[English] 日本語
Yorodumi
- PDB-4rqt: Alcohol Dehydrogenase Crystal Structure -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4rqt
TitleAlcohol Dehydrogenase Crystal Structure
ComponentsAlcohol dehydrogenase class-P
KeywordsOXIDOREDUCTASE / Rossmann fold / alcohol dehydrogenase
Function / homology
Function and homology information


response to flooding / S-(hydroxymethyl)glutathione dehydrogenase [NAD(P)+] activity / positive regulation of cellular response to hypoxia / formaldehyde catabolic process / alcohol dehydrogenase (NAD+) activity / response to sucrose / alcohol dehydrogenase (NAD+) activity, zinc-dependent / response to water deprivation / response to abscisic acid / alcohol dehydrogenase ...response to flooding / S-(hydroxymethyl)glutathione dehydrogenase [NAD(P)+] activity / positive regulation of cellular response to hypoxia / formaldehyde catabolic process / alcohol dehydrogenase (NAD+) activity / response to sucrose / alcohol dehydrogenase (NAD+) activity, zinc-dependent / response to water deprivation / response to abscisic acid / alcohol dehydrogenase / response to caffeine / response to osmotic stress / response to salt stress / response to cold / response to hydrogen peroxide / response to estradiol / cellular response to hypoxia / response to hypoxia / nucleotide binding / protein homodimerization activity / zinc ion binding / plasma membrane / 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 / GroES-like superfamily / NAD(P)-binding Rossmann-like Domain ...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 / 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
ACETIC ACID / Alcohol dehydrogenase class-P
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsXu, Y.W.
CitationJournal: Biochimie / Year: 2014
Title: Structural insight into the conformational change of alcohol dehydrogenase from arabidopsis Thalianal during coenzyme binding.
Authors: Chen, F. / Wang, P. / An, Y. / Huang, J. / Xu, Y.
History
DepositionNov 5, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 17, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: 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 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Alcohol dehydrogenase class-P
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,3187
Polymers40,8391
Non-polymers4796
Water3,243180
1
A: Alcohol dehydrogenase class-P
hetero molecules

A: Alcohol dehydrogenase class-P
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,63514
Polymers81,6772
Non-polymers95812
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_566x,x-y+1,-z+7/61
Buried area4680 Å2
ΔGint-120 kcal/mol
Surface area28090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.604, 103.604, 168.127
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-509-

HOH

-
Components

#1: Protein Alcohol dehydrogenase class-P


Mass: 40838.605 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: ADH, ADH1, Arabidopsis thaliana, At1g77120, F22K20.19 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P06525, 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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 180 / 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: 3.19 Å3/Da / Density % sol: 61.43 %
Crystal growTemperature: 295 K / Method: evaporation / pH: 5.9
Details: 2.0M ammonium sulfate, 0.1M acetate pH5.9, 1% glycerol, EVAPORATION, temperature 295K

-
Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: May 1, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 24400 / Num. obs: 24387 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.2 % / Rmerge(I) obs: 0.076
Reflection shellResolution: 2.3→2.37 Å / Redundancy: 12.2 % / Rmerge(I) obs: 0.513 / Mean I/σ(I) obs: 5.8 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2FZW

2fzw


Resolution: 2.3→49.505 Å / SU ML: 0.17 / σ(F): 1.34 / Phase error: 18.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2005 1717 7.05 %RANDOM
Rwork0.1621 ---
obs0.1648 24362 99.91 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→49.505 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2863 0 21 180 3064
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052948
X-RAY DIFFRACTIONf_angle_d0.8384000
X-RAY DIFFRACTIONf_dihedral_angle_d13.2281070
X-RAY DIFFRACTIONf_chiral_restr0.048438
X-RAY DIFFRACTIONf_plane_restr0.002519
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.36770.20841280.17621842X-RAY DIFFRACTION100
2.3677-2.44410.2211570.16471817X-RAY DIFFRACTION100
2.4441-2.53150.22481480.16041846X-RAY DIFFRACTION100
2.5315-2.63280.22171430.17041851X-RAY DIFFRACTION100
2.6328-2.75260.22361300.17011862X-RAY DIFFRACTION100
2.7526-2.89780.21761490.17321869X-RAY DIFFRACTION100
2.8978-3.07930.21961290.18041871X-RAY DIFFRACTION100
3.0793-3.3170.19931470.17291872X-RAY DIFFRACTION100
3.317-3.65070.21931550.1581882X-RAY DIFFRACTION100
3.6507-4.17870.19061470.14191905X-RAY DIFFRACTION100
4.1787-5.26380.15641440.13821940X-RAY DIFFRACTION100
5.2638-49.51690.19691400.18012088X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 27.4989 Å / Origin y: 51.7213 Å / Origin z: 89.1612 Å
111213212223313233
T0.2166 Å20.0246 Å2-0.0483 Å2-0.21 Å2-0.0075 Å2--0.174 Å2
L1.0189 °2-1.2139 °20.127 °2-2.5104 °2-0.178 °2--0.2618 °2
S0.0799 Å °0.1538 Å °-0.0921 Å °-0.117 Å °-0.0409 Å °0.1657 Å °0.0466 Å °0.0073 Å °-0.0339 Å °
Refinement TLS groupSelection details: all

+
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