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- PDB-4v3f: Crystal structure of betaine aldehyde dehydrogenase from spinach ... -

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Basic information

Entry
Database: PDB / ID: 4v3f
TitleCrystal structure of betaine aldehyde dehydrogenase from spinach showing a thiohemiacetal with betaine aldehyde
Components(BETAINE ALDEHYDE DEHYDROGENASE, ...) x 2
KeywordsOXIDOREDUCTASE / BETAINE ALDEHYDE DEHYDROGENASE / ALDH10.
Function / homology
Function and homology information


4-trimethylammoniobutyraldehyde dehydrogenase / 4-trimethylammoniobutyraldehyde dehydrogenase activity / aminobutyraldehyde dehydrogenase activity / aminobutyraldehyde dehydrogenase / betaine-aldehyde dehydrogenase / betaine-aldehyde dehydrogenase activity / glycine betaine biosynthetic process from choline / cellular aldehyde metabolic process / Oxidoreductases; Acting on the aldehyde or oxo group of donors; With NAD+ or NADP+ as acceptor / cellular detoxification of aldehyde ...4-trimethylammoniobutyraldehyde dehydrogenase / 4-trimethylammoniobutyraldehyde dehydrogenase activity / aminobutyraldehyde dehydrogenase activity / aminobutyraldehyde dehydrogenase / betaine-aldehyde dehydrogenase / betaine-aldehyde dehydrogenase activity / glycine betaine biosynthetic process from choline / cellular aldehyde metabolic process / Oxidoreductases; Acting on the aldehyde or oxo group of donors; With NAD+ or NADP+ as acceptor / cellular detoxification of aldehyde / potassium ion binding / protein homodimerization activity
Similarity search - Function
Aldehyde dehydrogenase NAD(P)-dependent / 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 NAD(P)-dependent / 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
CHOLINE ION / 2-ETHOXYETHANOL / IODIDE ION / Aminoaldehyde dehydrogenase BADH
Similarity search - Component
Biological speciesSPINACIA OLERACEA (spinach)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.998 Å
AuthorsZarate-Romero, A. / Munoz-Clares, R.A.
CitationJournal: Biochem.J. / Year: 2016
Title: Reversible, Partial Inactivation of Plant Betaine Aldehyde Dehydrogenase by Betaine Aldehyde: Mechanism and Possible Physiological Implications.
Authors: Zarate-Romero, A. / Murillo-Melo, D.S. / Mujica-Jimenez, C. / Montiel, C. / Munoz-Clares, R.A.
History
DepositionOct 18, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 20, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 3, 2016Group: Database references
Revision 1.2Apr 13, 2016Group: Database references
Revision 1.3Aug 9, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.type
Revision 1.4Oct 30, 2019Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Other
Category: pdbx_database_status / pdbx_validate_close_contact / struct_conn
Item: _pdbx_database_status.status_code_sf
Revision 1.5Jan 10, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BETAINE ALDEHYDE DEHYDROGENASE, CHLOROPLASTIC
B: BETAINE ALDEHYDE DEHYDROGENASE, CHLOROPLASTIC
C: BETAINE ALDEHYDE DEHYDROGENASE, CHLOROPLASTIC
D: BETAINE ALDEHYDE DEHYDROGENASE, CHLOROPLASTIC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)220,46128
Polymers217,3884
Non-polymers3,07324
Water11,908661
1
A: BETAINE ALDEHYDE DEHYDROGENASE, CHLOROPLASTIC
B: BETAINE ALDEHYDE DEHYDROGENASE, CHLOROPLASTIC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,32315
Polymers108,6862
Non-polymers1,63713
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10630 Å2
ΔGint-28.8 kcal/mol
Surface area32310 Å2
MethodPISA
2
C: BETAINE ALDEHYDE DEHYDROGENASE, CHLOROPLASTIC
D: BETAINE ALDEHYDE DEHYDROGENASE, CHLOROPLASTIC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,13813
Polymers108,7022
Non-polymers1,43611
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11050 Å2
ΔGint-26.4 kcal/mol
Surface area32410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.440, 82.256, 88.516
Angle α, β, γ (deg.)79.44, 84.89, 77.32
Int Tables number1
Space group name H-MP1

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Components

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BETAINE ALDEHYDE DEHYDROGENASE, ... , 2 types, 4 molecules ABDC

#1: Protein BETAINE ALDEHYDE DEHYDROGENASE, CHLOROPLASTIC / BADH / BETAINE ALDEHYDE DEHYDROGENASE


Mass: 54343.027 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SPINACIA OLERACEA (spinach) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P17202, betaine-aldehyde dehydrogenase
#2: Protein BETAINE ALDEHYDE DEHYDROGENASE, CHLOROPLASTIC / BADH / BETAINE ALDEHYDE DEHYDROGENASE


Mass: 54359.027 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SPINACIA OLERACEA (spinach) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P17202, betaine-aldehyde dehydrogenase

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Non-polymers , 6 types, 685 molecules

#3: Chemical
ChemComp-IOD / IODIDE ION / Iodide


Mass: 126.904 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: I
#4: Chemical ChemComp-CHT / CHOLINE ION / Choline


Mass: 104.171 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C5H14NO
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-ETX / 2-ETHOXYETHANOL / 2-Ethoxyethanol


Mass: 90.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 661 / 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: 2.15 Å3/Da / Density % sol: 42.7 % / Description: NONE
Crystal growpH: 6.2
Details: AMMONIUM IODIDE 0.2 M, POLY ETHYLENE GLYCOL 3350 20% (W/V), PH 6.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9791
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Mar 13, 2014
RadiationMonochromator: SI (1 1 1) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2→29 Å / Num. obs: 122131 / % possible obs: 96.1 % / Observed criterion σ(I): 2 / Redundancy: 2.4 % / Rmerge(I) obs: 0.048 / Rsym value: 0.048 / Net I/σ(I): 9.1
Reflection shellResolution: 2→2.11 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.268 / Mean I/σ(I) obs: 2.3 / % possible all: 88

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.8.4_1496)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4A0M

4a0m


Resolution: 1.998→28.968 Å / SU ML: 0.23 / σ(F): 1.96 / Phase error: 23.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2114 5965 4.9 %
Rwork0.1961 --
obs0.1968 122084 96.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.998→28.968 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15246 0 90 661 15997
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00915951
X-RAY DIFFRACTIONf_angle_d1.25921724
X-RAY DIFFRACTIONf_dihedral_angle_d14.7255824
X-RAY DIFFRACTIONf_chiral_restr0.0542434
X-RAY DIFFRACTIONf_plane_restr0.0082795
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9981-2.02080.28441580.28223030X-RAY DIFFRACTION75
2.0208-2.04460.30831620.28853669X-RAY DIFFRACTION90
2.0446-2.06950.31981960.27583644X-RAY DIFFRACTION91
2.0695-2.09570.27442040.27463736X-RAY DIFFRACTION93
2.0957-2.12320.29791830.26293813X-RAY DIFFRACTION94
2.1232-2.15230.26151890.24613848X-RAY DIFFRACTION95
2.1523-2.18310.24312050.23973817X-RAY DIFFRACTION95
2.1831-2.21560.26232100.24223881X-RAY DIFFRACTION96
2.2156-2.25020.26562010.23643886X-RAY DIFFRACTION97
2.2502-2.28710.29182340.23543881X-RAY DIFFRACTION97
2.2871-2.32650.24322180.23153889X-RAY DIFFRACTION97
2.3265-2.36880.24622000.23483869X-RAY DIFFRACTION97
2.3688-2.41440.26811970.23923944X-RAY DIFFRACTION97
2.4144-2.46360.27561920.22893908X-RAY DIFFRACTION97
2.4636-2.51720.24431740.22633954X-RAY DIFFRACTION97
2.5172-2.57570.24952010.2183979X-RAY DIFFRACTION97
2.5757-2.64010.26481980.22013915X-RAY DIFFRACTION98
2.6401-2.71140.23911890.21833923X-RAY DIFFRACTION98
2.7114-2.79110.20922050.21623974X-RAY DIFFRACTION98
2.7911-2.88110.26792130.22283948X-RAY DIFFRACTION98
2.8811-2.9840.24751940.21753946X-RAY DIFFRACTION98
2.984-3.10330.22491940.21413963X-RAY DIFFRACTION98
3.1033-3.24440.25591940.20843984X-RAY DIFFRACTION98
3.2444-3.41520.22792250.20023966X-RAY DIFFRACTION98
3.4152-3.62880.18282010.17493969X-RAY DIFFRACTION99
3.6288-3.90840.18372130.16093974X-RAY DIFFRACTION99
3.9084-4.30050.15092160.15173963X-RAY DIFFRACTION99
4.3005-4.92020.13352080.13453990X-RAY DIFFRACTION99
4.9202-6.1890.17211930.16213988X-RAY DIFFRACTION99
6.189-28.97120.15151980.16043868X-RAY DIFFRACTION96

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