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- PDB-5a2d: CRYSTAL STRUCTURE OF BETAINE ALDEHYDE DEHYDROGENASE FROM SPINACH ... -

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Basic information

Entry
Database: PDB / ID: 5a2d
TitleCRYSTAL STRUCTURE OF BETAINE ALDEHYDE DEHYDROGENASE FROM SPINACH SHOWING A THIOHEMIACETAL WITH BETAINE ALDEHYDE
Components(BETAINE ALDEHYDE DEHYDROGENASE, ...) x 3
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


3-aminopropanal dehydrogenase (NAD+) activity / 4-trimethylammoniobutyraldehyde dehydrogenase / 4-trimethylammoniobutyraldehyde dehydrogenase activity / aminobutyraldehyde dehydrogenase / aminobutyraldehyde dehydrogenase (NAD+) activity / betaine-aldehyde dehydrogenase (NAD+) activity / betaine-aldehyde dehydrogenase / aldehyde metabolic process / glycine betaine biosynthetic process from choline / Oxidoreductases; Acting on the aldehyde or oxo group of donors; With NAD+ or NADP+ as acceptor ...3-aminopropanal dehydrogenase (NAD+) activity / 4-trimethylammoniobutyraldehyde dehydrogenase / 4-trimethylammoniobutyraldehyde dehydrogenase activity / aminobutyraldehyde dehydrogenase / aminobutyraldehyde dehydrogenase (NAD+) activity / betaine-aldehyde dehydrogenase (NAD+) activity / betaine-aldehyde dehydrogenase / aldehyde metabolic process / glycine betaine biosynthetic process from choline / 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, C-terminal / Aldehyde dehydrogenase, N-terminal / Aldehyde/histidinol dehydrogenase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
2-(2-ETHOXYETHOXY)ETHANOL / CHOLINE ION / 2-ETHOXYETHANOL / : / Aminoaldehyde dehydrogenase BADH
Similarity search - Component
Biological speciesSPINACIA OLERACEA (spinach)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 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
DepositionMay 17, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 3, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 13, 2016Group: Database references
Revision 1.2Jun 20, 2018Group: Advisory / Data collection / Derived calculations
Category: pdbx_struct_conn_angle / pdbx_validate_close_contact ...pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_conn / struct_conn_type
Item: _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id ..._pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_type.id
Revision 1.3Feb 20, 2019Group: Advisory / Data collection / Derived calculations
Category: pdbx_data_processing_status / pdbx_validate_close_contact / struct_conn
Item: _pdbx_data_processing_status.task_name
Revision 1.4Jan 10, 2024Group: 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 / struct_conn / struct_conn_type / 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 / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_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_conn_type.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)218,32215
Polymers217,3564
Non-polymers96511
Water12,088671
1
A: BETAINE ALDEHYDE DEHYDROGENASE, CHLOROPLASTIC
B: BETAINE ALDEHYDE DEHYDROGENASE, CHLOROPLASTIC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,2258
Polymers108,6542
Non-polymers5716
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9610 Å2
ΔGint-22.4 kcal/mol
Surface area32830 Å2
MethodPISA
2
C: BETAINE ALDEHYDE DEHYDROGENASE, CHLOROPLASTIC
D: BETAINE ALDEHYDE DEHYDROGENASE, CHLOROPLASTIC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,0977
Polymers108,7022
Non-polymers3955
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8950 Å2
ΔGint-26.4 kcal/mol
Surface area32670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.720, 82.286, 87.717
Angle α, β, γ (deg.)79.41, 84.75, 77.40
Int Tables number1
Space group name H-MP1

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Components

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BETAINE ALDEHYDE DEHYDROGENASE, ... , 3 types, 4 molecules ABCD

#1: Protein BETAINE ALDEHYDE DEHYDROGENASE, CHLOROPLASTIC / BADH


Mass: 54327.027 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: THIOHEMIACETAL BOND BETWEEN BETAINE ALDEHYDE AND C450 IN CHAIN A AND B
Source: (gene. exp.) SPINACIA OLERACEA (spinach) / Plasmid: PET28B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P17202, betaine-aldehyde dehydrogenase
#2: Protein BETAINE ALDEHYDE DEHYDROGENASE, CHLOROPLASTIC / BADH


Mass: 54343.027 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SPINACIA OLERACEA (spinach) / References: UniProt: P17202, betaine-aldehyde dehydrogenase
#3: Protein BETAINE ALDEHYDE DEHYDROGENASE, CHLOROPLASTIC / BADH


Mass: 54359.027 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SPINACIA OLERACEA (spinach) / References: UniProt: P17202, betaine-aldehyde dehydrogenase

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Non-polymers , 7 types, 682 molecules

#4: Chemical ChemComp-CHT / CHOLINE ION


Mass: 104.171 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H14NO
#5: Chemical ChemComp-ETX / 2-ETHOXYETHANOL


Mass: 90.121 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O2
#6: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#7: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#8: Chemical ChemComp-AE3 / 2-(2-ETHOXYETHOXY)ETHANOL


Mass: 134.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O3
#9: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 671 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.14 Å3/Da / Density % sol: 42.47 % / Description: NONE
Crystal growpH: 7
Details: POLYETHYLENE GLYCOL 3350 20% (V/V), 0.2 M MAGNESIUM FORMATE DIHYDRATE, pH 7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792
DetectorType: ADSC CCD / Detector: CCD / Date: Mar 12, 2014 / Details: MIRRORS
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.98→28.7 Å / Num. obs: 126693 / % possible obs: 97.4 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Biso Wilson estimate: 34.6 Å2 / Rmerge(I) obs: 0.08 / Rsym value: 0.08 / Net I/σ(I): 7.2
Reflection shellResolution: 1.98→2.09 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 2.2 / Rsym value: 0.62 / % possible all: 96.9

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Processing

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

4a0m


Resolution: 1.98→28.7 Å / SU ML: 0.25 / σ(F): 1.96 / Phase error: 27.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2375 6191 4.9 %
Rwork0.1939 --
obs0.1961 125897 96.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50 Å2 / ksol: 0.37 e/Å3
Displacement parametersBiso mean: 52.08 Å2
Refinement stepCycle: LAST / Resolution: 1.98→28.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15164 0 57 671 15892
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0115772
X-RAY DIFFRACTIONf_angle_d1.35721471
X-RAY DIFFRACTIONf_dihedral_angle_d16.0765751
X-RAY DIFFRACTIONf_chiral_restr0.0612415
X-RAY DIFFRACTIONf_plane_restr0.0082758
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.98-2.00250.35962250.30843904X-RAY DIFFRACTION96
2.0025-2.0260.34342130.29743912X-RAY DIFFRACTION96
2.026-2.05070.32141900.29124094X-RAY DIFFRACTION95
2.0507-2.07670.36561940.32043888X-RAY DIFFRACTION96
2.0767-2.1040.33021710.28583974X-RAY DIFFRACTION96
2.104-2.13280.29331960.27164023X-RAY DIFFRACTION97
2.1328-2.16330.30472300.25763951X-RAY DIFFRACTION96
2.1633-2.19560.25672120.25093935X-RAY DIFFRACTION96
2.1956-2.22990.29641960.2583963X-RAY DIFFRACTION96
2.2299-2.26640.31462000.27773940X-RAY DIFFRACTION96
2.2664-2.30550.28442000.24213983X-RAY DIFFRACTION96
2.3055-2.34740.29241990.23624036X-RAY DIFFRACTION97
2.3474-2.39250.29572000.24013977X-RAY DIFFRACTION97
2.3925-2.44130.28932270.22914009X-RAY DIFFRACTION97
2.4413-2.49440.28652000.23324032X-RAY DIFFRACTION97
2.4944-2.55240.25492060.22313958X-RAY DIFFRACTION97
2.5524-2.61610.27182000.21983999X-RAY DIFFRACTION98
2.6161-2.68680.24972010.21884082X-RAY DIFFRACTION98
2.6868-2.76580.2942260.22264001X-RAY DIFFRACTION98
2.7658-2.8550.25842110.21734041X-RAY DIFFRACTION98
2.855-2.9570.27091850.21354064X-RAY DIFFRACTION98
2.957-3.07520.25021920.20884043X-RAY DIFFRACTION98
3.0752-3.2150.25932260.19554051X-RAY DIFFRACTION99
3.215-3.38430.23012190.19134086X-RAY DIFFRACTION99
3.3843-3.59590.23342100.1744052X-RAY DIFFRACTION99
3.5959-3.8730.19142310.16274072X-RAY DIFFRACTION99
3.873-4.26160.19432330.14954063X-RAY DIFFRACTION99
4.2616-4.87560.15942080.12724096X-RAY DIFFRACTION99
4.8756-6.13290.21832120.15494053X-RAY DIFFRACTION99
6.1329-28.70290.20261780.17473424X-RAY DIFFRACTION83

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