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- PDB-1bxs: SHEEP LIVER CLASS 1 ALDEHYDE DEHYDROGENASE WITH NAD BOUND -

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Basic information

Entry
Database: PDB / ID: 1bxs
TitleSHEEP LIVER CLASS 1 ALDEHYDE DEHYDROGENASE WITH NAD BOUND
ComponentsALDEHYDE DEHYDROGENASE
KeywordsOXIDOREDUCTASE / ALDEHYDE DEHYDROGENASE / RETINAL / CLASS 1 / TETRAMER / NAD / CYTOSOLIC
Function / homology
Function and homology information


fructosamine catabolic process / 3-deoxyglucosone dehydrogenase activity / benzaldehyde dehydrogenase (NAD+) / benzaldehyde dehydrogenase (NAD+) activity / maintenance of lens transparency / retinal dehydrogenase / gamma-aminobutyric acid biosynthetic process / aminobutyraldehyde dehydrogenase / aminobutyraldehyde dehydrogenase (NAD+) activity / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (non-phosphorylating) activity ...fructosamine catabolic process / 3-deoxyglucosone dehydrogenase activity / benzaldehyde dehydrogenase (NAD+) / benzaldehyde dehydrogenase (NAD+) activity / maintenance of lens transparency / retinal dehydrogenase / gamma-aminobutyric acid biosynthetic process / aminobutyraldehyde dehydrogenase / aminobutyraldehyde dehydrogenase (NAD+) activity / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (non-phosphorylating) activity / aldehyde dehydrogenase (NAD+) / cellular detoxification of aldehyde / aldehyde dehydrogenase (NAD+) activity / retinal dehydrogenase activity / retinol metabolic process / retinoid metabolic process / NAD binding / axon / synapse / cytosol
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 / Aldehyde dehydrogenase 1A1
Similarity search - Component
Biological speciesOvis aries (sheep)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsMoore, S.A. / Baker, H.M. / Blythe, T.J. / Kitson, K.E. / Kitson, T.M. / Baker, E.N.
CitationJournal: Structure / Year: 1998
Title: Sheep liver cytosolic aldehyde dehydrogenase: the structure reveals the basis for the retinal specificity of class 1 aldehyde dehydrogenases.
Authors: Moore, S.A. / Baker, H.M. / Blythe, T.J. / Kitson, K.E. / Kitson, T.M. / Baker, E.N.
History
DepositionOct 8, 1998Processing site: BNL
Revision 1.0Apr 27, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)222,1968
Polymers219,5424
Non-polymers2,6544
Water2,306128
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25560 Å2
ΔGint-107 kcal/mol
Surface area58220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.689, 87.625, 90.840
Angle α, β, γ (deg.)110.47, 105.63, 103.56
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
33
44
/ NCS ensembles :
ID
1
2
3
4

NCS oper:
IDCodeMatrixVector
1given(-0.999997, -0.00049, -0.002274), (-0.001395, 0.908631, 0.417598), (0.001862, 0.4176, -0.908629)93.3033, -17.0627, 78.1712
2given(0.999998, 0.000776, -0.001812), (0.000762, -0.999971, -0.007575), (-0.001818, 0.007574, -0.99997)0.0376, 95.6668, 102.6063
3given(-1, -0.000146, -0.000456), (0.000325, -0.906408, -0.422404), (-0.000352, -0.422404, 0.906408)93.2306, 112.5753, 24.8866

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Components

#1: Protein
ALDEHYDE DEHYDROGENASE


Mass: 54885.590 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Cellular location: CYTOSOL / Organ: LIVER / References: UniProt: P51977, aldehyde dehydrogenase (NAD+)
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


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


Mass: 18.015 Da / Num. of mol.: 128 / 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: 2.6 Å3/Da / Density % sol: 53 %
Crystal growpH: 7.2 / Details: pH 7.2
Crystal
*PLUS
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
21 mMNAD+1drop
3170 mM1reservoirMgCl2
4100 mMBis-Tris propane1reservoir
56-7 %(w/v)mPEG50001reservoir

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Oct 1, 1997 / Details: 0.1 MM COLLIMATION
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. obs: 83641 / % possible obs: 95.5 % / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Biso Wilson estimate: 27.8 Å2 / Rmerge(I) obs: 0.096 / Net I/σ(I): 11.3
Reflection shellResolution: 2.35→2.43 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 2.7 / % possible all: 93.7
Reflection shell
*PLUS
% possible obs: 93.7 %

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Processing

Software
NameVersionClassification
AMoREphasing
CNS0.3Crefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AG8

1ag8


Resolution: 2.35→100 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.259 8274 9.5 %RANDOM
Rwork0.235 ---
obs0.235 83206 95.5 %-
Displacement parametersBiso mean: 29 Å2
Baniso -1Baniso -2Baniso -3
1-1.84 Å2-2.12 Å2-5.12 Å2
2---5.35 Å2-2.78 Å2
3---3.51 Å2
Refinement stepCycle: LAST / Resolution: 2.35→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15144 0 176 140 15460
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.61
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.061.5
X-RAY DIFFRACTIONc_mcangle_it1.662
X-RAY DIFFRACTIONc_scbond_it1.822
X-RAY DIFFRACTIONc_scangle_it2.582.5
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Weight Biso : 2

Ens-IDDom-IDNCS model detailsRms dev Biso (Å2)Rms dev position (Å)Weight position
11RESTRAINTS1.60.009800
221.90.09100
331.30.03100
442.30.0550
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMWATER.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMNAD.TOP
X-RAY DIFFRACTION3NAD.PARAM
X-RAY DIFFRACTION4PROTEIN.TOP
Software
*PLUS
Name: CNS / Version: 0.3C / Classification: refinement
Refine LS restraints
*PLUS
Type: c_planar_d / Dev ideal: 0.018

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