[English] 日本語
Yorodumi
- PDB-6qap: Structure of the human aldehyde dehydrogenase 9A1 in C2 space group -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6qap
TitleStructure of the human aldehyde dehydrogenase 9A1 in C2 space group
Components4-trimethylaminobutyraldehyde dehydrogenase
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


formaldehyde dehydrogenase / 1-pyrroline dehydrogenase activity / 4-trimethylammoniobutyraldehyde dehydrogenase / 4-trimethylammoniobutyraldehyde dehydrogenase activity / formaldehyde dehydrogenase activity / Carnitine synthesis / carnitine biosynthetic process / aminobutyraldehyde dehydrogenase activity / aminobutyraldehyde dehydrogenase / cellular aldehyde metabolic process ...formaldehyde dehydrogenase / 1-pyrroline dehydrogenase activity / 4-trimethylammoniobutyraldehyde dehydrogenase / 4-trimethylammoniobutyraldehyde dehydrogenase activity / formaldehyde dehydrogenase activity / Carnitine synthesis / carnitine biosynthetic process / aminobutyraldehyde dehydrogenase activity / aminobutyraldehyde dehydrogenase / cellular aldehyde metabolic process / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (non-phosphorylating) activity / aldehyde dehydrogenase (NAD+) / aldehyde dehydrogenase (NAD+) activity / small molecule binding / protein homotetramerization / extracellular exosome / cytosol / cytoplasm
Similarity search - Function
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; 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
DI(HYDROXYETHYL)ETHER / 4-trimethylaminobutyraldehyde dehydrogenase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsMorera, S. / Vigouroux, A.
CitationJournal: Biosci.Rep. / Year: 2019
Title: Kinetic and structural analysis of human ALDH9A1.
Authors: Koncitikova, R. / Vigouroux, A. / Kopecna, M. / Sebela, M. / Morera, S. / Kopecny, D.
History
DepositionDec 19, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 10, 2019Provider: repository / Type: Initial release
Revision 1.1May 8, 2019Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Jan 24, 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_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 4-trimethylaminobutyraldehyde dehydrogenase
B: 4-trimethylaminobutyraldehyde dehydrogenase
C: 4-trimethylaminobutyraldehyde dehydrogenase
D: 4-trimethylaminobutyraldehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)223,44131
Polymers221,9014
Non-polymers1,53927
Water6,449358
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22900 Å2
ΔGint-140 kcal/mol
Surface area62380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)164.290, 160.030, 84.600
Angle α, β, γ (deg.)90.00, 91.09, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein
4-trimethylaminobutyraldehyde dehydrogenase / TMABADH / Aldehyde dehydrogenase E3 isozyme / Aldehyde dehydrogenase family 9 member A1 / Gamma- ...TMABADH / Aldehyde dehydrogenase E3 isozyme / Aldehyde dehydrogenase family 9 member A1 / Gamma-aminobutyraldehyde dehydrogenase / R-aminobutyraldehyde dehydrogenase


Mass: 55475.355 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ALDH9A1, ALDH4, ALDH7, ALDH9 / Production host: Escherichia coli (E. coli)
References: UniProt: P49189, 4-trimethylammoniobutyraldehyde dehydrogenase, aldehyde dehydrogenase (NAD+), aminobutyraldehyde dehydrogenase
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 358 / 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: 2.51 Å3/Da / Density % sol: 50.91 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / Details: 14% PEG 4K, 0.1 M sodium citrate pH 5.6

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.3→47.74 Å / Num. obs: 96851 / % possible obs: 99.7 % / Redundancy: 7 % / Biso Wilson estimate: 59.02 Å2 / Rmerge(I) obs: 0.152 / Rsym value: 0.141 / Net I/σ(I): 9.89
Reflection shellResolution: 2.3→2.44 Å

-
Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6QAK

6qak


Resolution: 2.3→47.74 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.91 / SU R Cruickshank DPI: 0.318 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.305 / SU Rfree Blow DPI: 0.22 / SU Rfree Cruickshank DPI: 0.226
RfactorNum. reflection% reflectionSelection details
Rfree0.251 4843 5 %RANDOM
Rwork0.22 ---
obs0.222 96847 99.7 %-
Displacement parametersBiso mean: 63.21 Å2
Baniso -1Baniso -2Baniso -3
1--5.214 Å20 Å2-0.3395 Å2
2---3.3647 Å20 Å2
3---8.5786 Å2
Refine analyzeLuzzati coordinate error obs: 0.35 Å
Refinement stepCycle: 1 / Resolution: 2.3→47.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14408 0 96 358 14862
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0114783HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1619958HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d5123SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes2528HARMONIC5
X-RAY DIFFRACTIONt_it14783HARMONIC20
X-RAY DIFFRACTIONt_nbd5SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.09
X-RAY DIFFRACTIONt_other_torsion19.32
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1914SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact17389SEMIHARMONIC4
LS refinement shellResolution: 2.3→2.31 Å / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.3473 -5.01 %
Rwork0.2926 1840 -
all0.2953 1937 -
obs--88.69 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.98540.6748-0.16851.0311-0.11330.4935-0.09910.03420.5059-0.06050.14360.28290.0197-0.1731-0.0445-0.3162-0.0059-0.0407-0.26790.0077-0.221-61.106115.160114.1702
22.4871.10630.33461.25660.34240.549-0.05860.0269-0.7291-0.02260.1763-0.4466-0.03150.1901-0.1177-0.3298-0.00060.0223-0.3033-0.0221-0.1865-21.643423.010614.8793
30.5670.4628-0.08022.5328-0.74970.74010.11230.00650.14510.1380.01850.5529-0.1092-0.0634-0.1308-0.2062-0.01550.022-0.3183-0.0194-0.243-38.976839.1239-23.9195
40.61580.450.0522.33930.56520.51470.1059-0.0005-0.11890.1159-0.0077-0.50.09460.0123-0.0982-0.2035-0.0248-0.0204-0.31290.0162-0.2457-42.368-0.9216-23.8999
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }

+
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