[English] 日本語
Yorodumi
- PDB-5yat: Crystal structure of mitochondrial alcohol dehydrogenase isozyme ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5yat
TitleCrystal structure of mitochondrial alcohol dehydrogenase isozyme III from Komagataella phaffii GS115
ComponentsMitochondrial alcohol dehydrogenase isozyme III
KeywordsOXIDOREDUCTASE / alcohol dehydrogenase / catalytic zinc / yeast / dimer
Function / homology
Function and homology information


oxidoreductase activity / zinc ion binding
Similarity search - Function
Alcohol dehydrogenase, zinc-type, conserved site / Zinc-containing alcohol dehydrogenases signature. / Quinone Oxidoreductase; Chain A, domain 1 / Medium-chain alcohol dehydrogenases, catalytic domain / Alcohol dehydrogenase-like, C-terminal / Zinc-binding dehydrogenase / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / Polyketide synthase, enoylreductase domain / Enoylreductase ...Alcohol dehydrogenase, zinc-type, conserved site / Zinc-containing alcohol dehydrogenases signature. / Quinone Oxidoreductase; Chain A, domain 1 / Medium-chain alcohol dehydrogenases, catalytic domain / Alcohol dehydrogenase-like, C-terminal / Zinc-binding dehydrogenase / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / Polyketide synthase, enoylreductase domain / Enoylreductase / GroES-like superfamily / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ISOPROPYL ALCOHOL / Mitochondrial alcohol dehydrogenase isozyme III
Similarity search - Component
Biological speciesKomagataella phaffii (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.745 Å
AuthorsZhang, H.D. / Li, Q.
CitationJournal: Biochim. Biophys. Acta / Year: 2018
Title: Investigation of structure and function of mitochondrial alcohol dehydrogenase isozyme III from Komagataella phaffii GS115.
Authors: Zhang, H. / Li, Q. / Wang, L. / Chen, Y.
History
DepositionSep 1, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 21, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: 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: Mitochondrial alcohol dehydrogenase isozyme III
B: Mitochondrial alcohol dehydrogenase isozyme III
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,82712
Polymers74,0762
Non-polymers75010
Water9,332518
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2870 Å2
ΔGint-13 kcal/mol
Surface area29480 Å2
Unit cell
Length a, b, c (Å)111.856, 111.856, 105.520
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number172
Space group name H-MP64
Components on special symmetry positions
IDModelComponents
11A-650-

HOH

21A-749-

HOH

-
Components

#1: Protein Mitochondrial alcohol dehydrogenase isozyme III


Mass: 37038.176 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Komagataella phaffii (strain GS115 / ATCC 20864) (fungus)
Strain: GS115 / ATCC 20864 / Gene: PAS_chr2-1_0472 / Production host: Pichia (fungus) / References: UniProt: C4R0S8
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 518 / 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: 2.57 Å3/Da / Density % sol: 52.19 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 13% (v/v) 2-propanol, 0.2 M Zinc acetate, 0.1M Sodium cacodylate/Hydrochloric acid, pH 6.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979158 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 18, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979158 Å / Relative weight: 1
ReflectionResolution: 1.745→96.88 Å / Num. obs: 72896 / % possible obs: 99.9 % / Redundancy: 21.9 % / Rmerge(I) obs: 0.205 / Net I/σ(I): 14.3

-
Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4W6Z

4w6z


Resolution: 1.745→36.613 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 21.92
RfactorNum. reflection% reflection
Rfree0.2116 3558 5.03 %
Rwork0.1825 --
obs0.184 70682 92.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.745→36.613 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5171 0 36 518 5725
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045299
X-RAY DIFFRACTIONf_angle_d0.7477190
X-RAY DIFFRACTIONf_dihedral_angle_d11.6863102
X-RAY DIFFRACTIONf_chiral_restr0.051823
X-RAY DIFFRACTIONf_plane_restr0.005918
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.745-1.76890.33611020.2912305X-RAY DIFFRACTION80
1.7689-1.79420.32841310.26982402X-RAY DIFFRACTION83
1.7942-1.8210.28071330.25262413X-RAY DIFFRACTION85
1.821-1.84940.29471330.24392475X-RAY DIFFRACTION86
1.8494-1.87970.24311350.24252502X-RAY DIFFRACTION87
1.8797-1.91220.27621300.27192279X-RAY DIFFRACTION79
1.9122-1.94690.34521330.30352372X-RAY DIFFRACTION83
1.9469-1.98440.25481180.21522624X-RAY DIFFRACTION91
1.9844-2.02490.24481330.20032777X-RAY DIFFRACTION94
2.0249-2.06890.21971320.20372676X-RAY DIFFRACTION93
2.0689-2.1170.24261460.19542690X-RAY DIFFRACTION94
2.117-2.170.23141440.18852776X-RAY DIFFRACTION95
2.17-2.22860.21711430.1952725X-RAY DIFFRACTION94
2.2286-2.29420.29641370.23782572X-RAY DIFFRACTION90
2.2942-2.36820.21221530.17942778X-RAY DIFFRACTION97
2.3682-2.45290.2031470.17162844X-RAY DIFFRACTION98
2.4529-2.5510.20991410.1652848X-RAY DIFFRACTION99
2.551-2.66710.20211570.17122836X-RAY DIFFRACTION99
2.6671-2.80770.19571510.17322870X-RAY DIFFRACTION99
2.8077-2.98350.20711680.16752845X-RAY DIFFRACTION99
2.9835-3.21370.18881560.17372879X-RAY DIFFRACTION100
3.2137-3.53690.19011560.16322891X-RAY DIFFRACTION100
3.5369-4.04810.16951490.15522912X-RAY DIFFRACTION100
4.0481-5.09810.17711620.14422905X-RAY DIFFRACTION100
5.0981-36.62150.20851680.18412928X-RAY DIFFRACTION100

+
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://pdbjlvh1.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