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- PDB-9ju5: Structure of aldehyde dehydrogenase SbzJ in complex with NAD+ -

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Basic information

Entry
Database: PDB / ID: 9ju5
TitleStructure of aldehyde dehydrogenase SbzJ in complex with NAD+
ComponentsAldehyde dehydrogenase
KeywordsOXIDOREDUCTASE / altemicidin / biosynthesis / aldehyde dehydrogenase
Function / homologyoxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor / Aldehyde dehydrogenase domain / Aldehyde dehydrogenase family / Aldehyde dehydrogenase, C-terminal / Aldehyde dehydrogenase, N-terminal / Aldehyde/histidinol dehydrogenase / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Aldehyde dehydrogenase
Function and homology information
Biological speciesStreptomyces sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsHe, H. / Mori, T. / Abe, I.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Structure of aldehyde dehydrogenase SbzJ in complex with NAD+
Authors: He, H. / Mori, T. / Abe, I.
History
DepositionOct 7, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 8, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Aldehyde dehydrogenase
B: Aldehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,1644
Polymers101,8372
Non-polymers1,3272
Water16,646924
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7200 Å2
ΔGint-36 kcal/mol
Surface area31590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.116, 107.179, 110.990
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11B-618-

HOH

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Components

#1: Protein Aldehyde dehydrogenase


Mass: 50918.375 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sp. (bacteria) / Gene: sbzJ / Production host: Escherichia coli (E. coli) / References: UniProt: A0A3T0ZHH6
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 924 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.63 Å3/Da / Density % sol: 53.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 8% v/v Tacsimate, 20% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Aug 30, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→49.28 Å / Num. obs: 73223 / % possible obs: 100 % / Redundancy: 7.4 % / Biso Wilson estimate: 19.06 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.116 / Net I/σ(I): 14.3
Reflection shellResolution: 2→2.04 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 3.7 / Num. unique obs: 4446 / CC1/2: 0.861 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WNB

1wnb


Resolution: 2→45.06 Å / SU ML: 0.1751 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17.4371
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1883 2003 2.74 %
Rwork0.148 71147 -
obs0.1491 73150 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.17 Å2
Refinement stepCycle: LAST / Resolution: 2→45.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6587 0 88 924 7599
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00626911
X-RAY DIFFRACTIONf_angle_d0.80319481
X-RAY DIFFRACTIONf_chiral_restr0.05011085
X-RAY DIFFRACTIONf_plane_restr0.00841258
X-RAY DIFFRACTIONf_dihedral_angle_d15.63912619
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.050.21331500.17935013X-RAY DIFFRACTION100
2.05-2.110.24941310.17095025X-RAY DIFFRACTION100
2.11-2.170.21391420.16245006X-RAY DIFFRACTION99.94
2.17-2.240.2021490.1535043X-RAY DIFFRACTION100
2.24-2.320.23711390.15065037X-RAY DIFFRACTION99.94
2.32-2.410.2281420.15675027X-RAY DIFFRACTION99.94
2.41-2.520.22271410.15875053X-RAY DIFFRACTION99.92
2.52-2.650.1881410.15185065X-RAY DIFFRACTION99.88
2.65-2.820.18831410.15615060X-RAY DIFFRACTION99.96
2.82-3.040.1751440.15415079X-RAY DIFFRACTION99.94
3.04-3.340.19061440.14575099X-RAY DIFFRACTION99.89
3.34-3.830.17661420.13825112X-RAY DIFFRACTION99.89
3.83-4.820.13891450.12055174X-RAY DIFFRACTION99.85
4.82-45.060.17921520.15015354X-RAY DIFFRACTION99.57

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