[English] 日本語
Yorodumi
- PDB-6z5o: CRYSTAL STRUCTURE OF RAT PEROXISOMAL MULTIFUNCTIONAL ENZYME TYPE-... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6z5o
TitleCRYSTAL STRUCTURE OF RAT PEROXISOMAL MULTIFUNCTIONAL ENZYME TYPE-1 (RPMFE1) COMPLEXED WITH COENZYME-A AND OXIDISED NICOTINAMIDE ADENINE DINUCLEOTIDE
ComponentsPeroxisomal bifunctional enzyme
KeywordsOXIDOREDUCTASE / COENZYME-A / BETA OXIDATION / PEROXISOME / hydratase / 3S-hydroxyacyl-CoA-dehydrogenase
Function / homology
Function and homology information


Beta-oxidation of very long chain fatty acids / intramolecular oxidoreductase activity, transposing C=C bonds / Peroxisomal protein import / 3-hydroxyacyl-CoA dehydratase activity / fatty acid beta-oxidation using acyl-CoA oxidase / fatty acid derivative biosynthetic process / alpha-linolenic acid metabolic process / Delta3-Delta2-enoyl-CoA isomerase / delta(3)-delta(2)-enoyl-CoA isomerase activity / long-chain (3S)-3-hydroxyacyl-CoA dehydrogenase (NAD+) activity ...Beta-oxidation of very long chain fatty acids / intramolecular oxidoreductase activity, transposing C=C bonds / Peroxisomal protein import / 3-hydroxyacyl-CoA dehydratase activity / fatty acid beta-oxidation using acyl-CoA oxidase / fatty acid derivative biosynthetic process / alpha-linolenic acid metabolic process / Delta3-Delta2-enoyl-CoA isomerase / delta(3)-delta(2)-enoyl-CoA isomerase activity / long-chain (3S)-3-hydroxyacyl-CoA dehydrogenase (NAD+) activity / 3-hydroxyacyl-CoA dehydrogenase / enoyl-CoA hydratase / unsaturated fatty acid biosynthetic process / (3S)-3-hydroxyacyl-CoA dehydrogenase (NAD+) activity / enoyl-CoA hydratase activity / long-chain fatty acid biosynthetic process / fatty acid beta-oxidation / peroxisomal matrix / NAD+ binding / peroxisome / enzyme binding / cytosol
Similarity search - Function
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. / Enoyl-CoA hydratase/isomerase / Enoyl-CoA hydratase/isomerase ...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. / Enoyl-CoA hydratase/isomerase / Enoyl-CoA hydratase/isomerase / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / ClpP/crotonase-like domain superfamily / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
COENZYME A / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / NICOTINAMIDE / Peroxisomal bifunctional enzyme
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsWierenga, R.K. / Sridhar, S. / Kiema, T.R.
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2020
Title: Crystallographic binding studies of rat peroxisomal multifunctional enzyme type 1 with 3-ketodecanoyl-CoA: capturing active and inactive states of its hydratase and dehydrogenase catalytic sites.
Authors: Sridhar, S. / Schmitz, W. / Hiltunen, J.K. / Venkatesan, R. / Bergmann, U. / Kiema, T.R. / Wierenga, R.K.
History
DepositionMay 27, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 9, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 16, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Apr 21, 2021Group: Database references / Category: pdbx_related_exp_data_set
Revision 1.3Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
AAA: Peroxisomal bifunctional enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,05710
Polymers80,9311
Non-polymers2,1259
Water12,016667
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3240 Å2
ΔGint-43 kcal/mol
Surface area31110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.646, 106.664, 114.512
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 1 types, 1 molecules AAA

#1: Protein Peroxisomal bifunctional enzyme / PBFE


Mass: 80931.352 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: peroxisomal / Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Ehhadh / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P07896, enoyl-CoA hydratase, Delta3-Delta2-enoyl-CoA isomerase, 3-hydroxyacyl-CoA dehydrogenase

-
Non-polymers , 6 types, 676 molecules

#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-NCA / NICOTINAMIDE


Mass: 122.125 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H6N2O / Comment: medication*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 667 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 47.96 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 75mM MES, pH 6; 16%w/v PEG 4000; 125mM ammonium sulfate.

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.972957 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 31, 2018
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972957 Å / Relative weight: 1
ReflectionResolution: 1.7→48.9 Å / Num. obs: 80675 / % possible obs: 95.1 % / Redundancy: 8.13 % / Biso Wilson estimate: 21.4 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.126 / Rpim(I) all: 0.046 / Net I/σ(I): 9.9
Reflection shellResolution: 1.7→1.73 Å / Rmerge(I) obs: 1.005 / Mean I/σ(I) obs: 2 / Num. unique obs: 4187 / CC1/2: 0.811 / Rpim(I) all: 0.37 / % possible all: 94.9

-
Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
xia2data reduction
Aimlessdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5OMO

5omo


Resolution: 1.7→48.9 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.937 / SU B: 2.532 / SU ML: 0.082 / Cross valid method: NONE / ESU R: 0.119 / ESU R Free: 0.12
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2332 4190 5.198 %
Rwork0.189 76425 -
all0.191 --
obs-80615 94.77 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 25.328 Å2
Baniso -1Baniso -2Baniso -3
1-0.748 Å20 Å20 Å2
2--0.844 Å2-0 Å2
3----1.591 Å2
Refinement stepCycle: LAST / Resolution: 1.7→48.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5503 0 132 667 6302
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0125971
X-RAY DIFFRACTIONr_angle_refined_deg1.6121.6458147
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8785763
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.57421.179280
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.353151005
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7481541
X-RAY DIFFRACTIONr_chiral_restr0.1180.2768
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024518
X-RAY DIFFRACTIONr_nbd_refined0.2110.22970
X-RAY DIFFRACTIONr_nbtor_refined0.3180.23969
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1510.2535
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2160.2107
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1810.247
X-RAY DIFFRACTIONr_mcbond_it1.8612.1232912
X-RAY DIFFRACTIONr_mcangle_it2.5863.1743648
X-RAY DIFFRACTIONr_scbond_it2.9222.6663059
X-RAY DIFFRACTIONr_scangle_it4.3353.8854474
X-RAY DIFFRACTIONr_lrange_it6.59130.9359431
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.7440.2973130.2735519X-RAY DIFFRACTION93.9736
1.744-1.7920.283010.2715154X-RAY DIFFRACTION90.0908
1.792-1.8440.2792730.2375421X-RAY DIFFRACTION96.3126
1.844-1.9010.2792660.2225222X-RAY DIFFRACTION96.2807
1.901-1.9630.262370.2085132X-RAY DIFFRACTION96.3049
1.963-2.0320.2552820.1914883X-RAY DIFFRACTION96.0037
2.032-2.1080.2522320.1974549X-RAY DIFFRACTION92.1195
2.108-2.1940.2212470.194375X-RAY DIFFRACTION92.774
2.194-2.2920.2412350.1954471X-RAY DIFFRACTION97.071
2.292-2.4040.2552420.1814214X-RAY DIFFRACTION97.0383
2.404-2.5340.2232450.1834029X-RAY DIFFRACTION97.0922
2.534-2.6870.261990.193696X-RAY DIFFRACTION93.6073
2.687-2.8730.2222040.1873387X-RAY DIFFRACTION91.4438
2.873-3.1030.2291860.1883405X-RAY DIFFRACTION98.2759
3.103-3.3990.2311760.1893101X-RAY DIFFRACTION97.1827
3.399-3.80.191750.1652745X-RAY DIFFRACTION94.9285
3.8-4.3870.1811350.152335X-RAY DIFFRACTION90.5093
4.387-5.370.2441000.1522194X-RAY DIFFRACTION97.9087
5.37-7.5870.227850.2071630X-RAY DIFFRACTION92.9539
7.587-48.90.257570.208963X-RAY DIFFRACTION93.9227

+
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