFRACTION74
2.8152-2.96350.33872940.29374437X-RAY DIFFRACTION80
2.9635-3.14880.34242560.2754840X-RAY DIFFRACTION85
3.1488-3.39140.30482550.24724911X-RAY DIFFRACTION88
3.3914-3.73170.26682790.21065102X-RAY DIFFRACTION91
3.7317-4.26950.2032910.17225256X-RAY DIFFRACTION94
4.2695-5.37060.22732620.16145510X-RAY DIFFRACTION97
5.3706-25.27980.24122510.20025539X-RAY DIFFRACTION98
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)
13.6441-1.1887-0.15573.0571-1.71663.51080.0360.44250.2924-0.4169-0.3014-0.30920.24030.83760.12490.3846-0.07-0.03040.49450.02820.3302-9.107366.383632.4142
23.5308-1.02230.24822.2634-1.27813.8077-0.0826-0.4158-0.09840.0720.2320.03140.60850.5246-0.11090.42430.0391-0.02590.5852-0.02250.2007-13.417454.84744.0166
31.5408-0.1286-2.33810.07230.83440.7972-0.3854-1.3860.08080.03040.4175-0.05690.05481.32580.00930.62420.3795-0.08361.47920.0240.37953.946949.823651.6899
40.29520.16650.2891.54680.26850.99080.0434-0.7349-0.10340.351-0.01620.2692-0.1693-0.5445-0.1780.3816-0.05190.05220.7210.33250.49884.429525.019120.2432
52.39791.15075.70612.10351.545.687-0.3502-2.0917-0.7524-0.5833-0.04871.0964-0.4402-1.91650.16990.4029-0.12040.02591.33240.45790.9047-9.747722.235823.9163
63.4371-0.43081.28822.25251.19212.89170.0266-0.4384-0.39280.07590.0714-0.04510.5918-0.2724-0.09710.33970.070.09420.38760.2270.360614.690925.142217.8506
70.13580.65390.18971.617-0.42460.7124-0.0003-0.974-0.61990.2528-0.05180.12410.16050.14690.08610.53890.2199-0.01351.11160.50180.685723.254519.608344.3111
83.92940.26011.0691.42.3045-0.22891.5236-0.0273-0.21741.5625-0.14450.025-0.3122-0.3434-0.52491.49970.3920.28960.88810.75190.695420.699510.989454.6197
9-0.16661.10840.57112.9019-1.33641.9925-0.1192-0.93180.09060.64140.0991-0.4561-0.5480.04520.03310.3990.3835-0.00061.31250.24120.336826.238635.256743.3852
10-3.2103-0.67860.29541.9598-0.16351.01470.0941-0.69850.1236-0.066-0.2715-0.7097-0.10.54010.27160.35850.21150.02451.38450.33970.768835.121538.942339.4304
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 8:70)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 83:234)
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 235:293)
4X-RAY DIFFRACTION4CHAIN A AND (RESSEQ 294:361)
5X-RAY DIFFRACTION5CHAIN A AND (RESSEQ 362:383)
6X-RAY DIFFRACTION6CHAIN A AND (RESSEQ 384:502)
7X-RAY DIFFRACTION7CHAIN A AND (RESSEQ 503:575)
8X-RAY DIFFRACTION8CHAIN A AND (RESSEQ 597:611)
9X-RAY DIFFRACTION9CHAIN A AND (RESSEQ 612:691)
10X-RAY DIFFRACTION10CHAIN A AND (RESSEQ 692:719)

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