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- PDB-6sdm: NADH-dependent variant of TBADH -

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Basic information

Entry
Database: PDB / ID: 6sdm
TitleNADH-dependent variant of TBADH
ComponentsNADP-dependent isopropanol dehydrogenase
KeywordsOXIDOREDUCTASE / cofactor
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-dependent isopropanol dehydrogenase
Similarity search - Component
Biological speciesThermoanaerobacter brockii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsSelles Vidal, L. / Murray, J.W. / Heap, J.T.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/N503873/1 United Kingdom
CitationJournal: Nat Commun / Year: 2021
Title: Versatile selective evolutionary pressure using synthetic defect in universal metabolism.
Authors: Selles Vidal, L. / Murray, J.W. / Heap, J.T.
History
DepositionJul 28, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 26, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 16, 2022Group: Database references / Category: citation / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 24, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NADP-dependent isopropanol 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)151,9118
Polymers151,6494
Non-polymers2624
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15180 Å2
ΔGint-230 kcal/mol
Surface area47000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.123, 123.946, 169.240
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-ID
11
21
31
41

NCS domain segments:

Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: ALA / End label comp-ID: ALA / Auth seq-ID: 0 - 352 / Label seq-ID: 2 - 354

Dom-IDComponent-IDSelection detailsAuth asym-IDLabel asym-ID
11(chain 'A' and (resid 0 through 339 or (resid 340...AA
22(chain 'B' and (resid 0 through 339 or (resid 340...BB
33(chain 'C' and (resid 0 through 339 or (resid 340...CC
44(chain 'D' and (resid 0 through 339 or (resid 340...DD

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Components

#1: Protein
NADP-dependent isopropanol dehydrogenase


Mass: 37912.223 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoanaerobacter brockii (bacteria) / Gene: adh / 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
Has ligand of interestN

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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: 2.74 Å3/Da / Density % sol: 55.05 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 5.5 / Details: 20% w/v PEG 3K, sodium citrate pH 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 6, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.85→71.68 Å / Num. obs: 39642 / % possible obs: 99.87 % / Redundancy: 6.5 % / Biso Wilson estimate: 69.95 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.1918 / Net I/σ(I): 6.92
Reflection shellResolution: 2.85→2.952 Å / Rmerge(I) obs: 1.671 / Mean I/σ(I) obs: 1.11 / Num. unique obs: 3923 / CC1/2: 0.554 / % possible all: 99.62

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
PHENIX1.16_3549refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YKF

1ykf


Resolution: 2.85→71.68 Å / SU ML: 0.4182 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.433
RfactorNum. reflection% reflection
Rfree0.2385 2015 5.09 %
Rwork0.174 --
obs0.1774 39601 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 77.08 Å2
Refinement stepCycle: LAST / Resolution: 2.85→71.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10618 0 4 0 10622
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008610852
X-RAY DIFFRACTIONf_angle_d1.060814692
X-RAY DIFFRACTIONf_chiral_restr0.06061648
X-RAY DIFFRACTIONf_plane_restr0.00711906
X-RAY DIFFRACTIONf_dihedral_angle_d10.31796492
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.85-2.920.41481080.32922687X-RAY DIFFRACTION99.11
2.92-30.32051570.2932584X-RAY DIFFRACTION99.67
3-3.090.31871310.26572670X-RAY DIFFRACTION99.89
3.09-3.190.34181370.26362657X-RAY DIFFRACTION99.75
3.19-3.30.28641500.25062652X-RAY DIFFRACTION99.96
3.3-3.430.2831450.20962639X-RAY DIFFRACTION99.93
3.43-3.590.32561520.1952661X-RAY DIFFRACTION99.96
3.59-3.780.30551420.18272672X-RAY DIFFRACTION99.96
3.78-4.020.22931280.15192671X-RAY DIFFRACTION99.93
4.02-4.330.19721550.12742673X-RAY DIFFRACTION99.96
4.33-4.760.15021670.11192690X-RAY DIFFRACTION100
4.76-5.450.21831380.12982721X-RAY DIFFRACTION100
5.45-6.870.23071440.17052743X-RAY DIFFRACTION99.93
6.87-71.680.20651610.16552866X-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)
11.47075460359-1.54033762188-1.990324728682.443029945220.7741742293675.707988957891.068035768610.8139550926130.74901084749-0.9880912542810.0980499597976-0.287185684817-3.27955176305-0.488251721238-0.6623515529271.388885373360.2041165827110.2253976520540.8153825426270.2448572240370.853973558643-45.464058074823.0349839692.8493406647
22.63574794334-0.4304035131740.8919745184911.96846770926-0.5404245341596.12284073960.1920227027070.500576501706-0.0426502314782-0.580680234176-0.00453440078150.314779003838-0.134553159049-0.322342939167-0.1624657086930.449978123810.0612719033744-0.09533865855460.428693429050.03525490346830.544117862144-38.61771410747.42322350447.78452072071
34.086208628540.6208060929111.984685398592.789233842360.7987425084043.501050166010.0716205742513-0.282683518690.3438412347930.1153637539270.002682192515160.0488916438785-0.2470085972320.0559865285013-0.1079991445050.3650372836410.06286178711510.04352145166360.3726564796370.03143640072360.596812114105-29.202343307510.528078671225.4964473725
46.69978942302-2.34973787307-0.6526682580714.6575888654-1.743283003734.669917115750.353476826966-0.159518356720.157840525433-0.150277181538-0.1165636700451.37034315882-0.532762687192-0.674082340182-0.2082780173280.3636756056330.0314022448018-0.08105266221420.5189432077710.04209682995720.736190123373-51.181739769414.288150536217.0300612259
53.290759917942.81285360166-0.4098410606357.514686787770.667500102631.671173634860.186173327176-0.18922496425-0.1289702717670.329228262007-0.117918770945-0.05562271035250.03661009884430.0409836583767-0.08173682389380.3016389852540.0671717364823-0.1285069908220.516043665061-0.08276584424810.61078924825310.03373855035.2933578051836.84973628
62.176801934213.238840415440.1431765567145.68867248301-1.148734555045.277840823510.0677920989402-0.301238925246-0.1477568844070.212370329633-0.0451665999776-0.05335348598520.115354831459-0.133892130362-0.02820947118680.3500793056790.0850561516157-0.05029002891680.392770582515-0.08137897800110.6056044618262.83562187284-0.27319192773729.8639133774
74.26300733-1.583152416731.361207847714.9633802598-1.585967046952.90621963799-0.05432830579030.142396899390.371707713038-0.05500607811060.123548388386-0.254244271731-0.3605659488470.0966492276731-0.06560497186990.342546727915-0.05170515381670.05828216923390.434476624668-0.02505603303340.433337469732-6.2926306637813.464048536411.8946295903
87.694748782094.847912513434.739800928835.253760405564.448802371588.50030161744-0.2612940282290.5485104528960.533912855027-0.3533542130710.175912865532-0.48834311966-0.6977914084050.3838560547010.1124783320640.3708759862230.06055174329570.01191170442840.4576631851640.01636593448410.78690465798714.854393760212.490493455221.3900391073
93.67313713521-0.670746648759-0.6062460032951.022719777111.567591232962.971132202970.316826149030.869283765339-0.750854070652-0.810816267843-0.1827624534130.3439531797420.438895129241-0.156512611921-0.1313840783741.239886998330.267361740949-0.1304631370920.850264401973-0.1343960157950.661631019053-20.9445414781-5.63315217807-19.3210209385
102.92795547846-1.726843166451.23252157392.8217226473-1.686888619623.643886834330.322120640360.5575210979820.0452453655966-0.875510440574-0.296310700165-0.2266065446690.5103999646310.0886599508115-0.114906936550.7493909607270.1490740941220.05255666215870.647388432527-0.1482946252550.55803598348-9.34527683139-4.78690714273-7.75145430971
111.82845742576-0.4637719706960.3273066322553.15232758799-0.8313163907112.946565360460.1893186762490.469444100161-0.635884415411-0.500450098455-0.121218410552-0.0864391033540.6572285447140.193729680554-0.01495575438980.7711779803750.1266159353780.01790916152870.644265335319-0.2368596490540.737046245567-6.61977919417-16.81492992012.52525230154
122.365087204191.500935661750.9893119872610.9881749922410.8478018287371.561736699650.4635923384211.26072273637-0.636078472156-1.15206488394-0.626669837199-0.759877195540.2034398140350.708683247033-0.1808314172181.477015100450.5056528971960.1504329889761.18293422759-0.2493820166640.671240099875-2.40363350477-9.28895813315-19.8894743734
132.624691359590.1421012950480.03884246016285.10831339814-0.8334198997492.235906395620.0814894314681-0.0341003195393-0.255186836604-0.184858114810.0949240135921-0.05573887782310.06643795956470.120410131611-0.1886561272940.3909012192650.0134426779216-0.1064665300270.436937098430.04369537219770.536114599386-17.2600819964-24.390612584837.3795971841
142.46970208244-0.5008850503540.1572250720182.657119748670.5505994769026.107891570430.1425988187620.359547149709-0.785758585509-0.5634451924550.07392457781760.1268991992460.727807402294-0.156094654191-0.1480692308440.531678071326-0.0300058002851-0.1817885291190.412475798855-0.0409441885970.813251176175-30.6865225315-19.052164279114.3886556474
156.21251961476-3.28599488998-0.8611518174557.65485356777-2.274536311963.576757096020.1046534052190.053680625957-1.44334197752-0.3557852548310.458173085171.140454648070.58342131156-0.595340134923-0.505194774490.483784137754-0.110106017767-0.1869915618110.6116694912480.2274270762011.01063380999-34.1126415451-29.018308086135.170299907
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -1 through 59 )
2X-RAY DIFFRACTION2chain 'A' and (resid 60 through 198 )
3X-RAY DIFFRACTION3chain 'A' and (resid 199 through 310 )
4X-RAY DIFFRACTION4chain 'A' and (resid 311 through 352 )
5X-RAY DIFFRACTION5chain 'B' and (resid -1 through 79 )
6X-RAY DIFFRACTION6chain 'B' and (resid 80 through 150 )
7X-RAY DIFFRACTION7chain 'B' and (resid 151 through 310 )
8X-RAY DIFFRACTION8chain 'B' and (resid 311 through 352 )
9X-RAY DIFFRACTION9chain 'C' and (resid -1 through 112 )
10X-RAY DIFFRACTION10chain 'C' and (resid 113 through 198 )
11X-RAY DIFFRACTION11chain 'C' and (resid 199 through 310 )
12X-RAY DIFFRACTION12chain 'C' and (resid 311 through 352 )
13X-RAY DIFFRACTION13chain 'D' and (resid -1 through 150 )
14X-RAY DIFFRACTION14chain 'D' and (resid 151 through 310 )
15X-RAY DIFFRACTION15chain 'D' and (resid 311 through 352 )

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