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- PDB-9d7j: Clostridium acetobutylicum alcohol dehydrogenase bound to NADP+ -

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Basic information

Entry
Database: PDB / ID: 9d7j
TitleClostridium acetobutylicum alcohol dehydrogenase bound to NADP+
ComponentsOxidoreductase
KeywordsOXIDOREDUCTASE / alcohol dehydrogenase / loop disorder
Function / homologyshort chain dehydrogenase / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Short-chain dehydrogenase/reductase SDR / oxidoreductase activity / NAD(P)-binding domain superfamily / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Oxidoreductase
Function and homology information
Biological speciesClostridium acetobutylicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.39 Å
AuthorsMadzelan, P. / Wilson, M.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CBET-2023250 United States
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2025
Title: Is a Malleable Active Site Loop the Key to High Substrate Promiscuity? Hybrid, Biocatalytic Route to Structurally Diverse Taxoid Side Chains with Remarkable Dual Stereocontrol.
Authors: Kudalkar, G.P. / Leidner, F. / Kumar, N. / Hass, J.L. / Madzelan, P. / Powell, D.R. / Day, V.W. / Le Magueres, P. / Ferrara, J.D. / Daniels, L.M. / Yamano, A. / Ito, S. / Niu, W. / ...Authors: Kudalkar, G.P. / Leidner, F. / Kumar, N. / Hass, J.L. / Madzelan, P. / Powell, D.R. / Day, V.W. / Le Magueres, P. / Ferrara, J.D. / Daniels, L.M. / Yamano, A. / Ito, S. / Niu, W. / Grubmueller, H. / Wilson, M.A. / Berkowitz, D.B.
History
DepositionAug 16, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 2, 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: Oxidoreductase
B: Oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,4186
Polymers61,8072
Non-polymers1,6114
Water7,674426
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, dimer in the ASU
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6620 Å2
ΔGint-28 kcal/mol
Surface area19840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.261, 62.592, 123.579
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Oxidoreductase


Mass: 30903.576 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium acetobutylicum (bacteria) / Gene: CA_P0001 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q97TU5
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 426 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 1.95 Å3/Da / Density % sol: 36.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 6% PEG 6000, 0.1M HEPES pH=7.5, 4% 2,4-methylpentanediol (MPD)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 4, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.39→35.92 Å / Num. obs: 94445 / % possible obs: 97.1 % / Redundancy: 5.1 % / Biso Wilson estimate: 18.18 Å2 / CC1/2: 0.997 / Rrim(I) all: 0.063 / Net I/σ(I): 13.3
Reflection shellResolution: 1.39→1.41 Å / Mean I/σ(I) obs: 1.2 / Num. unique obs: 4493 / CC1/2: 0.413 / Rrim(I) all: 1.598

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
autoXDSdata reduction
Aimlessdata scaling
SHELXCDphasing
RefinementMethod to determine structure: SAD / Resolution: 1.39→34.41 Å / SU ML: 0.1487 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.244
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1742 4884 5.18 %
Rwork0.1394 89412 -
obs0.1412 94296 96.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.97 Å2
Refinement stepCycle: LAST / Resolution: 1.39→34.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3760 0 104 426 4290
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054157
X-RAY DIFFRACTIONf_angle_d1.06195639
X-RAY DIFFRACTIONf_chiral_restr0.0697632
X-RAY DIFFRACTIONf_plane_restr0.005707
X-RAY DIFFRACTIONf_dihedral_angle_d14.41721575
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.39-1.410.33061620.30222818X-RAY DIFFRACTION93.53
1.41-1.420.2811380.25882962X-RAY DIFFRACTION95.24
1.42-1.440.29871410.23752904X-RAY DIFFRACTION96.15
1.44-1.460.23691310.22212958X-RAY DIFFRACTION95.69
1.46-1.480.24761590.20022936X-RAY DIFFRACTION96.36
1.48-1.50.27391610.18792939X-RAY DIFFRACTION96.51
1.5-1.520.2161640.18172972X-RAY DIFFRACTION96.67
1.52-1.540.20571440.16442940X-RAY DIFFRACTION97.01
1.54-1.570.21871730.1592972X-RAY DIFFRACTION96.68
1.57-1.590.19311400.15992782X-RAY DIFFRACTION91.4
1.59-1.620.22331420.1492897X-RAY DIFFRACTION95.06
1.62-1.650.19631870.14282973X-RAY DIFFRACTION97.2
1.65-1.680.17581810.13842910X-RAY DIFFRACTION96.2
1.68-1.720.21241590.16052970X-RAY DIFFRACTION97.26
1.72-1.750.21141580.15182979X-RAY DIFFRACTION97.06
1.75-1.790.18471740.13853017X-RAY DIFFRACTION97.67
1.79-1.840.18781810.12352961X-RAY DIFFRACTION97.58
1.84-1.890.15121990.11542970X-RAY DIFFRACTION97.54
1.89-1.940.16241490.11383014X-RAY DIFFRACTION97.65
1.94-2.010.18321620.11472816X-RAY DIFFRACTION91.77
2.01-2.080.16111750.12182967X-RAY DIFFRACTION97.19
2.08-2.160.16751650.11933055X-RAY DIFFRACTION98.86
2.16-2.260.15561730.11443034X-RAY DIFFRACTION98.68
2.26-2.380.15841760.10943066X-RAY DIFFRACTION99.17
2.38-2.530.15181780.11333069X-RAY DIFFRACTION99.11
2.53-2.720.171300.1233116X-RAY DIFFRACTION98.9
2.72-30.17661420.13522958X-RAY DIFFRACTION94.17
3-3.430.1551810.14063122X-RAY DIFFRACTION99.61
3.43-4.320.17271850.13233145X-RAY DIFFRACTION99.14
4.32-34.410.16091740.17023190X-RAY DIFFRACTION95.7

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