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Basic information

Entry
Database: PDB / ID: 7ux4
TitleCrystallographic snapshots of ternary complexes of thermophilic secondary alcohol dehydrogenase from Thermoanaerobacter pseudoethanolicus reveal the dynamics of ligand exchange and the proton relay network.
Components
  • NADP-dependent isopropanol dehydrogenase
  • Secondary-alcohol dehydrogenase
KeywordsLYASE / alcohol dehydrogenase / zinc / NADP
Function / homology
Function and homology information


isopropanol dehydrogenase (NADP+) / isopropanol dehydrogenase (NADP+) activity / zinc ion binding
Similarity search - Function
Alcohol dehydrogenase, zinc-type, conserved site / Zinc-containing alcohol dehydrogenases signature. / Alcohol dehydrogenase-like, C-terminal / Zinc-binding dehydrogenase / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / Polyketide synthase, enoylreductase domain / Enoylreductase / GroES-like superfamily / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
: / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / (1S,3S)-3-methylcyclohexan-1-ol / NADP-dependent isopropanol dehydrogenase
Similarity search - Component
Biological speciesThermoanaerobacter pseudethanolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.23 Å
AuthorsPhillips, R.S. / Dinh, T.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Proteins / Year: 2022
Title: Crystallographic snapshots of ternary complexes of thermophilic secondary alcohol dehydrogenase from Thermoanaerobacter pseudoethanolicus reveal the dynamics of ligand exchange and the proton relay network.
Authors: Dinh, T. / Rahn, K.T. / Phillips, R.S.
History
DepositionMay 4, 2022Deposition site: RCSB / Processing site: RCSB
SupersessionMay 18, 2022ID: 7JNS
Revision 1.0May 18, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 20, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Secondary-alcohol dehydrogenase
B: NADP-dependent isopropanol dehydrogenase
C: NADP-dependent isopropanol dehydrogenase
D: NADP-dependent isopropanol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,65725
Polymers150,6954
Non-polymers3,96221
Water5,639313
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.000, 122.960, 165.440
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
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 3 through 61 or resid 63...
d_2ens_1(chain "B" and (resid 3 through 61 or resid 63...
d_3ens_1(chain "C" and (resid 3 through 61 or resid 63...
d_4ens_1(chain "D" and (resid 3 through 61 or resid 63...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-IDBeg label alt-IDEnd label alt-ID
d_11GLYALAA1 - 59
d_12GLYASPA61 - 77
d_13VALALAA79 - 244
d_14ILEGLYA246 - 324
d_15ASPMETA326 - 333
d_16METALAA335 - 350
d_17ZNZNB
d_18NAPNAPC
d_21GLYALAG3 - 61
d_22GLYASPG63 - 79
d_23VALALAG81 - 246
d_24ILEGLYG248 - 326
d_25ASPMETG328 - 335
d_26METALAG337 - 352
d_27ZNZNH
d_28NAPNAPI
d_31GLYALAM3 - 61
d_32GLYASPM63 - 79
d_33VALALAM81 - 246
d_34ILEGLYM248 - 326
d_35ASPMETM328 - 335
d_36METALAM337 - 352
d_37ZNZNNAA
d_38NAPNAPO
d_41GLYALAR3 - 61
d_42GLYASPR63 - 79
d_43VALALAR81 - 246
d_44ILEGLYR248 - 326
d_45ASPMETR328 - 335
d_46METALAR337 - 352
d_47ZNZNS
d_48NAPNAPT

NCS oper:
IDCodeMatrixVector
1given(-0.99990310363, 0.00168649927765, -0.0138180704392), (0.0105089791103, 0.742434399026, -0.66983634158), (0.00912933231603, -0.669916650684, -0.742380183213)37.1110305883, -9.22840165718, -24.120375181
2given(-0.549984727235, 0.325997476235, 0.768922912454), (0.282964108304, -0.793485631003, 0.538805963964), (0.785778666814, 0.5139126374, 0.34415939316)39.5625653769, -3.97912785703, -21.5406363895
3given(0.537869739933, -0.310863806683, -0.783619701487), (-0.308696263187, -0.937596553357, 0.160060364323), (-0.784476105409, 0.155808847077, -0.6002673098)-2.33537863505, 2.11202958363, -5.19923530363

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Components

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Protein , 2 types, 4 molecules ABCD

#1: Protein Secondary-alcohol dehydrogenase


Mass: 37652.793 Da / Num. of mol.: 1 / Mutation: I86A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoanaerobacter pseudethanolicus (bacteria)
Production host: Escherichia coli (E. coli)
References: UniProt: P14941, isopropanol dehydrogenase (NADP+)
#2: Protein NADP-dependent isopropanol dehydrogenase


Mass: 37680.801 Da / Num. of mol.: 3 / Mutation: I86A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoanaerobacter pseudethanolicus (bacteria)
Production host: Escherichia coli (E. coli)
References: UniProt: P14941, isopropanol dehydrogenase (NADP+)

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Non-polymers , 6 types, 334 molecules

#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H28N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: K
#6: Chemical ChemComp-NWO / (1S,3S)-3-methylcyclohexan-1-ol


Mass: 114.185 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: C7H14O / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 313 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.7 Å3/Da / Density % sol: 54.52 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 0.6 M KCl,12% PEG 3350, 50 mM HEPES-K buffer, pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 12, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.23→68.63 Å / Num. obs: 61152 / % possible obs: 92.6 % / Redundancy: 6.7 % / Biso Wilson estimate: 54.92 Å2 / CC1/2: 0.996 / Net I/σ(I): 8.8
Reflection shellResolution: 2.23→2.47 Å / Mean I/σ(I) obs: 1.1 / Num. unique obs: 5096 / CC1/2: 0.384

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YKF

1ykf


Resolution: 2.23→68.63 Å / SU ML: 0.2506 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.6577
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.204 1998 3.27 %
Rwork0.1734 59058 -
obs0.1744 61056 75.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 68.79 Å2
Refinement stepCycle: LAST / Resolution: 2.23→68.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10549 0 230 313 11092
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00311055
X-RAY DIFFRACTIONf_angle_d0.640115008
X-RAY DIFFRACTIONf_chiral_restr0.04751671
X-RAY DIFFRACTIONf_plane_restr0.00451923
X-RAY DIFFRACTIONf_dihedral_angle_d11.00374001
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.748293326775
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS0.967410081569
ens_1d_4AX-RAY DIFFRACTIONTorsion NCS0.728591203192
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.23-2.280.602180.4584482X-RAY DIFFRACTION8.83
2.28-2.340.3164320.3272954X-RAY DIFFRACTION17.42
2.34-2.410.2951530.30351580X-RAY DIFFRACTION28.63
2.41-2.490.337940.30582758X-RAY DIFFRACTION49.97
2.49-2.580.29271320.29663901X-RAY DIFFRACTION70.42
2.58-2.680.28921560.27814635X-RAY DIFFRACTION84.33
2.68-2.80.29061810.26315372X-RAY DIFFRACTION96.93
2.8-2.950.281870.24715533X-RAY DIFFRACTION99.88
2.95-3.140.27021880.22485545X-RAY DIFFRACTION99.98
3.14-3.380.23251880.19585565X-RAY DIFFRACTION99.97
3.38-3.720.21951880.15615581X-RAY DIFFRACTION99.88
3.72-4.260.15891910.13535625X-RAY DIFFRACTION99.83
4.26-5.360.16151910.12475662X-RAY DIFFRACTION99.81
5.36-68.630.17011990.15435865X-RAY DIFFRACTION99.57
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)
13.036264070291.448004980020.5534833520151.860926608390.7418216356830.5462301336980.363199452898-1.13035369975-0.8527679890920.744370541458-0.203756155005-0.6905322885990.006817389449071.0757336332-0.2419145935081.32330978153-0.12751559038-0.08849027209081.424028252650.1765786694940.63397996507518.8323313583-10.043593933425.370126227
23.080815097030.982550931073-0.4457359873122.00430692818-0.08728045381681.614701930220.23779814638-1.18581670950.1135877391370.750420538721-0.1830791623630.0286402713489-0.1860239487230.175061392192-0.06222813930320.688719159524-0.06954594554270.02980327702890.7180212383670.01136667243760.34066260960213.1265414846-2.8444784580210.2849271993
33.48224333658-0.00802966742786-0.9742248012593.352421325650.7595614609452.07553830098-0.0337249477772-0.453410665311-0.8126549354060.5394136106870.02546491924960.1938671091320.569744062113-0.0326445544683-0.05669274929960.506689850039-0.0695191102429-0.009915911497340.4409867666970.1625513393520.479059381137.94191813236-20.8952872827-4.3294795003
43.30217939615-0.0218072856396-0.294196169171.24555317849-0.8551947064585.512198996880.342056143942-1.04996018457-0.283076177161.111181948040.003730016911120.2812009027630.0837624855684-0.439648216634-0.316053979440.925966858534-0.1333420247790.09748534970091.006262709730.05878484770640.4637685748124.39909254251-4.6840055952517.6766955965
53.20957862713-0.7728767524580.4483780750316.22698028987-0.2235210372812.47073733928-0.04185801149630.349364351373-0.733104707178-0.09410750629370.1700402743160.1533817135260.136553994685-0.174303572407-0.08799939317490.463893248781-0.0817461475205-0.03111729083430.503509436681-0.17838849680.46501862490317.6598199468-29.1464115682-38.7459837002
62.90127796958-0.001173426506160.4979299597931.589850845250.4268063978971.81140557167-0.003141998109090.213726965588-0.407070279362-0.06533997984770.0539979409329-0.1441521481690.05733318398980.00698971896081-0.07376971811690.366593688678-0.00613061958533-0.0151379836390.255260856823-0.01668438077570.40061196634724.9419249075-18.391027768-27.2976779119
72.598260510780.171323975676-0.1962698858081.32803018622-0.5660059324114.33494460552-0.0175039891019-0.530374131679-0.6479032322540.271173610565-0.00697590337165-0.1755437546980.4304795079470.014291149446-0.009434138982430.460768665349-0.0239780173053-0.06797345229630.3219097062070.05344926853780.50710808974328.691523282-20.1200879515-10.8411568394
84.029637939421.1242225457-0.1079581065475.906421775492.336376923442.535569442940.09857690794750.373863122583-1.11003217899-0.2137076973330.177475264772-0.7141700622520.3344536378850.170369622935-0.2790863882940.4723639195550.036591136113-0.02394889205560.549754978771-0.2019056498860.73649921738234.1492886441-29.2242000592-34.6035184145
92.766037689872.82941871899-0.4260398206386.65907139626-2.733751574483.908602335480.375791215732-0.8265431521870.8498812108091.13495231704-0.0345021613956-0.3999579898-1.612404009080.524477778783-0.3787999859791.13360857334-0.1463240711870.1221875429740.774931955845-0.3273576814750.91485787401847.643116319224.14776824241.50674702116
103.800447400821.88466462187-2.438984533131.774136795590.3898761477476.125699775270.403631396355-1.16275384650.612644421950.8209904446540.173046301597-0.167718485957-1.522176080560.159752013955-0.6055690686950.749638225671-0.0773717027618-0.01650100972980.701833775687-0.1718365897830.62815710047845.049881420415.8468954754-2.02196941987
115.6724948231-0.207346710431-1.501414408062.15084544345-1.392660637282.175077334580.455460367529-0.7861521323520.5391504956110.49899306947-0.166313857139-0.184349082251-0.3862075772030.348166851379-0.2608610899320.488184033274-0.0878767315985-0.09114933598570.558375361771-0.1275286305890.53415948947439.6170441579.91419470084-1.88690483217
120.420911416402-1.17467394633-1.439087872598.384881453511.621814994227.436887415370.0936350741290.1045446697980.04445134817810.187126866674-0.01942999808270.1266701525550.401283057332-0.148487940757-0.04716641032530.2289915742150.00956180870304-0.03757227624910.3046616339560.02539213552520.2630888337431.88054705844.28992253805-20.7409804758
136.78911555477-1.26233626843-1.409721836642.17484144399-0.03223916079791.499750455790.1650634330130.5650010980060.679577612496-0.340314483745-0.105916505223-0.13678627587-0.241212060972-0.0657047360645-0.06524532447470.366631643768-0.0236521439527-0.01584503166490.3212207065120.04118251616820.35197138095329.089177637311.0168311707-27.918724877
142.64721039481-0.076314740848-0.7049689718973.61181730995-0.5298207549162.133732288920.196545725558-0.343550955986-0.1688019223620.198079523594-0.284545178073-0.528722893332-0.008306744624370.2527902357420.09654682633190.32145051492-0.0210923376616-0.1068924317250.470420335357-0.06134647530560.42968115724544.77911947372.8923085359-12.3719554845
155.746055760010.485369046796-2.899852396439.48573359278-1.646596185887.609450119560.342001082702-0.2246863124930.7642077729761.0032091165-0.495959523464-0.479472070569-1.536059652750.7680023981520.1035460088460.397141075384-0.113031167666-0.06180377502080.556997493462-0.07994989397870.79958652860752.086098032219.7308213973-16.1753087063
162.39203218109-2.59992884419-0.6063155297577.48979334717-1.042731195621.721468801230.3914217271120.9571794201810.341540039608-0.654891369047-0.4486898476220.427985289854-0.0694148730758-0.1927812100810.00440954957220.444096082008-0.0137083826097-0.1410702080230.4692887360410.1319890564850.55942877233-11.9327612717.14166122641-41.0081789467
174.21125354196-0.154684928709-0.2759568378912.96157051405-0.5358901341692.199572899380.1032012109290.3852869914980.189419895291-0.231769726438-0.06456223135990.2711389403030.0738351181025-0.0659587957592-0.04320239871340.350244432486-0.0163407574388-0.08022367321850.3652576276270.02415795080650.475419955545-5.342494468351.08135491862-30.6987432822
184.53516066122-0.109291630663-0.1694515432241.805499820710.6508945170922.297643066390.0573299156023-0.2682484638980.6800365690480.2090577015540.04785942050280.166749423273-0.3003532445550.000374310489767-0.09576704614850.3362705221090.001715395561720.01940049432420.262729563968-0.06903758199460.4108661500417.5049647042715.8179183447-10.5763457703
196.46897538108-2.723222429850.4046419402033.15012306469-1.086590795091.85243996495-0.14982327915-0.224343387215-0.1235819369960.1165799047920.1953588107860.6789099679180.135408253693-0.0725262113755-0.04614191913840.332017236277-0.0601373253222-0.0008275380973310.380772228939-0.0310534810610.52994465597-7.708160842681.15452011591-16.5868943611
206.01032150515-4.17365662372-2.98179283517.948605216840.4375766881527.039492686480.3428010183310.6299695726631.00556454544-0.2558222076480.03510312034780.339121116995-0.486971658609-0.212985060371-0.2430175408970.3566944076020.0165340044227-0.05359397646560.4307441248490.09000531265990.797096554259-15.473617823916.0317068163-24.9554140598
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 3 through 59 )AA3 - 591 - 57
22chain 'A' and (resid 60 through 210 )AA60 - 21058 - 208
33chain 'A' and (resid 211 through 298 )AA211 - 298209 - 296
44chain 'A' and (resid 299 through 352 )AA299 - 352297 - 350
55chain 'B' and (resid 1 through 79 )BG1 - 791 - 79
66chain 'B' and (resid 80 through 210 )BG80 - 21080 - 210
77chain 'B' and (resid 211 through 310 )BG211 - 310211 - 310
88chain 'B' and (resid 311 through 352 )BG311 - 352311 - 352
99chain 'C' and (resid 1 through 26 )CM1 - 261 - 26
1010chain 'C' and (resid 27 through 79 )CM27 - 7927 - 79
1111chain 'C' and (resid 80 through 150 )CM80 - 15080 - 150
1212chain 'C' and (resid 151 through 176 )CM151 - 176151 - 176
1313chain 'C' and (resid 177 through 292 )CM177 - 292177 - 292
1414chain 'C' and (resid 293 through 326 )CM293 - 326293 - 326
1515chain 'C' and (resid 327 through 352 )CM327 - 352327 - 352
1616chain 'D' and (resid 1 through 26 )DR1 - 261 - 26
1717chain 'D' and (resid 27 through 150 )DR27 - 15027 - 150
1818chain 'D' and (resid 151 through 292 )DR151 - 292151 - 292
1919chain 'D' and (resid 293 through 326 )DR293 - 326293 - 326
2020chain 'D' and (resid 327 through 352 )DR327 - 352327 - 352

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