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- PDB-4a0m: CRYSTAL STRUCTURE OF BETAINE ALDEHYDE DEHYDROGENASE FROM SPINACH ... -

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Basic information

Entry
Database: PDB / ID: 4a0m
TitleCRYSTAL STRUCTURE OF BETAINE ALDEHYDE DEHYDROGENASE FROM SPINACH IN COMPLEX WITH NAD
ComponentsBETAINE ALDEHYDE DEHYDROGENASE, CHLOROPLASTIC
KeywordsOXIDOREDUCTASE / ALDEHYDE OXIDATION / NAD COMPLEX
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
: / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Aminoaldehyde dehydrogenase BADH
Similarity search - Component
Biological speciesSPINACIA OLERACEA (spinach)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsGonzalez-Segura, L. / Rudino-Pinera, E. / Diaz-Sanchez, A.G. / Munoz-Clares, R.A.
CitationJournal: Plant Physiol. / Year: 2012
Title: Amino Acid Residues Critical for the Specificity for Betaine Aldehyde of the Plant Aldh10 Isoenzyme Involved in the Synthesis of Glycine Betaine.
Authors: Diaz-Sanchez, A.G. / Gonzalez-Segura, L. / Mujica-Jimenez, C. / Rudino-Pinera, E. / Montiel, C. / Martinez-Castilla, L.P. / Munoz-Clares, R.A.
History
DepositionSep 9, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 11, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2012Group: Other
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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 / _struct_conn.ptnr2_label_seq_id / _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)220,53123
Polymers216,9204
Non-polymers3,61119
Water9,440524
1
C: BETAINE ALDEHYDE DEHYDROGENASE, CHLOROPLASTIC
D: BETAINE ALDEHYDE DEHYDROGENASE, CHLOROPLASTIC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,40413
Polymers108,4602
Non-polymers1,94411
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12500 Å2
ΔGint-64.2 kcal/mol
Surface area31390 Å2
MethodPISA
2
A: BETAINE ALDEHYDE DEHYDROGENASE, CHLOROPLASTIC
B: BETAINE ALDEHYDE DEHYDROGENASE, CHLOROPLASTIC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,12710
Polymers108,4602
Non-polymers1,6678
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11630 Å2
ΔGint-58.2 kcal/mol
Surface area31790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.406, 80.979, 85.540
Angle α, β, γ (deg.)79.06, 84.94, 77.99
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
BETAINE ALDEHYDE DEHYDROGENASE, CHLOROPLASTIC / BADH


Mass: 54229.914 Da / Num. of mol.: 4 / Fragment: RESIDUES 1-496
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SPINACIA OLERACEA (spinach) / Organ: LEAVES / Plasmid: PET28A-SPBADH-1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYS-RIL / References: UniProt: P17202, betaine-aldehyde dehydrogenase
#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: K
#3: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 524 / 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: 2.1 Å3/Da / Density % sol: 41.3 % / Description: NONE
Crystal growpH: 8.5
Details: CRYSTALS WERE GROWN IN 0.085 M TRIS HYDROCHLORIDE PH 8.5, 0.17 M SODIUM ACETATE TRIHYDRATE, 25.5% W/V POLYETHYLENE GLYCOL 4,000, 15% V/V GLYCEROL.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.9793
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 18, 2009 / Details: DOUBLE CRYSTAL CHANNEL CUT, SI(III) 1M LONG
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. obs: 76619 / % possible obs: 93.2 % / Observed criterion σ(I): 0 / Redundancy: 2.28 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 14.5
Reflection shellResolution: 2.3→2.43 Å / Redundancy: 2.22 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 2.56 / % possible all: 81.1

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3FG0

3fg0
PDB Unreleased entry


Resolution: 2.3→29.078 Å / SU ML: 0.4 / σ(F): 1.97 / Phase error: 30.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2467 3838 5 %
Rwork0.2131 --
obs0.2343 76619 96.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 51.43 Å2 / ksol: 0.372 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.8302 Å22.4863 Å2-1.5381 Å2
2---2.3988 Å2-0.0967 Å2
3---0.6802 Å2
Refinement stepCycle: LAST / Resolution: 2.3→29.078 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15212 0 226 524 15962
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01416005
X-RAY DIFFRACTIONf_angle_d1.44821836
X-RAY DIFFRACTIONf_dihedral_angle_d20.1665889
X-RAY DIFFRACTIONf_chiral_restr0.082417
X-RAY DIFFRACTIONf_plane_restr0.0212794
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.32910.3441280.32842173X-RAY DIFFRACTION80
2.3291-2.35970.35551280.33962621X-RAY DIFFRACTION93
2.3597-2.39210.38711350.34422774X-RAY DIFFRACTION96
2.3921-2.42620.3291300.33042654X-RAY DIFFRACTION97
2.4262-2.46240.35011260.32272726X-RAY DIFFRACTION97
2.4624-2.50090.34891500.31742685X-RAY DIFFRACTION97
2.5009-2.54180.35031500.29782676X-RAY DIFFRACTION97
2.5418-2.58560.33771330.30532736X-RAY DIFFRACTION97
2.5856-2.63260.34341480.30662680X-RAY DIFFRACTION97
2.6326-2.68320.34361180.30172733X-RAY DIFFRACTION96
2.6832-2.7380.3391500.29592708X-RAY DIFFRACTION98
2.738-2.79740.31111480.28422754X-RAY DIFFRACTION97
2.7974-2.86250.33491520.28662686X-RAY DIFFRACTION97
2.8625-2.9340.3571460.28152684X-RAY DIFFRACTION98
2.934-3.01320.3231530.27352739X-RAY DIFFRACTION97
3.0132-3.10180.35851340.26272718X-RAY DIFFRACTION98
3.1018-3.20180.29521400.25952736X-RAY DIFFRACTION97
3.2018-3.31610.26381270.24682721X-RAY DIFFRACTION98
3.3161-3.44870.25141280.22852728X-RAY DIFFRACTION98
3.4487-3.60530.23251610.22012704X-RAY DIFFRACTION98
3.6053-3.7950.22741470.21052761X-RAY DIFFRACTION98
3.795-4.03220.21161340.21222758X-RAY DIFFRACTION98
4.0322-4.34260.22921560.19962717X-RAY DIFFRACTION98
4.3426-4.77790.17741590.16652717X-RAY DIFFRACTION98
4.7779-5.46530.18561410.16982733X-RAY DIFFRACTION98
5.4653-6.87070.20741740.19262711X-RAY DIFFRACTION98
6.8707-29.08060.17191420.16472748X-RAY DIFFRACTION98

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