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- PDB-6vwf: Structure of ALDH9A1 complexed with NAD+ in space group C222 -

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Basic information

Entry
Database: PDB / ID: 6vwf
TitleStructure of ALDH9A1 complexed with NAD+ in space group C222
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, 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
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / 4-trimethylaminobutyraldehyde dehydrogenase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.64 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 19, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,0404
Polymers107,7132
Non-polymers1,3272
Water55831
1
A: 4-trimethylaminobutyraldehyde dehydrogenase
B: 4-trimethylaminobutyraldehyde dehydrogenase
hetero molecules

A: 4-trimethylaminobutyraldehyde dehydrogenase
B: 4-trimethylaminobutyraldehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)218,0808
Polymers215,4274
Non-polymers2,6544
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x+1/2,-y+1/2,z1
Buried area16330 Å2
ΔGint-93 kcal/mol
Surface area60690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)158.148, 163.466, 84.341
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number21
Space group name H-MC222
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 1 through 62 or (resid 63...
21(chain B and (resid 1 through 66 or (resid 67...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETPHEPHE(chain A and (resid 1 through 62 or (resid 63...AA1 - 621 - 62
12LYSLYSLYSLYS(chain A and (resid 1 through 62 or (resid 63...AA6363
13METMETPHEPHE(chain A and (resid 1 through 62 or (resid 63...AA1 - 4941 - 494
14METMETPHEPHE(chain A and (resid 1 through 62 or (resid 63...AA1 - 4941 - 494
15METMETPHEPHE(chain A and (resid 1 through 62 or (resid 63...AA1 - 4941 - 494
16METMETPHEPHE(chain A and (resid 1 through 62 or (resid 63...AA1 - 4941 - 494
21METMETSERSER(chain B and (resid 1 through 66 or (resid 67...BB1 - 661 - 66
22GLNGLNGLNGLN(chain B and (resid 1 through 66 or (resid 67...BB6767
23METMETPHEPHE(chain B and (resid 1 through 66 or (resid 67...BB1 - 4941 - 494
24METMETPHEPHE(chain B and (resid 1 through 66 or (resid 67...BB1 - 4941 - 494
25METMETPHEPHE(chain B and (resid 1 through 66 or (resid 67...BB1 - 4941 - 494

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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: 53856.680 Da / Num. of mol.: 2
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 / Nicotinamide adenine dinucleotide


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


Mass: 18.015 Da / Num. of mol.: 31 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.53 Å3/Da / Density % sol: 51.39 %
Crystal growTemperature: 281 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1 M succinic acid pH 7.0, 15% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.00003 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Sep 25, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 2.64→47.13 Å / Num. obs: 32497 / % possible obs: 100 % / Redundancy: 7.1 % / CC1/2: 0.996 / Rmerge(I) obs: 0.151 / Rpim(I) all: 0.061 / Rrim(I) all: 0.163 / Net I/σ(I): 11.6 / Num. measured all: 229337 / Scaling rejects: 9
Reflection shellResolution: 2.64→2.77 Å / Redundancy: 7 % / Rmerge(I) obs: 1.07 / Num. measured all: 30035 / Num. unique obs: 4262 / CC1/2: 0.803 / Rpim(I) all: 0.434 / Rrim(I) all: 1.156 / Net I/σ(I) obs: 1.7 / % possible all: 100

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Processing

Software
NameVersionClassification
Aimless0.7.2data scaling
PHENIX1.14refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1A4S

1a4s


Resolution: 2.64→47.13 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 27.43
RfactorNum. reflection% reflection
Rfree0.2729 1595 4.91 %
Rwork0.2179 --
obs0.2207 32467 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 121.92 Å2 / Biso mean: 50.772 Å2 / Biso min: 19.54 Å2
Refinement stepCycle: final / Resolution: 2.64→47.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6729 0 46 31 6806
Biso mean--58.57 30.93 -
Num. residues----900
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A4007X-RAY DIFFRACTION7.661TORSIONAL
12B4007X-RAY DIFFRACTION7.661TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.64-2.72520.33231590.2882741100
2.7252-2.82260.32481350.28042786100
2.8226-2.93560.32961200.26462785100
2.9356-3.06920.31371560.25312776100
3.0692-3.2310.3231500.26552774100
3.231-3.43340.32551470.22432775100
3.4334-3.69840.29841120.21952826100
3.6984-4.07040.27561510.19882807100
4.0704-4.65890.22371650.17692796100
4.6589-5.86790.22471430.19582849100
5.8679-47.130.23541570.2052295799
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)
11.3934-0.4627-0.33271.3147-0.35411.00290.24030.01370.3255-0.0945-0.1436-0.2154-0.1020.2322-0.1020.37720.06690.03680.3819-0.00880.3061-43.8974-21.1605-27.3585
22.0487-0.19650.09390.5903-0.03740.74460.0448-0.2154-0.2740.0230.0399-0.01440.15870.0644-0.08810.31640.0789-0.0150.3992-0.00340.2492-59.6722-38.8185-66.1894
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A')A1 - 494
2X-RAY DIFFRACTION2(chain 'B')B1 - 494

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