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- PDB-1o04: Cys302Ser mutant of human mitochondrial aldehyde dehydrogenase co... -

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Basic information

Entry
Database: PDB / ID: 1o04
TitleCys302Ser mutant of human mitochondrial aldehyde dehydrogenase complexed with NAD+ and Mg2+
ComponentsAldehyde dehydrogenase, mitochondrial precursor
KeywordsOXIDOREDUCTASE / ALDH / NAD / NADH / isomerization
Function / homology
Function and homology information


Metabolism of serotonin / regulation of dopamine biosynthetic process / regulation of serotonin biosynthetic process / phenylacetaldehyde dehydrogenase (NAD+) activity / nitroglycerin metabolic process / aldehyde catabolic process / alcohol metabolic process / ethanol catabolic process / aldehyde dehydrogenase [NAD(P)+] activity / Ethanol oxidation ...Metabolism of serotonin / regulation of dopamine biosynthetic process / regulation of serotonin biosynthetic process / phenylacetaldehyde dehydrogenase (NAD+) activity / nitroglycerin metabolic process / aldehyde catabolic process / alcohol metabolic process / ethanol catabolic process / aldehyde dehydrogenase [NAD(P)+] activity / Ethanol oxidation / aldehyde dehydrogenase (NAD+) / carboxylesterase activity / aldehyde dehydrogenase (NAD+) activity / Smooth Muscle Contraction / Mitochondrial protein degradation / NAD binding / carbohydrate metabolic process / electron transfer activity / mitochondrial matrix / mitochondrion / extracellular exosome
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
GUANIDINE / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Aldehyde dehydrogenase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.42 Å
AuthorsPerez-Miller, S.J. / Hurley, T.D.
CitationJournal: Biochemistry / Year: 2003
Title: Coenzyme isomerization is integral to catalysis in aldehyde dehydrogenase
Authors: Perez-Miller, S.J. / Hurley, T.D.
History
DepositionFeb 20, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aldehyde dehydrogenase, mitochondrial precursor
B: Aldehyde dehydrogenase, mitochondrial precursor
C: Aldehyde dehydrogenase, mitochondrial precursor
D: Aldehyde dehydrogenase, mitochondrial precursor
E: Aldehyde dehydrogenase, mitochondrial precursor
F: Aldehyde dehydrogenase, mitochondrial precursor
G: Aldehyde dehydrogenase, mitochondrial precursor
H: Aldehyde dehydrogenase, mitochondrial precursor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)444,60482
Polymers435,8698
Non-polymers8,73574
Water90,5255025
1
A: Aldehyde dehydrogenase, mitochondrial precursor
B: Aldehyde dehydrogenase, mitochondrial precursor
C: Aldehyde dehydrogenase, mitochondrial precursor
D: Aldehyde dehydrogenase, mitochondrial precursor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)222,30241
Polymers217,9344
Non-polymers4,36837
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area31590 Å2
ΔGint-141 kcal/mol
Surface area57080 Å2
MethodPISA
2
E: Aldehyde dehydrogenase, mitochondrial precursor
F: Aldehyde dehydrogenase, mitochondrial precursor
G: Aldehyde dehydrogenase, mitochondrial precursor
H: Aldehyde dehydrogenase, mitochondrial precursor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)222,30241
Polymers217,9344
Non-polymers4,36837
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area31230 Å2
ΔGint-140 kcal/mol
Surface area56950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)141.211, 152.487, 177.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 8 molecules ABCDEFGH

#1: Protein
Aldehyde dehydrogenase, mitochondrial precursor / ALDH class 2 / ALDHI / ALDH-E2


Mass: 54483.566 Da / Num. of mol.: 8
Fragment: Complete mature sequence (does not contain mitochondrial leader sequence).
Mutation: C302S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ALDH2 OR ALDM / Plasmid: PET7-7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P05091, aldehyde dehydrogenase (NAD+)

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Non-polymers , 6 types, 5099 molecules

#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#5: Chemical
ChemComp-GAI / GUANIDINE


Mass: 59.070 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: CH5N3
#6: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 32 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5025 / 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: 1.88 Å3/Da / Density % sol: 34.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.4
Details: ACES, PEG 6000, Guanidine HCl, MgCl2, DTT., pH 6.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, sitting drop / PH range low: 6.6 / PH range high: 6.2
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
1100 mMsodium-ACES1reservoirpH6.2-6.6
215-19 %(w/v)PEG6000MW1reservoir
3100 mMguanidine-HCl1reservoir
410 mM1reservoirMgCl2
58 mMdithiothreitol1reservoir
68 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Dec 1, 2001
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.42→50 Å / Num. all: 713549 / Num. obs: 683580 / % possible obs: 95.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Biso Wilson estimate: 10.9 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 20.7
Reflection shellResolution: 1.42→1.47 Å / Rmerge(I) obs: 0.439 / Mean I/σ(I) obs: 1.8 / Num. unique all: 52512 / % possible all: 74
Reflection
*PLUS
Num. measured all: 3220059 / Rmerge(I) obs: 0.06
Reflection shell
*PLUS
% possible obs: 74 %

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1CW3

1cw3


Resolution: 1.42→50 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.963 / SU B: 0.942 / SU ML: 0.036 / Isotropic thermal model: Restrained / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.057 / ESU R Free: 0.059 / Stereochemistry target values: Engh & Huber / Details: MLKF refinement
RfactorNum. reflection% reflectionSelection details
Rfree0.1712 34234 5 %RANDOM
Rwork0.1453 ---
all0.1466 676347 --
obs0.1466 648549 95.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 12.891 Å2
Baniso -1Baniso -2Baniso -3
1-0.4 Å20 Å20 Å2
2---0.09 Å20 Å2
3----0.31 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.18 Å0.16 Å
Luzzati d res low-5 Å
Refinement stepCycle: LAST / Resolution: 1.42→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms30568 0 568 5025 36161
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02131798
X-RAY DIFFRACTIONr_angle_refined_deg1.5011.96243158
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.10853992
X-RAY DIFFRACTIONr_chiral_restr0.0970.24720
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0224360
X-RAY DIFFRACTIONr_nbd_refined0.1980.216569
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1280.23825
X-RAY DIFFRACTIONr_metal_ion_refined0.0520.232
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2270.291
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1840.2119
X-RAY DIFFRACTIONr_mcbond_it1.314319782
X-RAY DIFFRACTIONr_mcangle_it2.092531728
X-RAY DIFFRACTIONr_scbond_it3.237612016
X-RAY DIFFRACTIONr_scangle_it5.129811430
LS refinement shellResolution: 1.42→1.457 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.288 1907
Rwork0.255 36402
obs-38309
Refinement
*PLUS
Lowest resolution: 50 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.171 / Rfactor Rwork: 0.145
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.014
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.5

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