[English] 日本語
Yorodumi
- PDB-5jbx: Crystal structure of LiuC in complex with coenzyme A and malonic acid -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5jbx
TitleCrystal structure of LiuC in complex with coenzyme A and malonic acid
Components3-hydroxybutyryl-CoA dehydratase
KeywordsLYASE / Dehydratase / isovalerate / Myxococcus xanthus
Function / homology
Function and homology information


3-hydroxybutyryl-CoA dehydratase / hydro-lyase activity / fatty acid beta-oxidation
Similarity search - Function
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, conserved site / Enoyl-CoA hydratase/isomerase signature. / Enoyl-CoA hydratase/isomerase / Enoyl-CoA hydratase/isomerase / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / ClpP/crotonase-like domain superfamily ...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, conserved site / Enoyl-CoA hydratase/isomerase signature. / Enoyl-CoA hydratase/isomerase / Enoyl-CoA hydratase/isomerase / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / ClpP/crotonase-like domain superfamily / Alpha-Beta Complex / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
COENZYME A / MALONATE ION / 3-hydroxybutyryl-CoA dehydratase
Similarity search - Component
Biological speciesMyxococcus xanthus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å
AuthorsBock, T. / Reichelt, J. / Mueller, R. / Blankenfeldt, W.
CitationJournal: Chembiochem / Year: 2016
Title: The Structure of LiuC, a 3-Hydroxy-3-Methylglutaconyl CoA Dehydratase Involved in Isovaleryl-CoA Biosynthesis in Myxococcus xanthus, Reveals Insights into Specificity and Catalysis.
Authors: Bock, T. / Reichelt, J. / Muller, R. / Blankenfeldt, W.
History
DepositionApr 14, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 22, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 14, 2016Group: Database references
Revision 1.2Jan 10, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 3-hydroxybutyryl-CoA dehydratase
B: 3-hydroxybutyryl-CoA dehydratase
C: 3-hydroxybutyryl-CoA dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,1369
Polymers83,1933
Non-polymers1,9436
Water20,2851126
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14300 Å2
ΔGint-46 kcal/mol
Surface area28710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.834, 84.773, 128.634
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein 3-hydroxybutyryl-CoA dehydratase


Mass: 27730.842 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Myxococcus xanthus (strain DK 1622) (bacteria)
Strain: DK 1622 / Gene: crt, MXAN_3757 / Production host: Escherichia coli (E. coli)
References: UniProt: Q1D5Y4, 3-hydroxybutyryl-CoA dehydratase
#2: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#3: Chemical
ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H2O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1126 / 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: 2.45 Å3/Da / Density % sol: 49.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 60% Tacsimate pH 6

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.7994 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Aug 27, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7994 Å / Relative weight: 1
ReflectionResolution: 1.1→42.88 Å / Num. obs: 326543 / % possible obs: 99.1 % / Redundancy: 13.3 % / Biso Wilson estimate: 11.41 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.073 / Net I/σ(I): 16
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.1-1.1212.91.288197.9
6.02-42.8812.70.03199.8

-
Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
Aimless0.3.11data scaling
PDB_EXTRACT3.2data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JBW

5jbw


Resolution: 1.1→42.387 Å / SU ML: 0.08 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 12.47
RfactorNum. reflection% reflection
Rfree0.1446 16101 4.93 %
Rwork0.1249 --
obs0.1259 326352 99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 59.2 Å2 / Biso mean: 16.8208 Å2 / Biso min: 6.71 Å2
Refinement stepCycle: final / Resolution: 1.1→42.387 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5781 0 205 1174 7160
Biso mean--23.42 30.41 -
Num. residues----780
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076322
X-RAY DIFFRACTIONf_angle_d1.0978631
X-RAY DIFFRACTIONf_chiral_restr0.075999
X-RAY DIFFRACTIONf_plane_restr0.0071145
X-RAY DIFFRACTIONf_dihedral_angle_d22.8742486
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.1-1.11250.22275250.2109101391066498
1.1125-1.12560.19155520.1942100711062398
1.1256-1.13930.20665300.1835101271065798
1.1393-1.15370.19454980.1702102291072798
1.1537-1.16890.18375310.1617101471067898
1.1689-1.18490.16795230.1553101251064898
1.1849-1.20190.17935180.151102391075798
1.2019-1.21980.17515160.1544102161073298
1.2198-1.23890.16625310.1496102231075498
1.2389-1.25920.15895520.1362101971074999
1.2592-1.28090.15685240.1315102401076499
1.2809-1.30420.15465130.1315103131082699
1.3042-1.32930.1655410.1257102381077999
1.3293-1.35640.13945160.1161102641078099
1.3564-1.38590.14295370.1136103191085699
1.3859-1.41810.14655320.1112103331086599
1.4181-1.45360.13455390.1105103201085999
1.4536-1.49290.12755370.1049103321086999
1.4929-1.53680.12065190.101103851090499
1.5368-1.58650.12635750.10021037210947100
1.5865-1.64320.12595630.10281035810921100
1.6432-1.7090.13085140.10541042710941100
1.709-1.78670.13335330.11081044710980100
1.7867-1.88090.12345340.11311048711021100
1.8809-1.99880.13035280.12211044810976100
1.9988-2.15310.13035580.11511050311061100
2.1531-2.36980.12855340.1171052711061100
2.3698-2.71260.1485760.12411056811144100
2.7126-3.41740.155660.13161067111237100
3.4174-42.4180.15245860.13151098611572100

+
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