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- PDB-9nyo: Clostridium acetobutylicum alcohol dehydrogenase bound to NADP+, ... -

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Basic information

Entry
Database: PDB / ID: 9nyo
TitleClostridium acetobutylicum alcohol dehydrogenase bound to NADP+, disordered nicotinamide
ComponentsOxidoreductase
KeywordsOXIDOREDUCTASE / short chain alcohol dehydrogenase
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 / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsMadzelan, P. / Wilson, M.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35153337 United States
Citation
Journal: 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.
#1: Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionMar 28, 2025Deposition 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
B: Oxidoreductase
A: Oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,4186
Polymers61,8072
Non-polymers1,6114
Water5,368298
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6490 Å2
ΔGint-28 kcal/mol
Surface area19990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.289, 62.660, 124.479
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: pET15b / 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.: 298 / 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: 1.97 Å3/Da / Density % sol: 37.5 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 7% PEG 1500 and 0.1M imidazole pH7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.8856 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 13, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8856 Å / Relative weight: 1
ReflectionResolution: 1.75→36.02 Å / Num. obs: 49905 / % possible obs: 99.9 % / Redundancy: 10.4 % / Biso Wilson estimate: 29.56 Å2 / CC1/2: 1 / Rrim(I) all: 0.105 / Net I/σ(I): 14.6
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 10 % / Mean I/σ(I) obs: 0.7 / Num. unique obs: 2707 / CC1/2: 0.341 / Rrim(I) all: 4.022 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
autoXDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→34.6 Å / SU ML: 0.2108 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.9117
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2146 2531 5.11 %
Rwork0.1891 46963 -
obs0.1904 49494 99.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.29 Å2
Refinement stepCycle: LAST / Resolution: 1.75→34.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3709 0 104 298 4111
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00844201
X-RAY DIFFRACTIONf_angle_d0.91285713
X-RAY DIFFRACTIONf_chiral_restr0.0556632
X-RAY DIFFRACTIONf_plane_restr0.0057721
X-RAY DIFFRACTIONf_dihedral_angle_d14.3241601
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.780.34071390.3522385X-RAY DIFFRACTION91.92
1.78-1.820.38491310.33752526X-RAY DIFFRACTION98.66
1.82-1.860.32181200.30852609X-RAY DIFFRACTION99.42
1.86-1.90.33661220.29632608X-RAY DIFFRACTION99.42
1.9-1.950.32781550.27742570X-RAY DIFFRACTION99.74
1.95-20.24821550.24782577X-RAY DIFFRACTION99.74
2-2.060.27971300.22512610X-RAY DIFFRACTION99.85
2.06-2.130.21711370.22422591X-RAY DIFFRACTION99.49
2.13-2.20.251350.2032587X-RAY DIFFRACTION98.8
2.2-2.290.23391380.18642607X-RAY DIFFRACTION99.75
2.29-2.40.2181710.17322604X-RAY DIFFRACTION99.82
2.4-2.520.19651400.17622611X-RAY DIFFRACTION99.75
2.52-2.680.22351250.18092646X-RAY DIFFRACTION99.96
2.68-2.890.20611380.17442638X-RAY DIFFRACTION99.89
2.89-3.180.19561540.17822620X-RAY DIFFRACTION99.28
3.18-3.640.20211310.16352663X-RAY DIFFRACTION99.82
3.64-4.580.17231540.14812688X-RAY DIFFRACTION99.79
4.58-34.60.20261560.19312823X-RAY DIFFRACTION99.67
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.358934909961.26923900482-1.120543496444.217815982310.2067243712674.885500465260.110887813426-0.781939727428-0.4185173276310.512280883309-0.008594575648910.7396771196180.27666894307-0.847706287635-0.07236143715350.296870794475-0.06001246093490.07940310248560.5540652109430.1797837668320.4504058066-9.48650479004-10.0599269687-8.19342180464
24.215527151851.08667469181-0.1081523701862.82237309896-0.09758048988272.274363266280.0973848025603-0.655361330128-0.2435630406460.301087412116-0.02339303561740.06500153674790.150412200778-0.0571709573012-0.04287378992830.175823796008-0.0003584484882050.002090417754720.2377477320750.04013200541710.1956369885848.29182842938-3.6259796594-13.3997205676
32.81202311533-5.06934870284.465661011119.1152689505-7.972163161887.272626004460.07039074002770.3710220230720.846865815540.4313500419970.0952037095172-0.168227983526-0.384003209936-0.0579883288911-0.2024842992980.3202205105950.02750881476410.05280598231040.270493052410.1104704787750.519543250361-8.311219817048.94989700439-25.9820406418
46.716861729021.03024571391-1.355556394082.30299830104-0.6039477747282.91715603884-0.03970313427340.5323861411310.040362710676-0.4091630538840.2087985538450.1487138057750.0645250488924-0.27679724192-0.1574640004970.269261852367-0.0356018927593-0.04438396006510.1951000833060.00129102027250.2370129380961.19054622106-4.39743167572-28.3450012196
54.418647243372.109101416571.015174763918.018581012582.114615436523.640799865250.271575527166-0.623073879707-0.04699121208840.315844477611-0.406568958678-0.507669220431-0.3804353563790.9398650017940.02647930294910.275451313331-0.122635401056-0.03480895550640.509921214885-0.02538084573980.21786880870337.936253040514.6335629207-12.9644929972
63.855631271312.281296050940.5562513165283.75730257616-1.331838539362.796387425670.263538067248-0.619599219148-0.2657173467980.437123195574-0.426205875282-0.587905875436-0.2574095945390.8606843714980.1429860192460.431260034716-0.151843179188-0.06987049915420.6826352820340.008319268714490.33956226098640.50668176214.3962512861-6.19807648251
73.504272243371.189340692770.07292821153882.5566353649-0.1995862850971.482899361740.174647606293-0.6348749743490.03806643004420.378223776162-0.177188261746-0.130299042006-0.1065781624850.153845249854-0.008955321009560.205384779264-0.0328173712818-0.001550805217590.298114363124-0.04184737763250.16380526314322.45681859828.02315902301-13.5303482028
86.07950380207-2.95932364057-1.720236196335.783859232652.181393106134.17268289071-0.0479148052829-0.3035031279671.14682314631-0.2428723783230.184932300182-0.0761935381337-0.6975989708420.231308808842-0.118960333430.281589282483-0.073706377378-0.02878600232740.205615371954-0.03976442351970.35459624472722.838804386519.8116428448-22.9471189025
95.10978129511-4.4084700332-3.864109886593.970068501092.677983580526.541503824370.2279480649630.405601203041-0.7411267420220.169940257810.0562058502921-0.1467310417470.4415347745740.209578153748-0.303384895090.2751823904690.0184483294081-0.07504191406870.352130891825-0.08923040200310.47219359859439.5480536845-4.72413910878-25.5438150653
107.191924203291.157111028811.075761107143.004911092640.1568925752532.4707212227-0.1188024591310.284249391044-0.223362223265-0.2826520131080.157758061671-0.1023443506290.06964620031490.237777819773-0.03281273284480.263966153817-0.03186995559590.03522907762850.252477471121-0.01354740701350.17340733757529.97352076329.27781236361-28.3317902504
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'B' and (resid 2 through 61 )BA2 - 611 - 60
22chain 'B' and (resid 62 through 184 )BA62 - 18461 - 183
33chain 'B' and (resid 185 through 214 )BA185 - 214184 - 196
44chain 'B' and (resid 215 through 251 )BA215 - 251197 - 233
55chain 'A' and (resid 4 through 26 )AC4 - 261 - 23
66chain 'A' and (resid 27 through 66 )AC27 - 6624 - 63
77chain 'A' and (resid 67 through 173 )AC67 - 17364 - 170
88chain 'A' and (resid 174 through 184 )AC174 - 184171 - 181
99chain 'A' and (resid 185 through 214 )AC185 - 214182 - 193
1010chain 'A' and (resid 215 through 251 )AC215 - 251194 - 230

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