[English] 日本語
Yorodumi
- PDB-2wtb: Arabidopsis thaliana multifuctional protein, MFP2 -

+
Open data


ID or keywords:

Loading...

-
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 / 3-hydroxyacyl-CoA dehydrogenase / enoyl-CoA hydratase / plant-type cell wall / 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 / 3-hydroxyacyl-CoA dehydrogenase / enoyl-CoA hydratase / plant-type cell wall / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more