[English] 日本語
Yorodumi
- PDB-1mg5: Crystal structure of Drosophila melanogaster alcohol dehydrogenas... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1mg5
TitleCrystal structure of Drosophila melanogaster alcohol dehydrogenase complexed with NADH and acetate at 1.6 A
Componentsalcohol dehydrogenase
KeywordsOXIDOREDUCTASE / SDR / ADH / Drosophila melanogaster / NADH / acetate
Function / homology
Function and homology information


alcohol catabolic process / ethanol metabolic process / acetaldehyde dehydrogenase (acetylating) activity / alcohol metabolic process / alcohol dehydrogenase (NAD+) activity / acetaldehyde metabolic process / : / behavioral response to ethanol / : / alcohol dehydrogenase ...alcohol catabolic process / ethanol metabolic process / acetaldehyde dehydrogenase (acetylating) activity / alcohol metabolic process / alcohol dehydrogenase (NAD+) activity / acetaldehyde metabolic process / : / behavioral response to ethanol / : / alcohol dehydrogenase / oxidoreductase activity / protein homodimerization activity / protein-containing complex / cytosol
Similarity search - Function
Alcohol dehydrogenase, Drosophila-type / short chain dehydrogenase / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / Alcohol dehydrogenase
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.63 Å
AuthorsBenach, J. / Atrian, S. / Gonzalez-Duarte, R. / Ladenstein, R.
Citation
Journal: J.Mol.Biol. / Year: 2005
Title: Drosophila alcohol dehydrogenase: acetate-enzyme interactions and novel insights into the effects of electrostatics on catalysis
Authors: Benach, J. / Winberg, J.O. / Svendsen, J.S. / Atrian, S. / Gonzalez-Duarte, R. / Ladenstein, R.
#1: Journal: J.Mol.Biol. / Year: 1998
Title: The refined crystal structure of Drosophila lebanonensis alcohol dehydrogenase at 1.9 A resolution
Authors: Benach, J. / Atrian, S. / Gonzalez-Duarte, R. / Ladenstein, R.
#2: Journal: J.Mol.Biol. / Year: 1999
Title: The catalytic reaction and inhibition mechanism of Drosophila alcohol dehydrogenase: Observation of an enzyme-bound NAD-ketone adduct at 1.4 A resolution by X-ray crystallography
Authors: Benach, J. / Atrian, S. / Gonzalez-Duarte, R. / Ladenstein, R.
History
DepositionAug 14, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 30, 2013Group: Non-polymer description
Revision 1.4Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999sequence Since the protein was purified directly from Drosophila melanogaster ADH. The first ...sequence Since the protein was purified directly from Drosophila melanogaster ADH. The first residue: Met1 is cleaved off in the matured Drosophila melanogaster ADH-S enzyme. For this reason it is not present in the crystal structure.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: alcohol dehydrogenase
B: alcohol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,7636
Polymers55,3142
Non-polymers1,4494
Water14,808822
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7990 Å2
ΔGint-54 kcal/mol
Surface area18210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.481, 69.519, 75.923
Angle α, β, γ (deg.)90.00, 89.13, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein alcohol dehydrogenase /


Mass: 27656.834 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: ADH-Slow allele / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: P00334, alcohol dehydrogenase
#2: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH / Nicotinamide adenine dinucleotide


Mass: 665.441 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H29N7O14P2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 822 / 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: 2.26 Å3/Da / Density % sol: 45.68 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M TRIS/HCl, 30% PEG4000, 0.2M NaAcetate trihydrate, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 277 K / pH: 8.6 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
220 mMTris-HCl1droppH8.6
310 mMdithiothreitol1reservoir
410 mMNADH1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 10, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.63→40 Å / Num. obs: 60633 / % possible obs: 96.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.5 % / Biso Wilson estimate: 15.3 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 19.7
Reflection shellResolution: 1.63→1.68 Å / Rmerge(I) obs: 0.36 / % possible all: 73.3
Reflection
*PLUS
Num. measured all: 438968
Reflection shell
*PLUS
% possible obs: 73.3 % / Rmerge(I) obs: 0.36

-
Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1a4u

1a4u


Resolution: 1.63→20 Å / Isotropic thermal model: isotropic / Cross valid method: free R-factor / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflection
Rfree0.205 2894 5 %
Rwork0.168 --
all-61653 -
obs-61653 -
Displacement parametersBiso mean: 14.6 Å2
Refine analyzeLuzzati coordinate error obs: 0.16 Å / Luzzati d res low obs: 5 Å
Refinement stepCycle: LAST / Resolution: 1.63→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3906 0 96 822 4824
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.01
X-RAY DIFFRACTIONp_angle_d2.1
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg2.14
X-RAY DIFFRACTIONp_dihedral_angle_d
X-RAY DIFFRACTIONp_dihedral_angle_deg24
X-RAY DIFFRACTIONp_improper_angle_d
X-RAY DIFFRACTIONp_improper_angle_deg1.91

+
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