[English] 日本語
Yorodumi
- PDB-1ad3: CLASS 3 ALDEHYDE DEHYDROGENASE COMPLEX WITH NICOTINAMIDE-ADENINE-... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1ad3
TitleCLASS 3 ALDEHYDE DEHYDROGENASE COMPLEX WITH NICOTINAMIDE-ADENINE-DINUCLEOTIDE
ComponentsALDEHYDE DEHYDROGENASE (CLASS 3)
KeywordsOXIDOREDUCTASE / NADP / AROMATIC ALDEHYDE
Function / homology
Function and homology information


aldehyde dehydrogenase [NAD(P)+] / Phase I - Functionalization of compounds / 3-chloroallyl aldehyde dehydrogenase activity / benzaldehyde dehydrogenase (NAD+) activity / alcohol dehydrogenase (NADP+) activity / : / cellular aldehyde metabolic process / response to xenobiotic stimulus => GO:0009410 / : / oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor ...aldehyde dehydrogenase [NAD(P)+] / Phase I - Functionalization of compounds / 3-chloroallyl aldehyde dehydrogenase activity / benzaldehyde dehydrogenase (NAD+) activity / alcohol dehydrogenase (NADP+) activity / : / cellular aldehyde metabolic process / response to xenobiotic stimulus => GO:0009410 / : / oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor / aldehyde dehydrogenase (NAD+) activity / response to glucocorticoid / response to cAMP / response to nutrient / response to organic cyclic compound / membrane => GO:0016020 / response to hypoxia / positive regulation of cell population proliferation / endoplasmic reticulum / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Aldehyde dehydrogenase NAD(P)-dependent / Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde dehydrogenase, glutamic acid active site / Aldehyde dehydrogenases glutamic acid active site. / Aldehyde dehydrogenase, cysteine active site / Aldehyde dehydrogenases cysteine active site. / Aldehyde dehydrogenase domain ...Aldehyde dehydrogenase NAD(P)-dependent / Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde dehydrogenase, glutamic acid active site / Aldehyde dehydrogenases glutamic acid active site. / Aldehyde dehydrogenase, cysteine active site / Aldehyde dehydrogenases cysteine active site. / Aldehyde dehydrogenase domain / Aldehyde dehydrogenase family / Aldehyde dehydrogenase, N-terminal / Aldehyde dehydrogenase, C-terminal / Aldehyde/histidinol dehydrogenase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Aldehyde dehydrogenase, dimeric NADP-preferring
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / ISIRAS / Resolution: 2.6 Å
AuthorsLiu, Z.-J. / Rose, J. / Wang, B.C.
Citation
Journal: Nat.Struct.Biol. / Year: 1997
Title: The first structure of an aldehyde dehydrogenase reveals novel interactions between NAD and the Rossmann fold.
Authors: Liu, Z.J. / Sun, Y.J. / Rose, J. / Chung, Y.J. / Hsiao, C.D. / Chang, W.R. / Kuo, I. / Perozich, J. / Lindahl, R. / Hempel, J. / Wang, B.C.
#1: Journal: Enzymology and Molecular Biology of Carbonyl Metabolism 6 (in: Adv.Exp. Med.Biol., V.414)
Year: 1997
Title: Crystal Structure of a Class 3 Aldehyde Dehydrogenase at 2.6 Angstroms Resolution
Authors: Liu, Z.-J. / Hempel, J. / Sun, J. / Rose, J. / Hsiao, D. / Chang, W.-R. / Chung, Y.-J. / Kuo, I. / Lindahl, R. / Wang, B.-C.
#2: Journal: Enzymology and Molecular Biology of Carbonyl Metabolism 6 (in: Adv.Exp. Med.Biol., V.414)
Year: 1997
Title: Conserved Residues in the Aldehyde Dehydrogenase Family
Authors: Hempel, J. / Liu, Z.-J. / Perozich, J. / Rose, J. / Lindahl, R. / Wang, B.-C.
#3: Journal: Proteins / Year: 1990
Title: Preliminary Crystallographic Analysis of Class 3 Rat Liver Aldehyde Dehydrogenase
Authors: Rose, J.P. / Hempel, J. / Kuo, I. / Lindahl, R. / Wang, B.C.
History
DepositionJun 25, 1996Processing site: BNL
Revision 1.0Jul 7, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _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: ALDEHYDE DEHYDROGENASE (CLASS 3)
B: ALDEHYDE DEHYDROGENASE (CLASS 3)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,9544
Polymers100,6272
Non-polymers1,3272
Water4,972276
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10170 Å2
ΔGint-43 kcal/mol
Surface area31370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.950, 170.950, 47.160
Angle α, β, γ (deg.)90.00, 110.25, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.1895, 0.0654, -0.9797), (0.0639, -0.9948, -0.0787), (-0.9798, -0.0776, 0.1843)
Vector: 85.5899, 101.2096, 77.5218)
DetailsALDEHYDE DEHYDROGENASE IS A HOMODIMER. THE FULL DIMER IS PRESENT IN THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT.

-
Components

#1: Protein ALDEHYDE DEHYDROGENASE (CLASS 3) / ALDH


Mass: 50313.438 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Organ: LIVER / Plasmid: PTA1DH / Production host: Escherichia coli (E. coli) / Strain (production host): BH101
References: UniProt: P11883, aldehyde dehydrogenase [NAD(P)+]
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 276 / 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: 2.45 Å3/Da / Density % sol: 50 %
Crystal growpH: 6.2 / Details: pH 6.2
Crystal grow
*PLUS
Method: vapor diffusion
Details: Rose, J.P., (1990) Proteins: Struct.,Funct., Genet., 8, 305.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.7 mg/mlprotein1drop
21.5 %(w/v)PEG80001drop
30.05 %(w/v)mercaptoethanol1drop
40.5 mMEDTA1drop
50.25 mg/mlNAD1drop
612.5 mMPIPES1drop
70.05 %(w/v)mercaptoethanol1reservoir
80.5 mMEDTA1reservoir
90.25 mg/mlNAD1reservoir
1012.5 mMPIPES1reservoir
112.5 %PEG80001reservoir

-
Data collection

DiffractionMean temperature: 289 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Jun 1, 1994 / Details: SUPPER MIRRORS (SMALL)
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionHighest resolution: 2.5 Å / Num. obs: 25656 / % possible obs: 80 % / Observed criterion σ(I): -3 / Redundancy: 2.3 % / Biso Wilson estimate: 23.62 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 17.444
Reflection shellResolution: 2.6→2.7 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.183 / Mean I/σ(I) obs: 2.29 / % possible all: 50
Reflection shell
*PLUS
% possible obs: 50 %

-
Processing

Software
NameVersionClassification
ISIRASmodel building
X-PLOR3.1refinement
XENGENV. 2.1data reduction
XENGENV. 2.1data scaling
ISIRASphasing
RefinementMethod to determine structure: ISIRAS / Resolution: 2.6→8 Å / Rfactor Rfree error: 0.006 / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.279 1914 8 %RANDOM
Rwork0.177 ---
obs0.177 22435 80 %-
Displacement parametersBiso mean: 18.4 Å2
Refine analyzeLuzzati coordinate error obs: 0.35 Å
Refinement stepCycle: LAST / Resolution: 2.6→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6964 0 88 284 7336
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.457
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.5
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.404
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.6→2.7 Å / Rfactor Rfree error: 0.031
RfactorNum. reflection% reflection
Rfree0.36 131 -
Rwork0.24 1464 -
obs--50 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Rfactor all: 0.192
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.5
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.404

+
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