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- PDB-8yen: Aldehyde dehydrogenase -

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Basic information

Entry
Database: PDB / ID: 8yen
TitleAldehyde dehydrogenase
ComponentsAldehyde dehydrogenase family protein
KeywordsOXIDOREDUCTASE / ALDEHYDE DEHYDROGENASE / ENZYME / ALDEHYDE / DEHYDROGENASE.
Function / homology
Function and homology information


oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor
Similarity search - Function
Putative aldehyde dehydrogenase FUS7/LUC3-like / Aldehyde dehydrogenase, glutamic acid active site / Aldehyde dehydrogenases glutamic acid active site. / Aldehyde dehydrogenase domain / Aldehyde dehydrogenase family / Aldehyde dehydrogenase, C-terminal / Aldehyde dehydrogenase, N-terminal / Aldehyde/histidinol dehydrogenase
Similarity search - Domain/homology
Aldehyde dehydrogenase family protein
Similarity search - Component
Biological speciesRhodococcus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.58 Å
AuthorsKim, S.B. / Park, H.H.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea) Korea, Republic Of
CitationJournal: To Be Published
Title: Aldehyde dehydrogenase
Authors: Kim, S.B. / Park, H.H.
History
DepositionFeb 22, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 26, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aldehyde dehydrogenase family protein
B: Aldehyde dehydrogenase family protein


Theoretical massNumber of molelcules
Total (without water)111,7452
Polymers111,7452
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4590 Å2
ΔGint-21 kcal/mol
Surface area32120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.310, 48.620, 112.640
Angle α, β, γ (deg.)90.000, 105.884, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:

Ens-ID: 1 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: ARG / End label comp-ID: ARG / Auth seq-ID: 7 - 483 / Label seq-ID: 43 - 519

Dom-IDComponent-IDSelection detailsAuth asym-IDLabel asym-ID
11chain 'A'AA
22chain 'B'BB

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Components

#1: Protein Aldehyde dehydrogenase family protein


Mass: 55872.699 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodococcus (bacteria) / Gene: E5769_03205 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A4P7RFW8
Has protein modificationN

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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: 2.2 Å3/Da / Density % sol: 44.07 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 20% (W/V) PEG 3350, 0.1M Bis-Tris propane pH8.5, 0.2M Sodium fluoride

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Data collection

DiffractionMean temperature: 125 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 11, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.58→29.92 Å / Num. obs: 30821 / % possible obs: 98.87 % / Redundancy: 6.8 % / Biso Wilson estimate: 56.84 Å2 / CC1/2: 0.997 / Net I/σ(I): 11.83
Reflection shellResolution: 2.58→2.672 Å / Num. unique obs: 3033 / CC1/2: 0.997

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Processing

Software
NameVersionClassification
PHENIX1.17_3644refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.58→29.92 Å / SU ML: 0.4068 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.4705
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2343 1540 5 %
Rwork0.1886 29265 -
obs0.1909 30805 98.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 56.72 Å2
Refinement stepCycle: LAST / Resolution: 2.58→29.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7230 0 0 0 7230
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00957378
X-RAY DIFFRACTIONf_angle_d1.16210058
X-RAY DIFFRACTIONf_chiral_restr0.06491154
X-RAY DIFFRACTIONf_plane_restr0.00781330
X-RAY DIFFRACTIONf_dihedral_angle_d5.02571030
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.58-2.660.381380.30362628X-RAY DIFFRACTION98.93
2.66-2.760.34851370.26522598X-RAY DIFFRACTION98.2
2.76-2.870.32641390.25892637X-RAY DIFFRACTION98.47
2.87-30.32491400.24522664X-RAY DIFFRACTION99.75
3-3.160.31221370.23642614X-RAY DIFFRACTION99.03
3.16-3.350.28071400.22462651X-RAY DIFFRACTION99.08
3.35-3.610.26261410.19842682X-RAY DIFFRACTION99.33
3.61-3.980.21541390.18482644X-RAY DIFFRACTION99.22
3.98-4.550.19821420.15712685X-RAY DIFFRACTION99.23
4.55-5.730.21121420.15582701X-RAY DIFFRACTION99.48
5.73-29.920.16761450.15322761X-RAY DIFFRACTION97.91

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