[English] 日本語
Yorodumi
- PDB-4u1a: Crystal structure of human peroxisomal delta3,delta2, enoyl-CoA i... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4u1a
TitleCrystal structure of human peroxisomal delta3,delta2, enoyl-CoA isomerase helix-10 deletion mutant (ISOB-ECI2)
ComponentsEnoyl-CoA delta isomerase 2
KeywordsISOMERASE / PECI / crotonase / beta-oxidation
Function / homology
Function and homology information


Delta3-Delta2-enoyl-CoA isomerase / delta(3)-delta(2)-enoyl-CoA isomerase activity / Beta-oxidation of very long chain fatty acids / fatty-acyl-CoA binding / fatty acid catabolic process / fatty acid beta-oxidation / peroxisomal matrix / Peroxisomal protein import / peroxisome / intracellular membrane-bounded organelle ...Delta3-Delta2-enoyl-CoA isomerase / delta(3)-delta(2)-enoyl-CoA isomerase activity / Beta-oxidation of very long chain fatty acids / fatty-acyl-CoA binding / fatty acid catabolic process / fatty acid beta-oxidation / peroxisomal matrix / Peroxisomal protein import / peroxisome / intracellular membrane-bounded organelle / mitochondrion / membrane / cytosol
Similarity search - Function
Acyl-CoA-binding protein, ACBP, conserved site / Acyl-CoA-binding (ACB) domain signature. / Acyl-CoA-binding protein, ACBP / Acyl-CoA binding protein superfamily / Acyl CoA binding protein / Acyl-CoA-binding (ACB) domain profile. / Lyase 2-enoyl-coa Hydratase, Chain A, domain 2 / Lyase 2-enoyl-coa Hydratase; Chain A, domain 2 / Enoyl-CoA hydratase, C-terminal / Enoyl-CoA hydratase/isomerase ...Acyl-CoA-binding protein, ACBP, conserved site / Acyl-CoA-binding (ACB) domain signature. / Acyl-CoA-binding protein, ACBP / Acyl-CoA binding protein superfamily / Acyl CoA binding protein / Acyl-CoA-binding (ACB) domain profile. / Lyase 2-enoyl-coa Hydratase, Chain A, domain 2 / Lyase 2-enoyl-coa Hydratase; Chain A, domain 2 / Enoyl-CoA hydratase, C-terminal / Enoyl-CoA hydratase/isomerase / Enoyl-CoA hydratase/isomerase / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / FERM/acyl-CoA-binding protein superfamily / ClpP/crotonase-like domain superfamily / Alpha-Beta Complex / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Enoyl-CoA delta isomerase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.85 Å
AuthorsOnwukwe, G.U. / Koski, M.K. / Wierenga, R.K.
Funding support Germany, 1items
OrganizationGrant numberCountry
Biostruct-XN283570 Germany
CitationJournal: Febs J. / Year: 2015
Title: Human Delta (3) , Delta (2) -enoyl-CoA isomerase, type 2: a structural enzymology study on the catalytic role of its ACBP domain and helix-10.
Authors: Onwukwe, G.U. / Kursula, P. / Koski, M.K. / Schmitz, W. / Wierenga, R.K.
History
DepositionJul 15, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 24, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 31, 2014Group: Database references
Revision 1.2Jan 14, 2015Group: Database references
Revision 1.3Feb 25, 2015Group: Database references
Revision 1.4May 8, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Enoyl-CoA delta isomerase 2
B: Enoyl-CoA delta isomerase 2
C: Enoyl-CoA delta isomerase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,6486
Polymers89,5413
Non-polymers1063
Water66737
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7480 Å2
ΔGint-80 kcal/mol
Surface area28500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.440, 95.340, 129.970
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
11B
21A
12C
22A

NCS domain segments:

Component-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: CYS / End label comp-ID: CYS / Refine code: 3 / Auth seq-ID: 103 - 345 / Label seq-ID: 24 - 266

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11BB
21AA
12CC
22AA

NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.453322, 0.349164, 0.820112), (0.147829, 0.936791, -0.317127), (-0.879003, -0.022524, -0.476285)1.29084, -0.34119, 0.81064
3given(1), (1), (1)
4given(-0.465263, 0.118329, -0.877228), (0.330104, 0.942728, -0.047916), (0.821317, -0.31187, -0.477677)1.07551, -0.57989, -0.79676

-
Components

#1: Protein Enoyl-CoA delta isomerase 2 / DRS-1 / Delta(3) / delta(2)-enoyl-CoA isomerase / D3 / D2-enoyl-CoA isomerase / Diazepam-binding ...DRS-1 / Delta(3) / delta(2)-enoyl-CoA isomerase / D3 / D2-enoyl-CoA isomerase / Diazepam-binding inhibitor-related protein 1 / DBI-related protein 1 / Dodecenoyl-CoA isomerase / Hepatocellular carcinoma-associated antigen 88 / Peroxisomal 3 / 2-trans-enoyl-CoA isomerase / pECI / Renal carcinoma antigen NY-REN-1


Mass: 29847.061 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ECI2, DRS1, HCA88, PECI / Production host: Escherichia coli (E. coli)
References: UniProt: O75521, Delta3-Delta2-enoyl-CoA isomerase
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 37 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 52.3 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 160mM calcium acetate, 0.08M sodium cacodylate pH 6.5, 14.4% PEG8000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: May 9, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.85→34.85 Å / Num. obs: 22266 / % possible obs: 99.6 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.147 / Net I/σ(I): 9.9
Reflection shellResolution: 2.85→3 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.71 / Mean I/σ(I) obs: 2.8 / % possible all: 97.6

-
Processing

SoftwareName: REFMAC / Version: 5.8.0049 / Classification: refinement
RefinementResolution: 2.85→34.85 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.924 / SU B: 16.474 / SU ML: 0.286 / Cross valid method: THROUGHOUT / ESU R Free: 0.353 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23295 1113 5 %RANDOM
Rwork0.17631 ---
obs0.17906 21084 99.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 51.899 Å2
Baniso -1Baniso -2Baniso -3
1--2.98 Å2-0 Å20 Å2
2--7.79 Å20 Å2
3----4.81 Å2
Refinement stepCycle: 1 / Resolution: 2.85→34.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5706 0 3 37 5746
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0195825
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4441.9677880
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9475734
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.54124.362243
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.89151019
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0671530
X-RAY DIFFRACTIONr_chiral_restr0.0940.2892
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214347
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.4264.8812945
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it5.5417.3113676
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.1325.432880
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined11.35340.8298548
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11B907loose positional0.065
22C907loose positional0.075
11B972tight thermal6.690.5
22C972tight thermal9.030.5
11B907loose thermal7.1110
22C907loose thermal8.8510
LS refinement shellResolution: 2.847→2.921 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.386 77 -
Rwork0.341 1459 -
obs--94.87 %

+
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