PDB-6sch: NADH-dependent variant of CBADH

ID or keywords:

Entry

Database: PDB / ID: 6sch

Title

NADH-dependent variant of CBADH

Components

NADP-dependent isopropanol dehydrogenase

Keywords

OXIDOREDUCTASE / cofactor

Function / homology

Function and homology information

isopropanol dehydrogenase (NADP+) / isopropanol dehydrogenase (NADP+) activity / zinc ion binding
Similarity search - Function

Biological species

Clostridium beijerinckii (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.2 Å

Authors

Selles Vidal, L. / Murray, J.W. / Heap, J.T.

Funding support

United Kingdom, 1items

Citation

Journal: 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

Deposition	Jul 24, 2019	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Aug 26, 2020	Provider: repository / Type: Initial release
Revision 1.1	Mar 16, 2022	Group: 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 1.2	Jan 24, 2024	Group: 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

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6sch.cif.gz	665.5 KB	Display	PDBx/mmCIF format
PDB format	pdb6sch.ent.gz	460.3 KB	Display	PDB format
PDBx/mmJSON format	6sch.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6sch_validation.pdf.gz	3 MB	Display	wwPDB validaton report
Full document	6sch_full_validation.pdf.gz	3 MB	Display
Data in XML	6sch_validation.xml.gz	56.4 KB	Display
Data in CIF	6sch_validation.cif.gz	76.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/sc/6sch ftp://data.pdbj.org/pub/pdb/validation_reports/sc/6sch	HTTPS FTP

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Related structure data

Related structure data	6sdmC 1kevS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	1kev-d 7jns-d 2b83-d 1y9a-1 7jnq-d 1jqb-d 4cpd-d 1r37-1 1ykf-d 3fsr-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#13 - Jan 2001 Alcohol Dehydrogenase similarity (10) #32 - Aug 2002 Chaperones similarity (1)

Deposited unit

A: NADP-dependent isopropanol dehydrogenase

B: NADP-dependent isopropanol dehydrogenase

C: NADP-dependent isopropanol dehydrogenase

D: NADP-dependent isopropanol dehydrogenase

hetero molecules

160 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	75.812, 99.570, 114.089
Angle α, β, γ (deg.)	90.000, 102.768, 90.000
Int Tables number	4
Space group name H-M	P12₁1
Space group name Hall	P2yb
Symmetry operation	#1: x,y,z #2: -x,y+1/2,-z

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID
1	1
2	1
3	1
4	1

NCS domain segments:

Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: HIS / End label comp-ID: HIS / Auth seq-ID: 1 - 352 / Label seq-ID: 1 - 352

Dom-ID	Component-ID	Selection details	Auth asym-ID	Label asym-ID
1	1	(chain 'A' and resid 1 through 352)	A	A
2	2	(chain 'B' and resid 1 through 352)	B	B
3	3	(chain 'C' and resid 1 through 352)	C	C
4	4	(chain 'D' and resid 1 through 352)	D	D

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Protein , 1 types, 4 molecules ABCD

#1: Protein	NADP-dependent isopropanol dehydrogenase / CbADH Mass: 38383.547 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridium beijerinckii (bacteria) / Gene: adh / Production host: Escherichia coli (E. coli) References: UniProt: P25984, isopropanol dehydrogenase (NADP+)

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Non-polymers , 5 types, 374 molecules

#2: Chemical	ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂₁H₂₇N₇O₁₄P₂ / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Chemical	ChemComp-2PE / NONAETHYLENE GLYCOL Mass: 414.488 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₁₈H₃₈O₁₀ / Comment: precipitant*YM
#4: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#5: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Mg
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 356 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.69 Å³/Da / Density % sol: 54.28 %
Crystal grow	Temperature: 290 K / Method: vapor diffusion / Details: 900 mM sodium citrate, 100 mM imidazole pH 8

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 28, 2018
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97625 Å / Relative weight: 1
Reflection	Resolution: 2.192→74.165 Å / Num. obs: 83162 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / B_iso Wilson estimate: 34.89 Å² / CC_1/2: 0.997 / R_merge(I) obs: 0.096 / R_rim(I) all: 0.115 / Net I/σ(I): 7.5
Reflection shell	Resolution: 2.192→2.229 Å / Redundancy: 2.2 % / R_merge(I) obs: 1.061 / Num. unique obs: 3576 / CC_1/2: 0.347 / R_rim(I) all: 1.346 / % possible all: 84.4

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Processing

Software

Name	Version	Classification
PHENIX	1.16_3549	refinement
PHENIX	1.16_3549	refinement
xia2		data reduction
xia2		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1kev

1kev

Resolution: 2.2→69.01 Å / SU ML: 0.255 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.699
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.208	4038	4.88 %	random
R_work	0.1636	78733	-	-
obs	0.1658	82771	98.42 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 45.12 Å²

Refinement step

Cycle: LAST / Resolution: 2.2→69.01 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10666	0	332	356	11354

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0075	11209
X-RAY DIFFRACTION	f_angle_d	1.0277	15105
X-RAY DIFFRACTION	f_chiral_restr	0.061	1673
X-RAY DIFFRACTION	f_plane_restr	0.0055	1906
X-RAY DIFFRACTION	f_dihedral_angle_d	12.9819	6675

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.2-2.22	0.2752	124	0.2494	2256	X-RAY DIFFRACTION	81.59
2.22-2.25	0.3045	110	0.258	2400	X-RAY DIFFRACTION	88.38
2.25-2.28	0.3001	130	0.2581	2539	X-RAY DIFFRACTION	93
2.28-2.31	0.3203	127	0.2428	2703	X-RAY DIFFRACTION	97.05
2.31-2.34	0.2886	153	0.2366	2676	X-RAY DIFFRACTION	98.5
2.34-2.38	0.2975	139	0.2254	2717	X-RAY DIFFRACTION	98.89
2.38-2.41	0.2932	132	0.2172	2731	X-RAY DIFFRACTION	99.72
2.41-2.45	0.2771	135	0.2121	2761	X-RAY DIFFRACTION	99.76
2.45-2.49	0.2559	130	0.2008	2768	X-RAY DIFFRACTION	99.83
2.49-2.53	0.2433	139	0.193	2743	X-RAY DIFFRACTION	99.93
2.53-2.58	0.256	126	0.1863	2727	X-RAY DIFFRACTION	99.93
2.58-2.63	0.2659	137	0.1923	2791	X-RAY DIFFRACTION	99.9
2.63-2.68	0.24	156	0.1921	2705	X-RAY DIFFRACTION	99.93
2.68-2.74	0.2504	155	0.1788	2722	X-RAY DIFFRACTION	99.79
2.74-2.8	0.2365	163	0.1802	2746	X-RAY DIFFRACTION	99.97
2.8-2.87	0.2274	135	0.1753	2743	X-RAY DIFFRACTION	99.93
2.87-2.95	0.2285	148	0.1757	2741	X-RAY DIFFRACTION	99.86
2.95-3.04	0.2454	130	0.1785	2791	X-RAY DIFFRACTION	99.97
3.04-3.14	0.2112	142	0.1818	2751	X-RAY DIFFRACTION	99.86
3.14-3.25	0.2268	126	0.1823	2744	X-RAY DIFFRACTION	100
3.25-3.38	0.251	136	0.1731	2773	X-RAY DIFFRACTION	99.83
3.38-3.53	0.2017	141	0.1587	2746	X-RAY DIFFRACTION	99.83
3.53-3.72	0.1792	158	0.1505	2751	X-RAY DIFFRACTION	99.76
3.72-3.95	0.1679	137	0.1355	2799	X-RAY DIFFRACTION	99.93
3.95-4.26	0.1536	136	0.1219	2752	X-RAY DIFFRACTION	99.93
4.26-4.68	0.1523	141	0.1158	2766	X-RAY DIFFRACTION	99.93
4.68-5.36	0.1517	157	0.129	2768	X-RAY DIFFRACTION	99.93
5.36-6.75	0.2101	142	0.1542	2799	X-RAY DIFFRACTION	99.97
6.75-69.01	0.1794	153	0.1417	2824	X-RAY DIFFRACTION	99.3

Refinement TLS params.

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

ID	L11 (°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)
1	2.67172250585	0.558904891743	0.705155568018	2.42568282191	0.00542847714474	1.67228509596	0.099129060893	-0.379762414275	0.0396767547304	0.267835048822	-0.0492206481587	-0.0975731036771	0.0175179227718	-0.0380406083775	-0.0491425919459	0.284412866664	0.00228408735696	0.022392425761	0.301967751832	0.0135880240386	0.227206810127	51.4677439934	-20.505958427	52.1118508377
2	2.45629872332	-0.607196207722	-0.00732570753378	2.47380311146	-0.223683538665	1.23456929407	0.0697962643153	-0.0891377159923	0.460827921956	0.04743172798	-0.0479730752329	-0.16243245053	-0.225007918607	0.138318150457	-0.0294660151937	0.258588083957	-0.0492299607013	0.0132300128122	0.259486693743	-0.00991060605683	0.325111759886	42.1096904067	-0.753570406932	36.2396522396
3	4.15928683536	1.94070856802	2.65540475199	4.23568421844	1.61505680772	2.07737943957	-0.106920271344	-0.293403623688	0.617259319413	0.370528101964	-0.0607302432798	-0.134456554235	-0.327022708274	0.437813766884	0.168357464695	0.270044467457	-0.00243040879589	0.0301371937099	0.365418578832	-0.0285157253523	0.420936879348	61.4598235086	-6.61134374534	47.407100511
4	2.68425555246	-0.219807161449	-0.146615413743	2.04715174277	0.447342266752	5.56100414993	0.159598683734	0.154419110338	0.658382736114	-0.0185660544859	-0.0277989187992	0.381509936516	-0.859965444245	-0.0889656423172	-0.0513941480486	0.410318638511	0.0992484035326	0.0261210248445	0.297719075917	0.0643106411435	0.603647115343	4.51292060539	9.79603778492	23.4229206366
5	4.65089806935	-0.833133628636	-0.196189971304	0.784825053926	-0.135718515791	2.08451243824	0.146037070202	0.180497615586	0.660131980025	-0.136523636971	-0.0849339992043	0.117939384488	-0.165957261471	-0.186067710212	-0.0405830254362	0.273049823919	0.0368517600337	0.00838847144905	0.217594491598	0.0476167020917	0.369655094839	10.5693592394	1.2959339843	21.4117180389
6	2.17316539859	-0.429195914477	3.14838058256	5.05179693526	-3.77698905892	7.07694830623	-0.0613463543073	-0.0140966760432	0.0673443587622	-0.13650499739	-0.0719259344374	-0.0709035263942	0.194457221189	-0.128247723643	0.140394759647	0.189533582214	-0.0222097750858	0.0745059845226	0.228281832615	-0.0328654593613	0.300925186978	15.9006545311	-12.7105828004	36.6238999386
7	8.23299699078	-0.62092711247	-0.781113922469	2.47187037849	-2.94106747357	5.36421548032	-0.0508975513664	-0.168488094334	0.271237659474	0.186154205365	0.161361442751	0.300840037153	-0.00171470847185	-0.73842762722	-0.038722370614	0.187238472543	-0.0456226481037	0.0331905982449	0.289863907107	-0.039149857251	0.255787952667	7.55020759269	-13.7602645597	41.8668885784
8	5.62776597707	0.359550822833	-0.850453329507	3.59708128383	-1.01692927212	7.90399276873	-0.0560091173249	-0.478637653582	0.0821473671018	0.464270200694	-0.0395308267971	0.209754742664	0.067176512782	-0.141424479212	0.0757341633202	0.252743861988	-0.0432341998159	0.049709751575	0.221781811582	-0.0730409268896	0.222198127035	15.6196961539	-13.5915337011	51.6463492374
9	2.57021155505	0.467704301153	1.20656275738	0.916133318978	-0.188766101058	2.23959416458	0.0399261988102	-0.165263659669	0.379009904153	0.163189024729	-0.13244353565	0.203126814416	-0.166559288307	-0.110891902888	0.120805414221	0.252261554419	0.00209801852623	0.0540084964662	0.220589537947	-0.0440423010756	0.318804490677	21.3750199501	-6.33067260029	39.327910455
10	5.67627340854	-4.15260292288	-2.67542177555	3.97418035657	1.81238876282	2.60921512018	0.0483543367343	-0.00542081062775	0.238166596932	0.155461546785	-0.20980706721	0.632966924949	0.00380316228611	-0.443679300339	0.202733744405	0.168904598236	-0.0256965488512	-0.0179103287369	0.387156538542	-0.0495109479721	0.496919785008	-2.31375461189	-9.51236845285	31.6750266167
11	4.2677298338	-0.7286299314	-3.40051844774	8.99404152207	-2.89591311556	7.00994423459	0.287190509188	-0.243050747336	0.787993143147	0.577497929227	0.146754655545	0.491636399624	-1.31956204493	-0.514600035905	-0.382430895937	0.371852685567	0.0978004617383	0.101140219378	0.3802839341	-0.0668052857496	0.553889188604	-4.13863014387	4.15880090922	36.3446809732
12	4.03827947747	1.29025676602	2.3418263309	5.28388812439	1.89754586657	3.70345392896	0.0733838099969	0.396126701326	-0.464770084159	-0.248314831591	0.0468909895545	-0.104054268238	0.252399770016	0.331191271613	-0.121929426099	0.387116282645	-0.0054791619839	0.0396644085085	0.284364883504	0.0566180826544	0.260006975535	28.0089614675	-51.1134150623	39.3463740047
13	1.17125992212	-0.472332972783	0.533987149931	1.56952544634	-0.792606541777	1.21020898795	0.101479336647	-0.104414158517	-0.134032415476	-0.0830838882343	-0.0260432929188	0.151979167354	0.199919723979	-0.15843285359	-0.0883238586572	0.311406800736	-0.0315400147877	0.0118585599368	0.240381154768	-0.0237342946522	0.228620631398	22.1256926077	-36.0623813116	33.1828686188
14	3.49819881718	0.115406302835	-1.20324806111	1.81691924168	-0.301093529408	2.35142864281	0.0747042616679	0.596817871299	-0.139129369035	-0.356448129919	-0.0416072569353	0.0881236086279	0.241191094794	-0.120659631042	-0.0500733985701	0.365451647129	0.0140298208245	-0.0345905349164	0.309896310241	-0.0322754198733	0.206038521397	21.0334732576	-29.3042608436	12.1311510899
15	3.06112540295	0.613993091217	0.367665035762	3.29179651525	-0.479030224118	1.5920722182	0.0937736991541	0.0946604599676	-0.413523079233	0.00817941520186	0.0492893649377	0.388184951453	0.466918095564	-0.237152703801	-0.157280461411	0.375457325052	-0.100334780556	0.00396038799547	0.286004388466	0.0215483363978	0.277362541662	14.8370432512	-44.3494088514	36.2231878237
16	2.0506087935	0.581128756875	-1.16990742606	1.15745223562	-0.617130702824	2.00692436907	0.0217916015455	0.30669218378	0.140400469214	-0.208736726689	0.00903273183369	0.0662729265633	-0.0481326649471	-0.0925680396654	-0.0177460582215	0.349896054998	0.0232972669638	-0.00787975937969	0.345359574939	0.121540001153	0.326894883593	34.8039955796	-2.46108870055	-0.292252891298
17	3.0991863924	0.859034802612	0.110357387261	2.19351480778	0.221667759938	1.12105798725	0.041043356851	0.400019837059	-0.0642560145283	-0.318074817865	-0.0794066063869	-0.266180699301	0.163435483949	0.208975711713	0.0377748201567	0.319162070747	0.0871517814853	0.0651822072267	0.313345026131	0.0326032063514	0.216652703746	45.8297577076	-24.3111114245	15.5221981139
18	2.45244532958	0.097724169737	-0.38680928671	1.34134703515	-0.431235453227	4.03058209629	0.0304635966785	0.172883857897	-0.0181546566211	-0.302033970935	-0.025832465242	-0.0311271301209	-0.0165554371923	0.383067119329	-0.00991404341356	0.350354072858	0.00514255577319	0.07661616433	0.305246288734	0.113234500799	0.365398507078	48.5291387746	-4.64285767014	3.24126222006

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 150 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 151 through 310 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 311 through 352 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 1 through 79 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 80 through 150 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 151 through 176 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 177 through 210 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 211 through 245 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 246 through 310 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 311 through 326 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 327 through 352 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 1 through 79 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 80 through 210 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 211 through 292 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 293 through 355 )
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 1 through 150 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 151 through 292 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 293 through 354 )

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