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- PDB-3iwk: Crystal structure of aminoaldehyde dehydrogenase 1 from Pisum sat... -

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Basic information

Entry
Database: PDB / ID: 3iwk
TitleCrystal structure of aminoaldehyde dehydrogenase 1 from Pisum sativum (PsAMADH1)
ComponentsAminoaldehyde dehydrogenase
KeywordsOXIDOREDUCTASE / Rossmann fold / dimer / aminoaldehyde dehydrogenase / betaine aldehyde dehydrogenase / NAD
Function / homology
Function and homology information


gamma-guanidinobutyraldehyde dehydrogenase / gamma-guanidinobutyraldehyde dehydrogenase (NAD+) activity / 3-aminopropanal dehydrogenase (NAD+) activity / aminobutyraldehyde dehydrogenase / aminobutyraldehyde dehydrogenase (NAD+) activity / glycine betaine biosynthetic process from choline / Oxidoreductases; Acting on the aldehyde or oxo group of donors; With NAD+ or NADP+ as acceptor / sodium ion binding / cellular detoxification of aldehyde / peroxisome ...gamma-guanidinobutyraldehyde dehydrogenase / gamma-guanidinobutyraldehyde dehydrogenase (NAD+) activity / 3-aminopropanal dehydrogenase (NAD+) activity / aminobutyraldehyde dehydrogenase / aminobutyraldehyde dehydrogenase (NAD+) activity / glycine betaine biosynthetic process from choline / Oxidoreductases; Acting on the aldehyde or oxo group of donors; With NAD+ or NADP+ as acceptor / sodium ion binding / cellular detoxification of aldehyde / peroxisome / nucleotide binding / protein homodimerization activity
Similarity search - Function
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; 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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Aminoaldehyde dehydrogenase 1, peroxisomal
Similarity search - Component
Biological speciesPisum sativum (garden pea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å
AuthorsKopecny, D. / Morera, S. / Briozzo, P.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Structural and functional characterization of plant aminoaldehyde dehydrogenase from Pisum sativum with a broad specificity for natural and synthetic aminoaldehydes.
Authors: Tylichova, M. / Kopecny, D. / Morera, S. / Briozzo, P. / Lenobel, R. / Snegaroff, J. / Sebela, M.
History
DepositionSep 2, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 19, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 4, 2013Group: Database references
Revision 1.3Nov 1, 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 / database_2 / 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_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.pdbx_dist_value / _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_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: Aminoaldehyde dehydrogenase
B: Aminoaldehyde dehydrogenase
C: Aminoaldehyde dehydrogenase
D: Aminoaldehyde dehydrogenase
E: Aminoaldehyde dehydrogenase
F: Aminoaldehyde dehydrogenase
G: Aminoaldehyde dehydrogenase
H: Aminoaldehyde dehydrogenase
I: Aminoaldehyde dehydrogenase
J: Aminoaldehyde dehydrogenase
K: Aminoaldehyde dehydrogenase
L: Aminoaldehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)668,53056
Polymers658,42512
Non-polymers10,10544
Water35,9761997
1
A: Aminoaldehyde dehydrogenase
B: Aminoaldehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,2958
Polymers109,7372
Non-polymers1,5576
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7900 Å2
ΔGint-49 kcal/mol
Surface area35110 Å2
MethodPISA
2
C: Aminoaldehyde dehydrogenase
D: Aminoaldehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,3218
Polymers109,7372
Non-polymers1,5836
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7930 Å2
ΔGint-53 kcal/mol
Surface area35310 Å2
MethodPISA
3
E: Aminoaldehyde dehydrogenase
F: Aminoaldehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,2027
Polymers109,7372
Non-polymers1,4655
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7830 Å2
ΔGint-52 kcal/mol
Surface area34990 Å2
MethodPISA
4
G: Aminoaldehyde dehydrogenase
H: Aminoaldehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,47910
Polymers109,7372
Non-polymers1,7418
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7750 Å2
ΔGint-49 kcal/mol
Surface area35260 Å2
MethodPISA
5
I: Aminoaldehyde dehydrogenase
J: Aminoaldehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,3879
Polymers109,7372
Non-polymers1,6497
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7810 Å2
ΔGint-49 kcal/mol
Surface area35380 Å2
MethodPISA
6
K: Aminoaldehyde dehydrogenase
L: Aminoaldehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,84714
Polymers109,7372
Non-polymers2,11012
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7720 Å2
ΔGint-51 kcal/mol
Surface area35000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.410, 216.870, 205.760
Angle α, β, γ (deg.)90.000, 98.020, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 12 molecules ABCDEFGHIJKL

#1: Protein
Aminoaldehyde dehydrogenase


Mass: 54868.746 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pisum sativum (garden pea) / Gene: amadh1 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q8VWZ1, aminobutyraldehyde dehydrogenase

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Non-polymers , 5 types, 2041 molecules

#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1997 / 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: 2.9 Å3/Da / Density % sol: 57.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M HEPES pH 7.5, 13% PEG 6000, 5% 2-methyl-2,4-pentanediol, 5mM NAD, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 29, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 291593 / Num. obs: 290858 / % possible obs: 99.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Biso Wilson estimate: 40.72 Å2 / Rmerge(I) obs: 0.103 / Net I/σ(I): 14.06
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.4-2.530.6223.72466134231899.5
2.53-2.680.4335.12393553925899.6
2.68-2.870.372471803872799.7
2.87-3.10.193102339493509299.8
3.1-3.390.12914.12194453172599.8
3.39-3.790.08619.92096552943399.9
3.79-4.380.06824.819085826086100
4.38-5.370.05628.515877022008100
5.37-7.590.05328.712703416895100
7.590.03634.468875931699.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
REFMAC5.5.0072refinement
PDB_EXTRACT3.005data extraction
DNAdata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1CW3

1cw3


Resolution: 2.4→47.84 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.916 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 8.016 / SU ML: 0.185 / Cross valid method: THROUGHOUT / ESU R: 0.373 / ESU R Free: 0.249 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2436 14543 5 %RANDOM
Rwork0.19979 ---
obs0.20198 276314 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 86.72 Å2 / Biso mean: 34.693 Å2 / Biso min: 14.36 Å2
Baniso -1Baniso -2Baniso -3
1-1.72 Å20 Å20.12 Å2
2--0.82 Å20 Å2
3----2.5 Å2
Refinement stepCycle: LAST / Resolution: 2.4→47.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms45663 0 645 1997 48305
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.02247361
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1141.98664364
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.24555958
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.33424.5421845
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.913158083
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.98915243
X-RAY DIFFRACTIONr_chiral_restr0.080.27326
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02134993
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3581.529631
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.698247790
X-RAY DIFFRACTIONr_scbond_it0.972317730
X-RAY DIFFRACTIONr_scangle_it1.7424.516565
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 1066 -
Rwork0.263 20270 -
all-21336 -
obs--100 %

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