[English] 日本語
Yorodumi
- PDB-9jhe: 3-hydroxybutyryl-CoA dehydrogenase with NAD -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9jhe
Title3-hydroxybutyryl-CoA dehydrogenase with NAD
Components3-hydroxyacyl-CoA dehydrogenase, NAD binding domain protein
KeywordsOXIDOREDUCTASE / Complex with NAD
Function / homology
Function and homology information


3-hydroxybutyryl-CoA dehydrogenase activity / fatty acid beta-oxidation / NAD+ binding
Similarity search - Function
3-hydroxyacyl-CoA dehydrogenase / 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 / 6-phosphogluconate dehydrogenase, domain 2 / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain protein
Similarity search - Component
Biological speciesFaecalibacterium duncaniae
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsPark, J.A. / Yang, J.W. / Park, S.H. / Kim, S.H. / Hwang, K.Y.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea) Korea, Republic Of
Citation
Journal: Int J Mol Sci / Year: 2024
Title: Structural Insights and Catalytic Mechanism of 3-Hydroxybutyryl-CoA Dehydrogenase from Faecalibacterium Prausnitzii A2-165.
Authors: Yang, J. / Jeon, H.J. / Park, S. / Park, J. / Jang, S. / Shin, B. / Bang, K. / Hawkes, H.K. / Park, S. / Kim, S. / Hwang, K.Y.
#1: Journal: Int J Mol Sci / Year: 2024
Title: Structural Insights and Catalytic Mechanism of 3-Hydroxybutyryl-CoA Dehydrogenase from
Authors: Yang, J. / Jeon, H.J. / Park, S. / Park, J. / Jang, S. / Shin, B. / Bang, K. / Hawkes, H.K. / Park, S. / Kim, S. / Hwang, K.Y.
History
DepositionSep 9, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 13, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain protein
B: 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain protein
C: 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain protein
D: 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain protein
E: 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain protein
F: 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)190,85912
Polymers186,8786
Non-polymers3,9816
Water1,40578
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24830 Å2
ΔGint-128 kcal/mol
Surface area66590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.821, 80.476, 128.345
Angle α, β, γ (deg.)90.00, 102.19, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
3-hydroxyacyl-CoA dehydrogenase, NAD binding domain protein / 3-hydroxybutyryl-CoA dehydrogenase


Mass: 31146.408 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Faecalibacterium duncaniae (strain DSM 17677 / JCM 31915 / A2-165) (bacteria)
Gene: FAEPRAA2165_01580, GXM22_07070 / Production host: Escherichia coli (E. coli)
References: UniProt: C7H5K9, 3-hydroxybutyryl-CoA dehydrogenase
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.45 Å3/Da / Density % sol: 49.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: ammonium acetate, bis-tris/HCl, PEG 3,350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 16, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.55→46.7 Å / Num. obs: 54528 / % possible obs: 91.7 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 26.9
Reflection shellResolution: 2.55→2.55 Å / Rmerge(I) obs: 0.305 / Mean I/σ(I) obs: 12.8 / Num. unique obs: 2381

-
Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.55→46.64 Å / SU ML: 0.39 / Cross valid method: NONE / σ(F): 1.51 / Phase error: 29.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2639 2000 3.67 %
Rwork0.2125 --
obs0.2144 54528 91.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.55→46.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12978 0 264 78 13320
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_dihedral_angle_d7.2411836
X-RAY DIFFRACTIONf_chiral_restr0.0452106
X-RAY DIFFRACTIONf_plane_restr0.0052298
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.55-2.610.37641230.31643253X-RAY DIFFRACTION79
2.61-2.680.36551280.30813342X-RAY DIFFRACTION83
2.68-2.760.35371300.28913419X-RAY DIFFRACTION84
2.76-2.850.33741360.2743580X-RAY DIFFRACTION88
2.85-2.950.32471370.26873568X-RAY DIFFRACTION88
2.95-3.070.30561420.26663725X-RAY DIFFRACTION91
3.07-3.210.3181440.26853789X-RAY DIFFRACTION93
3.21-3.380.31081450.24993820X-RAY DIFFRACTION94
3.38-3.590.3211490.2353920X-RAY DIFFRACTION97
3.59-3.870.30961520.21953983X-RAY DIFFRACTION98
3.87-4.260.23461520.19293998X-RAY DIFFRACTION98
4.26-4.870.23091530.17324004X-RAY DIFFRACTION97
4.87-6.140.25071530.18694015X-RAY DIFFRACTION97

+
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