[English] 日本語
Yorodumi
- PDB-5omo: CRYSTAL STRUCTURE OF RAT PEROXISOMAL MULTIFUNCTIONAL ENZYME TYPE-... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5omo
TitleCRYSTAL STRUCTURE OF RAT PEROXISOMAL MULTIFUNCTIONAL ENZYME TYPE-1 (RPMFE1) COMPLEXED WITH WITH 3S-HYDROXY-DECANOYL-COA AND 3-KETO-DECANOYL-COA
ComponentsPeroxisomal bifunctional enzyme
KeywordsOXIDOREDUCTASE / 3S-HYDROXY-DECANOYL-COA / 3-KETO-DECANOYL-COA / MFE1 / BETA-OXIDATION / FATTY ACID / CROTONASE / 3-HYDROXYACYL-COA- DEHYDROGENASE / HYDRATASE
Function / homology
Function and homology information


Beta-oxidation of very long chain fatty acids / intramolecular oxidoreductase activity, transposing C=C bonds / Peroxisomal protein import / Delta3-Delta2-enoyl-CoA isomerase / delta(3)-delta(2)-enoyl-CoA isomerase activity / long-chain-3-hydroxyacyl-CoA dehydrogenase activity / enoyl-CoA hydratase / 3-hydroxyacyl-CoA dehydrogenase / 3-hydroxyacyl-CoA dehydrogenase activity / enoyl-CoA hydratase activity ...Beta-oxidation of very long chain fatty acids / intramolecular oxidoreductase activity, transposing C=C bonds / Peroxisomal protein import / Delta3-Delta2-enoyl-CoA isomerase / delta(3)-delta(2)-enoyl-CoA isomerase activity / long-chain-3-hydroxyacyl-CoA dehydrogenase activity / enoyl-CoA hydratase / 3-hydroxyacyl-CoA dehydrogenase / 3-hydroxyacyl-CoA dehydrogenase activity / enoyl-CoA hydratase activity / fatty acid beta-oxidation / NAD+ binding / peroxisome / enzyme binding / 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
(S)-3-HYDROXYDECANOYL-COA / 3-KETO-DECANOYL-COA / Peroxisomal bifunctional enzyme
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.49 Å
AuthorsKasaragod, P. / Kiema, T.-R. / Schmitz, W. / Hiltunen, J.K. / Wierenga, R.K.
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
DepositionAug 1, 2017Deposition site: PDBE / Processing site: PDBE
SupersessionSep 6, 2017ID: 5AAJ
Revision 1.0Sep 6, 2017Provider: repository / Type: Initial release
Revision 1.1May 2, 2018Group: Data collection / Category: reflns / reflns_shell
Item: _reflns.pdbx_Rpim_I_all / _reflns_shell.pdbx_Rpim_I_all
Revision 1.2Mar 20, 2019Group: Data collection / Database references / Category: citation / Item: _citation.journal_abbrev
Revision 1.3Jan 17, 2024Group: 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.4Mar 19, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Peroxisomal bifunctional enzyme
B: Peroxisomal bifunctional enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,51914
Polymers161,8632
Non-polymers3,65612
Water5,080282
1
A: Peroxisomal bifunctional enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,2738
Polymers80,9311
Non-polymers2,3427
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Peroxisomal bifunctional enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,2456
Polymers80,9311
Non-polymers1,3145
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.960, 125.080, 223.530
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: HIS / Beg label comp-ID: HIS / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: _ / Auth seq-ID: 0 - 716 / Label seq-ID: 20 - 736

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Peroxisomal bifunctional enzyme / PBFE


Mass: 80931.352 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: 3S-HYDROXY-DECANOYL-COA BOUND IN THE CROTONASE DOMAIN AND 3-KETO-DECANOYL-COA BOUND IN THE 3-HYDROXYACYL-COA-DEHYDROGENASE DOMAIN
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Ehhadh / Plasmid: PET15B / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P07896, enoyl-CoA hydratase, Delta3-Delta2-enoyl-CoA isomerase, 3-hydroxyacyl-CoA dehydrogenase

-
Non-polymers , 5 types, 294 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-HSC / (S)-3-HYDROXYDECANOYL-COA


Mass: 933.751 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C31H50N7O18P3S / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-ZOZ / 3-KETO-DECANOYL-COA


Mass: 935.767 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C31H52N7O18P3S / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 282 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.81 Å3/Da / Density % sol: 56.24 %
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 6
Details: 100MM MES PH 6.0, 150MM AMMONIUM SULPHATE, 15% W/V PEG4000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.93928 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 29, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93928 Å / Relative weight: 1
ReflectionResolution: 2.49→47.9 Å / Num. obs: 64401 / % possible obs: 99.2 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.029 / Net I/σ(I): 16.6
Reflection shellResolution: 2.49→2.62 Å / Redundancy: 4 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 4.2 / Num. unique obs: 8976 / Rpim(I) all: 0.158 / % possible all: 96.1

-
Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
SCALAdata scaling
REFMAC5.8.0158phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 2X58

2x58


Resolution: 2.49→47.9 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.921 / SU B: 16.867 / SU ML: 0.189 / Cross valid method: THROUGHOUT / ESU R: 0.436 / ESU R Free: 0.253 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22831 3208 5 %RANDOM
Rwork0.19271 ---
obs0.19446 60931 98.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 53.337 Å2
Baniso -1Baniso -2Baniso -3
1--0.38 Å2-0 Å20 Å2
2---2.45 Å20 Å2
3---2.82 Å2
Refinement stepCycle: 1 / Resolution: 2.49→47.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11076 0 228 282 11586
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumberWeight
X-RAY DIFFRACTIONr_bond_refined_d0.010.01911557
X-RAY DIFFRACTIONr_bond_other_d0.0020.0211006
X-RAY DIFFRACTIONr_angle_refined_deg1.4511.98115665
X-RAY DIFFRACTIONr_angle_other_deg1.0392.98525563
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.92451441
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.62223.035458
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.153151934
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8591579
X-RAY DIFFRACTIONr_chiral_restr0.0820.21735
X-RAY DIFFRACTIONr_chiral_restr_other1.9750.216
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02112635
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022271
X-RAY DIFFRACTIONr_nbd_refined0.19145920.2
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1440.221098
X-RAY DIFFRACTIONr_nbtor_refined0.1670.211122
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0740.211554
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1260.2798
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1940.227
X-RAY DIFFRACTIONr_nbd_other0.2390.299
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1510.29
X-RAY DIFFRACTIONr_mcbond_it1.2393.3945770
X-RAY DIFFRACTIONr_mcbond_other1.243.3935769
X-RAY DIFFRACTIONr_mcangle_it2.1865.0877209
X-RAY DIFFRACTIONr_mcangle_other2.1865.0887210
X-RAY DIFFRACTIONr_scbond_it1.2983.675787
X-RAY DIFFRACTIONr_scbond_other1.2973.6665785
X-RAY DIFFRACTIONr_scangle_it2.2345.4418456
X-RAY DIFFRACTIONr_scangle_other2.2345.4418456
X-RAY DIFFRACTIONr_long_range_B_refined4.67339.67712671
X-RAY DIFFRACTIONr_long_range_B_other4.67339.68112672
X-RAY DIFFRACTIONr_ncsr_local_group_10.0870.0544904
Refine LS restraints NCS

Ens-ID: 1 / Number: 44904 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.09 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.487→2.552 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.279 217 -
Rwork0.254 4117 -
obs--92.06 %
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)
11.25130.64810.39770.76170.79930.96780.00460.0465-0.0894-0.00640.0053-0.0308-0.0309-0.0469-0.00990.04010.00990.02650.3007-0.00250.0923-71.6428.537-114.28
20.7525-1.11040.55121.99-0.37531.0616-0.0975-0.1177-0.24390.27680.28940.38240.1489-0.0941-0.19190.1510.00030.05260.26650.11460.1628-39.428-3.905-94.074
30.3806-0.16160.23410.6597-0.54711.6206-0.0563-0.00020.04930.15590.0011-0.0648-0.1061-0.06650.05520.11120.0143-0.01430.2817-0.00580.066-35.34922.356-88.997
41.42650.5156-1.15141.7393-0.35190.94910.14050.09690.33490.18420.11090.3893-0.1021-0.0133-0.25150.0695-0.01930.02570.30850.11450.1799-56.99813.811-17.402
50.192-0.4680.1521.445-0.3361.56340.0798-0.0835-0.122-0.30790.08320.2328-0.6887-0.0143-0.1630.5582-0.06130.03870.10550.06360.1034-39.80332.159-46.084
60.23690.1364-0.00110.8379-0.62981.98430.0727-0.2011-0.0037-0.3069-0.10780.05070.09930.24860.03510.2318-0.0551-0.01460.27470.04750.0234-22.7128.723-47.747
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-4 - 259
2X-RAY DIFFRACTION2A260 - 475
3X-RAY DIFFRACTION3A476 - 720
4X-RAY DIFFRACTION4B0 - 259
5X-RAY DIFFRACTION5B260 - 475
6X-RAY DIFFRACTION6B476 - 717

+
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