[English] 日本語
Yorodumi
- PDB-1is2: Crystal Structure of Peroxisomal Acyl-CoA Oxidase-II from Rat Liver -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1is2
TitleCrystal Structure of Peroxisomal Acyl-CoA Oxidase-II from Rat Liver
Componentsacyl-CoA oxidase
KeywordsOXIDOREDUCTASE / FAD
Function / homology
Function and homology information


very long-chain fatty acid beta-oxidation / : / alpha-linolenic acid (ALA) metabolism / acyl-CoA oxidase / Beta-oxidation of very long chain fatty acids / acyl-CoA oxidase activity / fatty acid beta-oxidation using acyl-CoA oxidase / Peroxisomal protein import / very long-chain fatty acid metabolic process / fatty acid catabolic process ...very long-chain fatty acid beta-oxidation / : / alpha-linolenic acid (ALA) metabolism / acyl-CoA oxidase / Beta-oxidation of very long chain fatty acids / acyl-CoA oxidase activity / fatty acid beta-oxidation using acyl-CoA oxidase / Peroxisomal protein import / very long-chain fatty acid metabolic process / fatty acid catabolic process / hydrogen peroxide biosynthetic process / peroxisomal membrane / prostaglandin metabolic process / fatty acid oxidation / peroxisomal matrix / FAD binding / fatty acid binding / generation of precursor metabolites and energy / PDZ domain binding / lipid metabolic process / peroxisome / flavin adenine dinucleotide binding / spermatogenesis / protein homodimerization activity / cytoplasm
Similarity search - Function
Peroxisomal acyl-coenzyme A oxidase / : / Acyl-CoA oxidase, C-terminal / Acyl-CoA oxidase / Acyl-coenzyme A oxidase, N-terminal / Acyl-CoA oxidase / Acyl-coenzyme A oxidase N-terminal / Acyl-CoA oxidase, C-alpha1 domain / Butyryl-Coa Dehydrogenase, subunit A; domain 1 / Acyl-CoA dehydrogenase/oxidase, N-terminal domain ...Peroxisomal acyl-coenzyme A oxidase / : / Acyl-CoA oxidase, C-terminal / Acyl-CoA oxidase / Acyl-coenzyme A oxidase, N-terminal / Acyl-CoA oxidase / Acyl-coenzyme A oxidase N-terminal / Acyl-CoA oxidase, C-alpha1 domain / Butyryl-Coa Dehydrogenase, subunit A; domain 1 / Acyl-CoA dehydrogenase/oxidase, N-terminal domain / Butyryl-CoA Dehydrogenase, subunit A, domain 2 / Butyryl-CoA Dehydrogenase, subunit A; domain 2 / Acyl-CoA oxidase/dehydrogenase, middle domain / Acyl-CoA dehydrogenase, middle domain / Acyl-CoA dehydrogenase/oxidase, N-terminal domain superfamily / Butyryl-CoA Dehydrogenase, subunit A, domain 3 / Acyl-CoA oxidase/dehydrogenase, middle domain superfamily / Acyl-CoA dehydrogenase/oxidase, N-terminal and middle domain superfamily / Acyl-CoA dehydrogenase-like, C-terminal / Butyryl-CoA Dehydrogenase, subunit A; domain 3 / Up-down Bundle / Beta Barrel / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Peroxisomal acyl-coenzyme A oxidase 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2.2 Å
AuthorsNakajima, Y. / Miyahara, I. / Hirotsu, K.
CitationJournal: J.Biochem. / Year: 2002
Title: Three-dimensional structure of the flavoenzyme acyl-CoA oxidase-II from rat liver, the peroxisomal counterpart of mitochondrial acyl-CoA dehydrogenase.
Authors: Nakajima, Y. / Miyahara, I. / Hirotsu, K. / Nishina, Y. / Shiga, K. / Setoyama, C. / Tamaoki, H. / Miura, R.
History
DepositionNov 7, 2001Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 10, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 23, 2019Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.pdbx_database_id_DOI
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: acyl-CoA oxidase
B: acyl-CoA oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,1404
Polymers149,5692
Non-polymers1,5712
Water7,981443
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13050 Å2
ΔGint-70 kcal/mol
Surface area45350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.030, 91.501, 214.477
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a dimer in the asymmetric unit.

-
Components

#1: Protein acyl-CoA oxidase


Mass: 74784.531 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Plasmid: pET11d / Production host: Escherichia coli (E. coli) / References: UniProt: P07872, acyl-CoA oxidase
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 443 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.36 Å3/Da / Density % sol: 47.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: PEG 20000, potassium phosphate, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
12.0 mg/mlprotein1drop
23.0 %(w/v)PEG200001drop
320 mMpotassium phosphate1droppH7.4
48-11 %(w/v)PEG200001reservoir
5100 mMpotassium phosphate1reservoirpH7.4

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 8, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. all: 69647 / Num. obs: 69647 / % possible obs: 94.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.06 / Net I/σ(I): 16
Reflection shellResolution: 2.2→2.27 Å / Rmerge(I) obs: 0.283 / Mean I/σ(I) obs: 2.1 / Num. unique all: 6152 / % possible all: 85.3
Reflection
*PLUS
Highest resolution: 2.2 Å / Num. measured all: 344046 / Rmerge(I) obs: 0.06
Reflection shell
*PLUS
% possible obs: 85.3 % / Num. unique obs: 6152 / Num. measured obs: 22267 / Rmerge(I) obs: 0.283

-
Processing

Software
NameVersionClassification
SOLVEphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MIRAS / Resolution: 2.2→10 Å / σ(F): 2 / Stereochemistry target values: RANDOM
RfactorNum. reflection% reflectionSelection details
Rfree0.26 6806 10.13 %RANDOM
Rwork0.209 ---
all-68689 --
obs-67164 93.3 %-
Displacement parametersBiso mean: 32.8 Å2
Refine analyzeLuzzati coordinate error obs: 0.28 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.21 Å
Refinement stepCycle: LAST / Resolution: 2.2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9939 0 106 443 10488
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.252
X-RAY DIFFRACTIONc_dihedral_angle_d20.5
X-RAY DIFFRACTIONc_improper_angle_d0.834
X-RAY DIFFRACTIONc_mcbond_it1.294
X-RAY DIFFRACTIONc_mcangle_it1.979
Refinement
*PLUS
Rfactor obs: 0.209 / Rfactor Rfree: 0.26 / Rfactor Rwork: 0.209
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg20.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.834

+
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