[English] 日本語
Yorodumi
- PDB-5vjg: horse liver alcohol dehydrogenase complexed with 2,2'bipyridine -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5vjg
Titlehorse liver alcohol dehydrogenase complexed with 2,2'bipyridine
ComponentsAlcohol dehydrogenase E chain
KeywordsOXIDOREDUCTASE / alcohol dehydrogenase / 2 / 2'bipyridine / horse liver / zinc chelation
Function / homology
Function and homology information


alcohol dehydrogenase (NAD+) activity, zinc-dependent / : / 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. / 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
2,2'-bipyridine / Alcohol dehydrogenase E chain
Similarity search - Component
Biological speciesEquus caballus (horse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsPlapp, B.V. / Baskar Raj, S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Alcohol Abuse and Alcoholism (NIH/NIAAA)AA00279 United States
Citation
Journal: Biochemistry / Year: 2017
Title: Horse Liver Alcohol Dehydrogenase: Zinc Coordination and Catalysis.
Authors: Plapp, B.V. / Savarimuthu, B.R. / Ferraro, D.J. / Rubach, J.K. / Brown, E.N. / Ramaswamy, S.
#1: Journal: Eur. J. Biochem. / Year: 1977
Title: X-ray investigation of the binding of 1,10-phenanthroline and imidazole to horse-liver alcohol dehydrogenase.
Authors: Boiwe, T. / Branden, C.I.
#2: Journal: J. Mol. Biol. / Year: 1976
Title: Three-dimensional structure of horse liver alcohol dehydrogenase at 2-4 A resolution.
Authors: Eklund, H. / Nordstrom, B. / Zeppezauer, E. / Soderlund, G. / Ohlsson, I. / Boiwe, T. / Soderberg, B.O. / Tapia, O. / Branden, C.I. / Akeson, A.
History
DepositionApr 19, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 3, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 5, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Aug 2, 2017Group: Author supporting evidence / Database references / Category: citation / pdbx_audit_support
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _pdbx_audit_support.funding_organization
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 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: Alcohol dehydrogenase E chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,1404
Polymers39,8531
Non-polymers2873
Water1,72996
1
A: Alcohol dehydrogenase E chain
hetero molecules

A: Alcohol dehydrogenase E chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,2818
Polymers79,7072
Non-polymers5746
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area3310 Å2
ΔGint-21 kcal/mol
Surface area27610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.450, 73.700, 181.140
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein Alcohol dehydrogenase E chain


Mass: 39853.273 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Equus caballus (horse) / References: UniProt: P00327, alcohol dehydrogenase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-0BP / 2,2'-bipyridine / 2,2′-Bipyridine


Mass: 156.184 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H8N2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 96 / 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: 2.32 Å3/Da / Density % sol: 47.02 %
Crystal growTemperature: 278 K / Method: microdialysis / pH: 8.4
Details: Dialysis of 10 mg protein/ml against 50 mM Tris-HCl, pH 8.4, as the concentration of 2-methyl-2,4-pentanediol concentration was raised to 25 %. Crysta was soaked for 3 hr iwth 30 mM 2,2'- ...Details: Dialysis of 10 mg protein/ml against 50 mM Tris-HCl, pH 8.4, as the concentration of 2-methyl-2,4-pentanediol concentration was raised to 25 %. Crysta was soaked for 3 hr iwth 30 mM 2,2'-bipyridine before flash vitrification with liquid N2.l

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 23, 2005 / Details: MSC Yale confocal osmic
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. obs: 27148 / % possible obs: 95.3 % / Redundancy: 6.99 % / Biso Wilson estimate: 29.2 Å2 / Rmerge(I) obs: 0.118 / Χ2: 0.96 / Net I/σ(I): 9.8
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 5.04 % / Rmerge(I) obs: 0.342 / Mean I/σ(I) obs: 3.5 / Num. unique obs: 2560 / Χ2: 0.83 / % possible all: 87.4

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
d*TREKdata reduction
d*TREKdata scaling
REFMAC5.8.0131refinement
PDB_EXTRACT3.22data extraction
Omodel building
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8ADH

8adh


Resolution: 1.9→20 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.922 / SU B: 5.554 / SU ML: 0.153 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.173 / ESU R Free: 0.181
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2836 1174 4.1 %RANDOM
Rwork0.2044 ---
obs0.2075 27148 95.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 110.23 Å2 / Biso mean: 41.412 Å2 / Biso min: 22.22 Å2
Baniso -1Baniso -2Baniso -3
1-2.42 Å20 Å2-0 Å2
2--0.91 Å20 Å2
3----3.33 Å2
Refinement stepCycle: final / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2785 0 14 96 2895
Biso mean--47.63 40.78 -
Num. residues----374
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0192850
X-RAY DIFFRACTIONr_bond_other_d0.0020.022801
X-RAY DIFFRACTIONr_angle_refined_deg1.8041.983852
X-RAY DIFFRACTIONr_angle_other_deg1.04336485
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0135373
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.47124.3397
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.01115498
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.961512
X-RAY DIFFRACTIONr_chiral_restr0.10.2448
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0213177
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02587
LS refinement shellResolution: 1.9→1.949 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.462 82 4.7 %
Rwork0.378 1739 -
obs--85.69 %

+
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