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- PDB-4zuk: Structure ALDH7A1 complexed with NAD+ -

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Basic information

Entry
Database: PDB / ID: 4zuk
TitleStructure ALDH7A1 complexed with NAD+
ComponentsAlpha-aminoadipic semialdehyde dehydrogenase
KeywordsOXIDOREDUCTASE / ALDEHYDE DEHYDROGENASE / NAD / LYSINE CATABOLISM
Function / homology
Function and homology information


L-aminoadipate-semialdehyde dehydrogenase / L-aminoadipate-semialdehyde dehydrogenase activity / Choline catabolism / choline catabolic process / betaine-aldehyde dehydrogenase / betaine-aldehyde dehydrogenase activity / glycine betaine biosynthetic process from choline / Lysine catabolism / cellular aldehyde metabolic process / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (non-phosphorylating) activity ...L-aminoadipate-semialdehyde dehydrogenase / L-aminoadipate-semialdehyde dehydrogenase activity / Choline catabolism / choline catabolic process / betaine-aldehyde dehydrogenase / betaine-aldehyde dehydrogenase activity / glycine betaine biosynthetic process from choline / Lysine catabolism / cellular aldehyde metabolic process / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (non-phosphorylating) activity / aldehyde dehydrogenase (NAD+) / aldehyde dehydrogenase (NAD+) activity / sensory perception of sound / mitochondrial matrix / mitochondrion / extracellular exosome / identical protein binding / nucleus / cytosol
Similarity search - Function
Aldehyde dehydrogenase family 7 member A1-like / 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 domain / Aldehyde dehydrogenase family / Aldehyde dehydrogenase, N-terminal ...Aldehyde dehydrogenase family 7 member A1-like / 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 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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Alpha-aminoadipic semialdehyde dehydrogenase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.001 Å
AuthorsLuo, M. / Tanner, J.J.
CitationJournal: Biochemistry / Year: 2015
Title: Structural Basis of Substrate Recognition by Aldehyde Dehydrogenase 7A1.
Authors: Luo, M. / Tanner, J.J.
History
DepositionMay 16, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 16, 2015Group: Database references
Revision 1.2Sep 27, 2023Group: 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 / citation / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alpha-aminoadipic semialdehyde dehydrogenase
B: Alpha-aminoadipic semialdehyde dehydrogenase
C: Alpha-aminoadipic semialdehyde dehydrogenase
D: Alpha-aminoadipic semialdehyde dehydrogenase
E: Alpha-aminoadipic semialdehyde dehydrogenase
F: Alpha-aminoadipic semialdehyde dehydrogenase
G: Alpha-aminoadipic semialdehyde dehydrogenase
H: Alpha-aminoadipic semialdehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)451,82424
Polymers444,9638
Non-polymers6,86116
Water24,2301345
1
A: Alpha-aminoadipic semialdehyde dehydrogenase
B: Alpha-aminoadipic semialdehyde dehydrogenase
C: Alpha-aminoadipic semialdehyde dehydrogenase
D: Alpha-aminoadipic semialdehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)225,91212
Polymers222,4814
Non-polymers3,4318
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21470 Å2
ΔGint-101 kcal/mol
Surface area60310 Å2
MethodPISA
2
E: Alpha-aminoadipic semialdehyde dehydrogenase
F: Alpha-aminoadipic semialdehyde dehydrogenase
G: Alpha-aminoadipic semialdehyde dehydrogenase
H: Alpha-aminoadipic semialdehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)225,91212
Polymers222,4814
Non-polymers3,4318
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20620 Å2
ΔGint-93 kcal/mol
Surface area60350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)155.666, 161.579, 158.932
Angle α, β, γ (deg.)90.000, 94.760, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Alpha-aminoadipic semialdehyde dehydrogenase / Alpha-AASA dehydrogenase / Aldehyde dehydrogenase family 7 member A1 / Antiquitin-1 / Betaine ...Alpha-AASA dehydrogenase / Aldehyde dehydrogenase family 7 member A1 / Antiquitin-1 / Betaine aldehyde dehydrogenase / Delta1-piperideine-6-carboxylate dehydrogenase / P6c dehydrogenase


Mass: 55620.367 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ALDH7A1, ATQ1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P49419, L-aminoadipate-semialdehyde dehydrogenase, aldehyde dehydrogenase (NAD+), betaine-aldehyde dehydrogenase
#2: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1345 / 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: 2.24 Å3/Da / Density % sol: 45.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Protein stock solution contained 3 mg/mL ALDH7A1 and 5 mM NAD+. The reservoir contained 0.2 M ammonium sulfate and 20% PEG 3350, 0.1 mM Bis-Tris pH 6.5.
PH range: 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Sep 24, 2014 / Details: Taurus-1 detector
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→62.89 Å / Num. obs: 261450 / % possible obs: 99.5 % / Redundancy: 3.8 % / Biso Wilson estimate: 24.87 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.106 / Rpim(I) all: 0.063 / Net I/σ(I): 12.7 / Num. measured all: 995590
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2-2.033.71.051.346379124720.6320.62696.1
10.96-62.893.60.02342593616430.9990.01598.6

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Processing

Software
NameVersionClassification
Aimless0.3.6data scaling
PHENIX1.9_1692refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2J6L

2j6l


Resolution: 2.001→62.89 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 23.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2183 12912 4.94 %
Rwork0.1706 248375 -
obs0.1729 261287 99.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 118.85 Å2 / Biso mean: 30.0948 Å2 / Biso min: 12.02 Å2
Refinement stepCycle: final / Resolution: 2.001→62.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms30434 0 304 1345 32083
Biso mean--42.1 29.75 -
Num. residues----4062
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00731383
X-RAY DIFFRACTIONf_angle_d1.02142653
X-RAY DIFFRACTIONf_chiral_restr0.0384802
X-RAY DIFFRACTIONf_plane_restr0.0045489
X-RAY DIFFRACTIONf_dihedral_angle_d16.19511329
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0007-2.02350.3523960.28827896829295
2.0235-2.04730.31214400.24378236867699
2.0473-2.07220.30494110.24238243865499
2.0722-2.09850.27934170.22238250866799
2.0985-2.12610.27524150.22298273868899
2.1261-2.15520.26784370.21988223866099
2.1552-2.1860.2964190.2218231865099
2.186-2.21860.28534100.21678251866199
2.2186-2.25330.27484590.20668246870599
2.2533-2.29020.28044160.2058341875799
2.2902-2.32970.25984330.19238217865099
2.3297-2.37210.24874570.19258235869299
2.3721-2.41770.26364180.193282788696100
2.4177-2.46710.25794110.189782948705100
2.4671-2.52070.23744680.184382958763100
2.5207-2.57940.23694150.175182818696100
2.5794-2.64390.24874690.174982448713100
2.6439-2.71540.2394670.181582638730100
2.7154-2.79530.25634830.18482998782100
2.7953-2.88550.22644230.179983378760100
2.8855-2.98860.22673940.177283068700100
2.9886-3.10830.24043910.182683898780100
3.1083-3.24970.24033970.180183318728100
3.2497-3.4210.19654280.168183218749100
3.421-3.63540.1924790.15382968775100
3.6354-3.9160.19643830.146383668749100
3.916-4.310.16444680.133483018769100
4.31-4.93350.14464160.115383458761100
4.9335-6.21480.16964500.142183758825100
6.2148-62.92190.16044420.13838412885499
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)
10.42290.23850.07270.58350.23640.79440.0189-0.07040.049-0.0090.0777-0.1664-0.05580.1614-0.09410.16540.0120.00320.1606-0.07390.236956.889658.606934.1937
20.7775-0.31430.27160.7264-0.00430.57430.0012-0.07390.03830.07270.00050.1234-0.0171-0.0662-0.00470.1671-0.03170.0310.1871-0.06080.198322.280858.193943.3009
31.2128-0.3301-0.11690.60180.07180.43840.02020.1698-0.2889-0.0787-0.04130.06570.0924-0.08650.01960.1808-0.0106-0.01160.1521-0.04960.243745.557518.732323.6837
40.8990.1365-0.09740.6211-0.08890.47630.0416-0.2725-0.13920.1698-0.025-0.07980.0680.0582-0.01780.2089-0.0167-0.03080.22290.00440.175435.952220.355558.1062
50.82110.5333-0.10260.6198-0.16630.3574-0.06670.0966-0.0595-0.06560.05530.02910.021-0.06210.01350.1864-0.01720.01140.2527-0.11260.21223.670598.352433.1934
60.3089-0.1596-0.16450.4716-0.07330.4249-0.03490.0166-0.0310.03980.0274-0.14220.02790.00220.0050.2004-0.0411-0.00810.2264-0.09720.26158.269898.996143.4665
70.4881-0.0387-0.050.4285-0.1780.5715-0.0109-0.08050.1679-0.0311-0.01890.0404-0.1162-0.12890.03140.19930.0329-0.02020.2063-0.090.221635.6068138.020320.5648
80.8369-0.0859-0.33210.46490.14540.57820.004-0.14770.08970.08730.02-0.0024-0.0784-0.0644-0.02070.21020.0120.00520.2286-0.07120.18143.9906137.407956.5462
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1Chain AA3 - 511
2X-RAY DIFFRACTION2Chain BB3 - 511
3X-RAY DIFFRACTION3Chain CC3 - 511
4X-RAY DIFFRACTION4Chain DD3 - 511
5X-RAY DIFFRACTION5Chain EE3 - 511
6X-RAY DIFFRACTION6Chain FF3 - 511
7X-RAY DIFFRACTION7Chain GG3 - 501
8X-RAY DIFFRACTION8Chain HH3 - 511

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