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- PDB-6qao: Structure of human aldehyde dehydrogenase 9A1 in P21 space group -

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Basic information

Entry
Database: PDB / ID: 6qao
TitleStructure of human aldehyde dehydrogenase 9A1 in P21 space group
Components4-trimethylaminobutyraldehyde dehydrogenase
KeywordsOXIDOREDUCTASE / Aldehyde dehydrogenase
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: 2.89 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 / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)443,9099
Polymers443,8038
Non-polymers1061
Water46826
1
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)222,0085
Polymers221,9014
Non-polymers1061
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18030 Å2
ΔGint-109 kcal/mol
Surface area61070 Å2
MethodPISA
2
E: 4-trimethylaminobutyraldehyde dehydrogenase
F: 4-trimethylaminobutyraldehyde dehydrogenase
G: 4-trimethylaminobutyraldehyde dehydrogenase
H: 4-trimethylaminobutyraldehyde dehydrogenase


Theoretical massNumber of molelcules
Total (without water)221,9014
Polymers221,9014
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17320 Å2
ΔGint-109 kcal/mol
Surface area61340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.730, 167.450, 116.140
Angle α, β, γ (deg.)90.00, 90.94, 90.00
Int Tables number4
Space group name H-MP1211

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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.: 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-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 26 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.49 Å3/Da / Density % sol: 50.63 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / Details: 14% PEG 4K, 0.1 M sodium citrate pH 5.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98 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: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.89→49.71 Å / Num. obs: 96373 / % possible obs: 99.5 % / Redundancy: 7.12 % / CC1/2: 0.995 / Rmerge(I) obs: 0.2 / Rsym value: 0.191 / Net I/σ(I): 7.33
Reflection shellResolution: 2.89→3.35 Å

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Processing

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

6qak


Resolution: 2.89→49.71 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.933 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.321
RfactorNum. reflection% reflectionSelection details
Rfree0.213 4819 5 %RANDOM
Rwork0.179 ---
obs0.18 96373 99.5 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-6.2189 Å20 Å26.2439 Å2
2---12.221 Å20 Å2
3---6.0021 Å2
Refine analyzeLuzzati coordinate error obs: 0.35 Å
Refinement stepCycle: 1 / Resolution: 2.89→49.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms28735 0 7 26 28768
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0129321HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1939666HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d10142SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes5029HARMONIC5
X-RAY DIFFRACTIONt_it29321HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.93
X-RAY DIFFRACTIONt_other_torsion21.61
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion3815SEMIHARMONIC5
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_contact34524SEMIHARMONIC4
LS refinement shellResolution: 2.89→2.92 Å / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.3349 -5.03 %
Rwork0.2563 1831 -
all0.2601 1928 -
obs--81.14 %
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)
11.1809-0.3861-0.37450.74150.44021.5511-0.01290.14540.08890.0120.01630.0498-0.0337-0.1384-0.00340.26820.00060.08360.29180.15610.2982153.3996-21.717762.5402
21.83910.1161-0.15340.9826-0.16061.5283-0.0677-0.02620.1683-0.20070.0871-0.1197-0.02740.368-0.01940.135-0.07440.06940.1494-0.01150.02177.4419-26.37129.9252
31.67820.24140.72111.36720.3531.6808-0.0362-0.2458-0.3104-0.39070.10250.34550.0665-0.3863-0.0663-0.2155-0.0847-0.1564-0.25390.1504-0.2742148.1677-61.467131.3435
41.7699-0.36790.38461.0376-0.2641.07360.05740.2823-0.0593-0.0024-0.00630.0264-0.02170.0167-0.05120.26510.0157-0.05470.2145-0.04390.1723171.6698-63.7664.5715
52.08610.72480.82081.37030.27651.10090.2682-0.43350.02140.2576-0.3351-0.0385-0.0079-0.27270.0669-0.0255-0.0837-0.01940.1679-0.0104-0.0812124.6107-23.4919114.7207
62.6425-0.46950.87280.8733-0.59651.7230.1460.22690.31760.0755-0.14540.1142-0.23050.3012-0.0006-0.0331-0.08640.0340.0939-0.0630.09892.2938-20.045590.3839
71.41350.1229-0.09810.89410.00481.60850.1991-0.37630.05290.154-0.14250.05150.202-0.0089-0.05670.0118-0.11150.07120.1939-0.0164-0.001586.3425-57.3176116.5802
82.8616-0.6344-1.45720.94640.89972.0292-0.05070.1057-0.38850.149-0.14080.00080.2523-0.14330.1916-0.0242-0.07730.02610.07850.06240.1018118.9341-63.505892.405
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }
5X-RAY DIFFRACTION5{ E|* }
6X-RAY DIFFRACTION6{ F|* }
7X-RAY DIFFRACTION7{ G|* }
8X-RAY DIFFRACTION8{ H|* }

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