[English] 日本語
Yorodumi
- PDB-8ecs: F93G Horse Liver Alcohol Dehydrogenase in Complex with NADH and N... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8ecs
TitleF93G Horse Liver Alcohol Dehydrogenase in Complex with NADH and N-Cyclohexylformamide
ComponentsAlcohol dehydrogenase E chain
KeywordsOXIDOREDUCTASE / Ternary complex
Function / homology
Function and homology information


all-trans-retinol dehydrogenase (NAD+) activity / alcohol dehydrogenase / retinoic acid metabolic process / retinol metabolic process / zinc ion binding / cytosol
Similarity search - Function
Alcohol dehydrogenase, zinc-type, conserved site / Zinc-containing alcohol dehydrogenases signature. / 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 ...Alcohol dehydrogenase, zinc-type, conserved site / Zinc-containing alcohol dehydrogenases signature. / 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 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
CYCLOHEXYLFORMAMIDE / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / Alcohol dehydrogenase E chain
Similarity search - Component
Biological speciesEquus caballus (horse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsZheng, C. / Mathews, I.I. / Boxer, S.G.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM118044 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P30GM133894 United States
CitationJournal: To Be Published
Title: Structure of F93G horse liver alcohol dehydrogenase at 1.20 Angstroms resolution
Authors: Zheng, C. / Mathews, I.I. / Boxer, S.G.
History
DepositionSep 2, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 13, 2023Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Alcohol dehydrogenase E chain
B: Alcohol dehydrogenase E chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,74410
Polymers79,8972
Non-polymers1,8478
Water17,619978
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6970 Å2
ΔGint-109 kcal/mol
Surface area26440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.100, 50.280, 92.570
Angle α, β, γ (deg.)92.750, 102.880, 108.970
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein Alcohol dehydrogenase E chain


Mass: 39948.332 Da / Num. of mol.: 2 / Mutation: F93G
Source method: isolated from a genetically manipulated source
Details: liver enzyme / Source: (gene. exp.) Equus caballus (horse) / Production host: Escherichia coli (E. coli) / References: UniProt: P00327, alcohol dehydrogenase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH


Mass: 665.441 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H29N7O14P2
#4: Chemical ChemComp-CXF / CYCLOHEXYLFORMAMIDE


Mass: 127.184 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H13NO / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 978 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.21 Å3/Da / Density % sol: 44.4 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: PEG400(10%-25%), 2mM NADH, 10mM N-cyclohexylformamide in Tris buffer at pH 8.20

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 15, 2020
Details: Rh coated collimating mirrors, K-B focusing mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.2→37.75 Å / Num. obs: 211968 / % possible obs: 92.5 % / Redundancy: 6.795 % / Biso Wilson estimate: 20.144 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.066 / Rrim(I) all: 0.072 / Χ2: 0.896 / Net I/σ(I): 11.8 / Num. measured all: 1440286 / Scaling rejects: 305
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.2-1.235.2641.0811.396457416927122680.7791.272.5
1.23-1.265.6620.9921.648074116511142590.8061.09386.4
1.26-1.36.1430.8182.118837816051143870.8660.89389.6
1.3-1.346.9060.7032.629917115619143610.9150.75991.9
1.34-1.387.0170.5583.339840115087140240.9450.60393
1.38-1.437.1860.4644.099866714650137300.960.593.7
1.43-1.487.0080.3615.059286814114132510.9720.3993.9
1.48-1.557.2220.2736.599227013539127770.9840.29494.4
1.55-1.617.0190.2058.358698613067123930.9880.22194.8
1.61-1.697.2060.16610.348528312427118350.9920.17995.2
1.69-1.787.0640.12912.778019411876113530.9950.1495.6
1.78-1.897.230.10316.337748911160107180.9950.11196
1.89-2.026.920.08219.947070510572102180.9960.08996.7
2.02-2.197.0470.06823.6966918979294960.9970.07497
2.19-2.397.2240.06127.563445902487820.9980.06697.3
2.39-2.687.0750.05729.4455821809478900.9970.06297.5
2.68-3.096.6210.05131.0446935722470890.9980.05698.1
3.09-3.797.0580.04635.3341874602659330.9980.0598.5
3.79-5.356.7860.04135.9331587470146550.9990.04599
5.35-37.757.0530.0436.8317979257525490.9980.04499

-
Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4DWV

4dwv


Resolution: 1.2→37.75 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 20.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.162 10590 5 %
Rwork0.1477 201228 -
obs0.1485 211818 92.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 88 Å2 / Biso mean: 23.0476 Å2 / Biso min: 11.13 Å2
Refinement stepCycle: final / Resolution: 1.2→37.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5556 0 110 978 6644
Biso mean--17.29 34.79 -
Num. residues----748
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.2-1.210.33522340.32924452468662
1.21-1.220.32413090.29825862617180
1.22-1.240.28253210.27936117643886
1.24-1.260.28033320.27686319665186
1.26-1.270.2623320.25056304663688
1.27-1.290.25673460.2346568691490
1.29-1.310.24133450.22236547689290
1.31-1.330.24383530.21336696704993
1.33-1.350.21383510.20246706705792
1.35-1.370.24023530.18676711706493
1.37-1.390.19513590.18346788714794
1.39-1.420.2093580.17036817717594
1.42-1.450.18743560.16066752710893
1.45-1.480.18563590.15166831719094
1.48-1.510.16323590.14116823718294
1.51-1.540.16843590.13816826718594
1.54-1.580.16183620.12996868723095
1.58-1.620.15833650.12936937730295
1.62-1.670.15453610.12956871723295
1.67-1.730.16123660.13326923728995
1.73-1.790.16813650.14166964732996
1.79-1.860.15913660.13796959732596
1.86-1.940.14773680.13196981734996
1.94-2.050.14943670.14066973734096
2.05-2.180.15673720.13897055742797
2.18-2.340.15983720.13917077744997
2.34-2.580.1533720.14137061743398
2.58-2.950.16773750.15317131750698
2.95-3.720.14863750.14747140751599
3.72-37.750.12963780.12547169754799

+
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