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- PDB-1a4z: ALDEHYDE DEHYDROGENASE FROM BOVINE MITOCHONDRIA COMPLEX WITH NAD ... -

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Basic information

Entry
Database: PDB / ID: 1a4z
TitleALDEHYDE DEHYDROGENASE FROM BOVINE MITOCHONDRIA COMPLEX WITH NAD (REDUCED) AND SAMARIUM (III)
ComponentsALDEHYDE DEHYDROGENASE
KeywordsOXIDOREDUCTASE / ALCOHOL METABOLISM / ALDEHYDE OXIDATION / ALPHA/BETA DOMAIN / DEHYDROGENASE
Function / homology
Function and homology information


Metabolism of serotonin / Ethanol oxidation / Smooth Muscle Contraction / : / regulation of dopamine biosynthetic process / regulation of serotonin biosynthetic process / phenylacetaldehyde dehydrogenase (NAD+) activity / aldehyde catabolic process / ethanol catabolic process / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (non-phosphorylating) activity ...Metabolism of serotonin / Ethanol oxidation / Smooth Muscle Contraction / : / regulation of dopamine biosynthetic process / regulation of serotonin biosynthetic process / phenylacetaldehyde dehydrogenase (NAD+) activity / aldehyde catabolic process / ethanol catabolic process / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (non-phosphorylating) activity / aldehyde dehydrogenase (NAD+) / carboxylesterase activity / aldehyde dehydrogenase (NAD+) activity / Mitochondrial protein degradation / NAD binding / mitochondrial matrix / mitochondrion
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 / SAMARIUM (III) ION / Aldehyde dehydrogenase, mitochondrial
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2.75 Å
AuthorsSteinmetz, C.G. / Hurley, T.D.
CitationJournal: Structure / Year: 1997
Title: Structure of mitochondrial aldehyde dehydrogenase: the genetic component of ethanol aversion.
Authors: Steinmetz, C.G. / Xie, P. / Weiner, H. / Hurley, T.D.
History
DepositionFeb 10, 1998Processing site: BNL
Revision 1.0Apr 8, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 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_struct_conn_angle / software / 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_asym_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.ptnr2_auth_asym_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_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _software.name / _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.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: ALDEHYDE DEHYDROGENASE
B: ALDEHYDE DEHYDROGENASE
C: ALDEHYDE DEHYDROGENASE
D: ALDEHYDE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)221,23412
Polymers217,9794
Non-polymers3,2558
Water1,58588
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26820 Å2
ΔGint-126 kcal/mol
Surface area56620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.600, 198.400, 91.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
33
44
/ NCS ensembles :
ID
1
2
3
4

NCS oper:
IDCodeMatrixVector
1given(0.255423, 0.966826, 0.002632), (0.966829, -0.255421, -0.001078), (-0.00037, 0.00282, -0.999996)-73.5257, 95.5341, 43.5809
2given(-0.504331, -0.633817, -0.586452), (-0.640469, -0.180961, 0.74636), (-0.57918, 0.752017, -0.314676)190.5928, 174.1226, -28.2339
3given(-0.747123, -0.336176, 0.573405), (-0.321781, -0.571912, -0.754568), (0.581605, -0.748266, 0.319114)143.36501, 235.7395, 71.4662

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Components

#1: Protein
ALDEHYDE DEHYDROGENASE


Mass: 54494.715 Da / Num. of mol.: 4 / Fragment: NAD BINDING DOMAIN / Source method: isolated from a natural source / Details: MITOCHONDRIAL ALDEHYDE DEHYDROGENASE / Source: (natural) Bos taurus (cattle) / Cellular location: MITOCHONDRIA / Organ: LIVER / Organelle: MITOCHONDRIA / References: UniProt: P20000, aldehyde dehydrogenase (NAD+)
#2: Chemical
ChemComp-SM / SAMARIUM (III) ION


Mass: 150.360 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Sm
#3: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


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


Mass: 18.015 Da / Num. of mol.: 88 / 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: 2.53 Å3/Da / Density % sol: 49 %
Crystal growpH: 6.5
Details: 14% PEG 8000, 100 MM MES, PH 6.5, 0.2 MM MGCL2, 1MM NAD; THEN SOAKED IN 1 MM SMCL3 OVERNIGHT.
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
1100 mMMES1drop
21 mMNAD+1drop
30.2 mM1dropMgCl2
414 %(w/v)PEG80001drop
58 mg/mlenzyme1drop

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Jun 1, 1996
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.74→48 Å / Num. obs: 50128 / % possible obs: 85 % / Observed criterion σ(I): 1 / Redundancy: 3.2 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 9.6
Reflection shellResolution: 2.74→2.83 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.18 / Mean I/σ(I) obs: 3.5 / % possible all: 59
Reflection
*PLUS
Num. measured all: 220626 / Rmerge(I) obs: 0.08
Reflection shell
*PLUS
% possible obs: 59 %

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Processing

Software
NameVersionClassification
PHASESphasing
X-PLOR3.1model building
XTALVIEWrefinement
X-PLOR3.1refinement
bioteXdata reduction
bioteXdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MIR / Resolution: 2.75→8 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0 / Isotropic thermal model: OVERALL ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 1
RfactorNum. reflection% reflectionSelection details
Rfree0.302 3345 7 %RANDOM
Rwork0.23 ---
obs0.23 42471 85 %-
Displacement parametersBiso mean: 10.7 Å2
Refine analyzeLuzzati coordinate error obs: 0.3 Å / Luzzati d res low obs: 8 Å
Refinement stepCycle: LAST / Resolution: 2.75→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15336 0 180 88 15604
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.48
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.1
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.22
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refine LS restraints NCS
Ens-IDDom-IDNCS model detailsRefine-IDRms dev position (Å)Weight position
11RESTRAINTSX-RAY DIFFRACTION0.06100
22X-RAY DIFFRACTION0.06100
33X-RAY DIFFRACTION0.06100
44X-RAY DIFFRACTION0.06100
LS refinement shellResolution: 2.75→2.87 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.333 329 4.8 %
Rwork0.23 3987 -
obs--62.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL
X-RAY DIFFRACTION3PARAM20.NADTOPH19.NAD
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.23 / Rfactor Rwork: 0.23
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.1
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.22
LS refinement shell
*PLUS
Rfactor Rwork: 0.23

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