[English] 日本語
Yorodumi
- PDB-6vr6: Structure of ALDH9A1 complexed with NAD+ in space group P1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6vr6
TitleStructure of ALDH9A1 complexed with NAD+ in space group P1
Components4-trimethylaminobutyraldehyde dehydrogenase
KeywordsOXIDOREDUCTASE / ALDEHYDE DEHYDROGENASE / NAD
Function / homology
Function and homology information


formaldehyde dehydrogenase / 4-trimethylammoniobutyraldehyde dehydrogenase / 4-trimethylammoniobutyraldehyde dehydrogenase activity / formaldehyde dehydrogenase (NAD+) activity / Carnitine synthesis / carnitine biosynthetic process / aminobutyraldehyde dehydrogenase / aminobutyraldehyde dehydrogenase (NAD+) activity / aldehyde metabolic process / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (non-phosphorylating) activity ...formaldehyde dehydrogenase / 4-trimethylammoniobutyraldehyde dehydrogenase / 4-trimethylammoniobutyraldehyde dehydrogenase activity / formaldehyde dehydrogenase (NAD+) activity / Carnitine synthesis / carnitine biosynthetic process / aminobutyraldehyde dehydrogenase / aminobutyraldehyde dehydrogenase (NAD+) activity / 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, 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, C-terminal / Aldehyde dehydrogenase, N-terminal / Aldehyde/histidinol dehydrogenase
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / 4-trimethylaminobutyraldehyde dehydrogenase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsWyatt, J.W. / Tanner, J.J.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM093123 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM065546 United States
CitationJournal: Arch.Biochem.Biophys. / Year: 2020
Title: Inhibition, crystal structures, and in-solution oligomeric structure of aldehyde dehydrogenase 9A1.
Authors: Wyatt, J.W. / Korasick, D.A. / Qureshi, I.A. / Campbell, A.C. / Gates, K.S. / Tanner, J.J.
History
DepositionFeb 6, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 26, 2020Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Oct 11, 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: 4-trimethylaminobutyraldehyde dehydrogenase
B: 4-trimethylaminobutyraldehyde dehydrogenase
C: 4-trimethylaminobutyraldehyde dehydrogenase
D: 4-trimethylaminobutyraldehyde dehydrogenase
E: 4-trimethylaminobutyraldehyde dehydrogenase
F: 4-trimethylaminobutyraldehyde dehydrogenase
G: 4-trimethylaminobutyraldehyde dehydrogenase
H: 4-trimethylaminobutyraldehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)435,11116
Polymers429,8048
Non-polymers5,3078
Water00
1
A: 4-trimethylaminobutyraldehyde dehydrogenase
B: 4-trimethylaminobutyraldehyde dehydrogenase
hetero molecules

C: 4-trimethylaminobutyraldehyde dehydrogenase
D: 4-trimethylaminobutyraldehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)217,5568
Polymers214,9024
Non-polymers2,6544
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Buried area16840 Å2
ΔGint-120 kcal/mol
Surface area63010 Å2
MethodPISA
2
E: 4-trimethylaminobutyraldehyde dehydrogenase
F: 4-trimethylaminobutyraldehyde dehydrogenase
hetero molecules

G: 4-trimethylaminobutyraldehyde dehydrogenase
H: 4-trimethylaminobutyraldehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)217,5568
Polymers214,9024
Non-polymers2,6544
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Buried area16120 Å2
ΔGint-114 kcal/mol
Surface area62590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.785, 90.297, 145.236
Angle α, β, γ (deg.)89.370, 84.040, 73.870
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and ((resid 67 through 69 and (name N...
21(chain B and ((resid 67 through 69 and (name N...
31(chain C and ((resid 67 through 69 and (name N...
41(chain D and ((resid 67 through 69 and (name N...
51(chain E and ((resid 67 through 69 and (name N...
61(chain F and ((resid 67 through 69 and (name N...
71(chain G and ((resid 67 through 69 and (name N...
81(chain H and ((resid 67 through 69 and (name N...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and ((resid 67 through 69 and (name N...A0
211(chain B and ((resid 67 through 69 and (name N...B0
311(chain C and ((resid 67 through 69 and (name N...C0
411(chain D and ((resid 67 through 69 and (name N...D0
511(chain E and ((resid 67 through 69 and (name N...E0
611(chain F and ((resid 67 through 69 and (name N...F0
711(chain G and ((resid 67 through 69 and (name N...G0
811(chain H and ((resid 67 through 69 and (name N...H0

-
Components

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


Mass: 53725.484 Da / Num. of mol.: 8
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-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.41 Å3/Da / Density % sol: 49.03 %
Crystal growTemperature: 281 K / Method: vapor diffusion, sitting drop
Details: 0.1 M NaCl, 0.05 M Bis-Tris pH 6.5, 0.1 M ammonium acetate, 0.05 M HEPES pH 9.5, 25% (w/v) PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 13, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.5→79.09 Å / Num. obs: 106567 / % possible obs: 76.7 % / Redundancy: 1.7 % / CC1/2: 0.991 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.09 / Rrim(I) all: 0.127 / Net I/σ(I): 4.5 / Num. measured all: 177440
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.5 / Num. measured all: 9039 / Num. unique obs: 5667 / CC1/2: 0.61 / Rpim(I) all: 0.5 / Rrim(I) all: 0.708 / Net I/σ(I) obs: 1 / % possible all: 82.8

-
Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
PHENIX1.14refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1A4S

1a4s


Resolution: 2.5→79.087 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.93 / Phase error: 31.77
RfactorNum. reflection% reflection
Rfree0.269 2131 2 %
Rwork0.2131 --
obs0.2143 106512 76.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 95.77 Å2 / Biso mean: 38.7491 Å2 / Biso min: 9.13 Å2
Refinement stepCycle: final / Resolution: 2.5→79.087 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms29077 0 233 0 29310
Biso mean--39.47 --
Num. residues----3939
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A13092X-RAY DIFFRACTION7.986TORSIONAL
12B13092X-RAY DIFFRACTION7.986TORSIONAL
13C13092X-RAY DIFFRACTION7.986TORSIONAL
14D13092X-RAY DIFFRACTION7.986TORSIONAL
15E13092X-RAY DIFFRACTION7.986TORSIONAL
16F13092X-RAY DIFFRACTION7.986TORSIONAL
17G13092X-RAY DIFFRACTION7.986TORSIONAL
18H13092X-RAY DIFFRACTION7.986TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.5-2.55820.3521620.2996743083
2.5582-2.62210.36091430.2856731280
2.6221-2.6930.35671300.2796650572
2.693-2.77230.37861440.2713744482
2.7723-2.86180.33211480.2644755683
2.8618-2.96410.3191470.258742382
2.9641-3.08270.33911570.2547727880
3.0827-3.22310.31111600.2452709678
3.2231-3.3930.34711360.225690276
3.393-3.60560.26681290.2175658772
3.6056-3.88390.21091120.2092621269
3.8839-4.27480.24021350.1654652272
4.2748-4.89330.16151290.1448678674
4.8933-6.16460.25441590.1923673475
6.1646-79.0870.20441400.1782659473
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)
10.15590.22610.0690.32290.10920.19460.03040.02350.01040.0205-0.0121-0.0203-0.01940.0349-0.01240.58350.15840.0560.29910.08170.19483.868-39.095295.1197
20.5172-0.0359-0.03490.8926-0.25260.23390.08110.0647-0.1374-0.1295-0.1077-0.17320.12070.10020.03750.59510.18480.04040.31450.07650.26738.3205-73.358182.2792
30.15010.08080.03510.1801-0.05830.1202-0.01790.10390.0653-0.08720.03450.0882-0.0234-0.0508-0.02610.6180.14790.02770.33080.12740.2425-29.4779-57.191664.3524
40.21020.0560.00450.3146-0.13470.17640.0617-0.01330.01590.10310.01670.0829-0.0419-0.0695-0.07610.58210.12750.06360.26690.09370.205-34.907-61.1876100.5406
50.1610.03340.05740.1004-0.04450.157-0.01590.02470.03530.01620.0123-0.0497-0.02120.07090.05950.52640.11720.0470.24530.1230.25211.8760.6722.6171
60.0529-0.00450.02630.1341-0.01630.0427-0.0114-0.062-0.09640.03210.0086-0.05630.07630.03010.0080.58060.18710.06050.29420.13350.3042-2.3467-30.229722.0291
70.0973-0.07890.0310.2235-0.12230.1616-0.0469-0.0661-0.0140.10260.05430.039-0.0568-0.0353-0.0070.56270.19190.05780.28350.11010.2602-36.39014.35526.1221
80.5274-0.00240.18710.03690.03310.40640.02050.0641-0.14260.0013-0.01440.03860.0843-0.0312-0.01250.51490.13610.04250.22750.06260.2315-41.2354-22.23181.5186
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA3 - 494
2X-RAY DIFFRACTION2chain BB3 - 494
3X-RAY DIFFRACTION3chain CC3 - 494
4X-RAY DIFFRACTION4chain DD3 - 494
5X-RAY DIFFRACTION5chain EE3 - 494
6X-RAY DIFFRACTION6chain FF3 - 494
7X-RAY DIFFRACTION7chain GG3 - 494
8X-RAY DIFFRACTION8chain HH3 - 494

+
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