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- PDB-6qap: Structure of the human aldehyde dehydrogenase 9A1 in C2 space group -

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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 / 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; 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, C-terminal / Aldehyde dehydrogenase, N-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

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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
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

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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.: 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


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


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


Mass: 18.015 Da / Num. of mol.: 358 / 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: 2.51 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

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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

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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: 2.3→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|* }

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