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- PDB-7utc: Crystal structure of secondary alcohol dehydrogenases from the Th... -

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Basic information

Entry
Database: PDB / ID: 7utc
TitleCrystal structure of secondary alcohol dehydrogenases from the Thermoanaerobacter ethanolicus with NADP and transition-state analogue inhibitor DMSO
ComponentsSecondary-alcohol dehydrogenase
KeywordsOXIDOREDUCTASE / secondary alcohol dehydrogenases / transition-state analogue inhibitor / DMSO / 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 / NADP-dependent isopropanol dehydrogenase
Similarity search - Component
Biological speciesThermoanaerobacter pseudethanolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsDinh, T. / Phillips, R.
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
DepositionApr 26, 2022Deposition site: RCSB / Processing site: RCSB
SupersessionMay 4, 2022ID: 7JNQ
Revision 1.0May 4, 2022Provider: repository / Type: Initial release
Revision 1.1May 11, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI ..._citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2May 18, 2022Group: Database references / Source and taxonomy / Structure summary
Category: entity / entity_src_gen ...entity / entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_ec / _entity.pdbx_mutation ..._entity.pdbx_ec / _entity.pdbx_mutation / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _struct_ref.db_code / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.pdbx_db_accession
Revision 1.3Jul 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 1.4Oct 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: Secondary-alcohol dehydrogenase
C: Secondary-alcohol dehydrogenase
D: Secondary-alcohol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,62147
Polymers150,6514
Non-polymers5,97043
Water8,863492
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.709, 125.325, 137.366
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
Secondary-alcohol dehydrogenase


Mass: 37662.809 Da / Num. of mol.: 4 / Mutation: C295A
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: Chemical
ChemComp-ZN / ZINC ION


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


Mass: 743.405 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H28N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical...
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 35 / Source method: obtained synthetically / Formula: C2H6OS / Feature type: SUBJECT OF INVESTIGATION / Comment: DMSO, precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 492 / Source method: isolated from a natural source / Formula: H2O
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: 2.28 Å3/Da / Density % sol: 45.99 %
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-BM / Wavelength: 1 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Oct 10, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→68.9 Å / Num. obs: 67445 / % possible obs: 93.9 % / Redundancy: 14.7 % / Biso Wilson estimate: 30.35 Å2 / CC1/2: 0.999 / Net I/σ(I): 16
Reflection shellResolution: 1.85→2.1 Å / Num. unique obs: 3372 / CC1/2: 0.427

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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: 1.85→67.26 Å / SU ML: 0.2588 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.3219
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2265 1999 2.97 %
Rwork0.1783 65416 -
obs0.1798 67415 56.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.42 Å2
Refinement stepCycle: LAST / Resolution: 1.85→67.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10568 0 336 492 11396
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004311163
X-RAY DIFFRACTIONf_angle_d0.702415126
X-RAY DIFFRACTIONf_chiral_restr0.04991677
X-RAY DIFFRACTIONf_plane_restr0.00531922
X-RAY DIFFRACTIONf_dihedral_angle_d11.8324025
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.890.263750.2717176X-RAY DIFFRACTION2.17
1.89-1.940.3203160.3399514X-RAY DIFFRACTION6.35
1.94-20.3324280.3022914X-RAY DIFFRACTION11.26
2-2.050.3666400.31351310X-RAY DIFFRACTION20.35
2.09-2.140.2739660.29392152X-RAY DIFFRACTION36.75
2.14-2.230.34441120.26993678X-RAY DIFFRACTION45.07
2.23-2.330.36671390.29324524X-RAY DIFFRACTION55.37
2.33-2.450.31391640.24785355X-RAY DIFFRACTION65.87
2.45-2.60.28181900.24166222X-RAY DIFFRACTION75.74
2.6-2.80.27672200.23377204X-RAY DIFFRACTION88.13
2.8-3.090.26542500.21818166X-RAY DIFFRACTION99.39
3.09-3.530.24592520.17188270X-RAY DIFFRACTION99.99
3.53-4.450.1852540.1318329X-RAY DIFFRACTION99.94
4.45-67.260.16342630.13328602X-RAY DIFFRACTION99.86
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)
11.25206590253-0.08637517032450.6478064618370.00429594665568-0.04921506734850.3300328901280.13503058008-1.08729657026-0.6289476092420.624261189891-0.1848859748310.02200797074490.0701333219788-0.1420037413450.08064466712420.919907985421-0.191721287091-0.1925230221550.8814980792460.5447019287690.879445340136-2.761-29.3923.44
20.532336380640.0904455564142-0.1509162527360.5186354930680.05088562269070.07611911358210.23936032224-0.610428912321-0.8009974177350.371264008264-0.155116716179-0.2457031594750.3159307089120.138763972219-0.03261827454090.522239588016-0.0708175524823-0.1915233478320.3865764271560.3024567628010.5857621758323.501-19.417-9.5
30.9892864923350.007233347967550.1575709122682.25371978940.7767750889211.143712978820.185367673641-0.7711395728-0.2429539611480.621608882482-0.0902183122303-0.1636034560510.148450265110.174418328927-0.0974475359590.4689476014-0.0974649143173-0.1232204859850.6100294467710.08985099000210.2462552767958.468-2.125-1.662
40.003035208786110.0639263545537-0.06981536312570.617389616932-0.6920916066661.055063266730.0218772000023-0.622657416095-0.4890147805120.5450216510180.13456386905-0.07619954312350.159383625288-0.286202418901-0.1159633626670.677913313560.00306901860558-0.3427805148510.7069733233750.5805556915910.87158727814913.849-26.82-0.288
50.4349383678540.0775940434705-0.04103198667580.0982378876384-0.009249774519550.003464908129620.26893959088-0.6531021319640.3170081006950.65726797393-0.1343823193520.0574431593182-0.066522404520.0219570193470.2443367532370.822337787696-0.2313078381990.25527929440.566983261967-0.5287423329680.798213052462-0.36934.0891.305
60.979229574859-0.0459380754922-0.2303420231870.488185192593-0.1139480595910.263538917520.300357978095-0.4065560120930.6648357637180.358033458121-0.2040758105630.126010065681-0.165965115597-0.0316676282667-0.1121714482870.386647511175-0.07193152237110.1393390899980.328058937941-0.1795671800160.381811206519-6.78123.363-10.987
70.689623539984-0.9283220609680.7297822025421.51874012473-0.4196808671331.95788848755-0.0508856980349-0.8627366527130.03855006541620.8219008438970.1127531338530.4304365768580.133362936987-0.174510965714-0.03074516310650.675456557009-0.1144732389830.1655393338370.716795451578-0.03162046839990.256905264783-16.4644.5131.227
81.05000362465-0.403313747110.1009038989611.91235414628-0.05832762978570.7449005646560.119603653965-0.7219054278280.2897546702870.609068887245-0.02186178653220.291361533526-0.258459534413-0.126226116901-0.06652360881850.338282471924-0.05357301776870.1391227060380.41380243845-0.149631321960.382817773704-9.98415.125-7.356
90.510045855017-0.420101525864-0.03454576111370.9780431883770.7884289357790.9807623196540.0521227033635-0.2407833996180.2612175564050.1341883485050.0611254568818-0.130571369998-0.1011000070040.189677146817-0.2602836594070.612948750589-0.1539942369810.3969186144670.822644626986-0.61899800650.826580637431-15.15133.0542.854
102.20884511396-0.2139315004350.1471981059732.34971243625-0.2650607369021.016940967380.2243284609530.0184658787561-0.523944534727-0.0293314156335-0.1934329250450.2826821130480.124466919895-0.104896769826-0.0147128371280.184351937206-0.0336895026099-0.01689087536090.170451606979-0.01286353121990.320333809524-26.07-15.237-30.089
112.741477624190.414425202307-0.3550037015151.76965210660.1099596219771.191222665780.07660135560580.281169761370.262986976571-0.129229255346-0.02410657748380.196236918073-0.0734963876254-0.12917479952-0.04566277773560.1075116026580.0111069624701-0.01641110050990.1470752724660.01524173004420.170793288381-13.8698.143-33.788
123.225715252150.7881314631772.222423387363.155538045751.770913828284.575863261950.1875195258570.1929825296690.0759129760936-0.245302414698-0.3101390274490.522663817337-0.0329477861269-0.2695030932260.08626028477810.1564389180390.046830752948-0.02504783808720.2079381985280.01149783353760.366287133666-34.673-1.056-35.832
132.04818758495-0.733206506018-0.5523256503684.255202014581.966022782443.612905258860.2712130935410.5361457361910.469739373161-1.0145383383-0.356990772141-0.212380132492-0.665966307554-0.09469835376420.09219666946290.312597183730.0601013839190.03764640629020.2752340120070.0337335707560.3448885493524.79518.3-39.984
141.769468586850.355527597261-0.1024443946481.65556304643-0.2371802086090.7833288812320.0724397940643-0.129039299622-0.06631516224540.0908352956454-0.0347323349508-0.255947312385-0.0922126630290.107230138044-0.03661149798320.114234732466-0.00859067545832-0.03819928240930.159792322237-0.03921210049680.19325091671919.1648.148-27.291
151.71244523090.3031721363440.39744711681.60269038473-0.01157453195821.193440904390.07841604455380.385181115156-0.44618907298-0.2063760070610.0180621950624-0.2367263039650.07633974253610.0516230062478-0.06165621268480.1392351881840.001589937678040.01191638041460.192900942517-0.07395323110390.2031528648677.285-5.186-35.3
162.763639224620.153123346996-2.034805312562.52341082684-1.183784816314.16209337310.1407511812080.218218490021-0.304083353583-0.269009239725-0.226301628695-0.4509188527810.03661773697510.300351175530.06824358991580.1463156281330.0310648897111-0.01777752258630.258735773424-0.04151113889410.40284268128131.2193.119-36.215
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 1:59 )A1 - 59
2X-RAY DIFFRACTION2( CHAIN A AND RESID 60:210 )A60 - 210
3X-RAY DIFFRACTION3( CHAIN A AND RESID 211:310 )A211 - 310
4X-RAY DIFFRACTION4( CHAIN A AND RESID 311:352 )A311 - 352
5X-RAY DIFFRACTION5( CHAIN B AND RESID 1:59 )B1 - 59
6X-RAY DIFFRACTION6( CHAIN B AND RESID 60:210 )B60 - 210
7X-RAY DIFFRACTION7( CHAIN B AND RESID 211:269 )B211 - 269
8X-RAY DIFFRACTION8( CHAIN B AND RESID 270:326 )B270 - 326
9X-RAY DIFFRACTION9( CHAIN B AND RESID 327:352 )B327 - 352
10X-RAY DIFFRACTION10( CHAIN C AND RESID 1:150 )C1 - 150
11X-RAY DIFFRACTION11( CHAIN C AND RESID 151:310 )C151 - 310
12X-RAY DIFFRACTION12( CHAIN C AND RESID 311:352 )C311 - 352
13X-RAY DIFFRACTION13( CHAIN D AND RESID 1:60 )D1 - 60
14X-RAY DIFFRACTION14( CHAIN D AND RESID 61:210 )D61 - 210
15X-RAY DIFFRACTION15( CHAIN D AND RESID 211:310 )D211 - 310
16X-RAY DIFFRACTION16( CHAIN D AND RESID 311:352 )D311 - 352

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