PDB-7dn1: Hetero-oligomers of SCR-SCR2 crystal structure with NADPH

ID or keywords:

Entry

Database: PDB / ID: 7dn1

Title

Hetero-oligomers of SCR-SCR2 crystal structure with NADPH

Components

(S)-specific carbonyl reductase
Carbonyl Reductase

Keywords

OXIDOREDUCTASE / Rossman fold / tetramer / tag-free / wild type with NADPH

Function / homology

oxidoreductase activity, acting on NAD(P)H, oxygen as acceptor / Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / metabolic process / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding domain superfamily / Chem-NDP / Carbonyl Reductase / (S)-specific carbonyl reductase

Function and homology information

Biological species

Candida parapsilosis (yeast)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.74 Å

Authors

Li, Y.H. / Zhang, R.Z. / Forouhar, F. / Wang, C. / Montelione, G.T. / Szyperski, T. / Xu, Y. / Hunt, J.F.

Funding support

China, 2items

Citation

Journal: EMBO J / Year: 2022
Title: Oligomeric interactions maintain active-site structure in a noncooperative enzyme family.
Authors: Yaohui Li / Rongzhen Zhang / Chi Wang / Farhad Forouhar / Oliver B Clarke / Sergey Vorobiev / Shikha Singh / Gaetano T Montelione / Thomas Szyperski / Yan Xu / John F Hunt /

Abstract: The evolutionary benefit accounting for widespread conservation of oligomeric structures in proteins lacking evidence of intersubunit cooperativity remains unclear. Here, crystal and cryo-EM ...

History

Deposition	Dec 8, 2020	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Apr 6, 2022	Provider: repository / Type: Initial release
Revision 1.1	Jul 27, 2022	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2	Aug 10, 2022	Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.3	Sep 14, 2022	Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.4	Nov 29, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7dn1.cif.gz	279.3 KB	Display	PDBx/mmCIF format
PDB format	pdb7dn1.ent.gz	186.8 KB	Display	PDB format
PDBx/mmJSON format	7dn1.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7dn1_validation.pdf.gz	1.1 MB	Display	wwPDB validaton report
Full document	7dn1_full_validation.pdf.gz	1.1 MB	Display
Data in XML	7dn1_validation.xml.gz	26.5 KB	Display
Data in CIF	7dn1_validation.cif.gz	36.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/dn/7dn1 ftp://data.pdbj.org/pub/pdb/validation_reports/dn/7dn1	HTTPS FTP

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Related structure data

Related structure data	32211C 32212C 32213C 7dldC 7dllC 7dlmC 7dmgC 7vyqC 3ctmS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	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	#34 - Oct 2002 Dihydrofolate Reductase similarity (1) #90 - Jun 2007 Fatty Acid Synthase similarity (1) #77 - May 2006 Glucose Oxidase similarity (1) #57 - Sep 2004 Catalase similarity (1)

Deposited unit

A: Carbonyl Reductase

B: (S)-specific carbonyl reductase

hetero molecules

61.8 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Carbonyl Reductase

B: (S)-specific carbonyl reductase

hetero molecules

A: Carbonyl Reductase

B: (S)-specific carbonyl reductase

hetero molecules

defined by author&software
Evidence: gel filtration
124 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	69.589, 114.676, 127.752
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	20
Space group name H-M	C222₁
Space group name Hall	C2c2
Symmetry operation	#1: x,y,z #2: x,-y,-z #3: -x,y,-z+1/2 #4: -x,-y,z+1/2 #5: x+1/2,y+1/2,z #6: x+1/2,-y+1/2,-z #7: -x+1/2,y+1/2,-z+1/2 #8: -x+1/2,-y+1/2,z+1/2

Components on special symmetry positions

ID	Model	Components
1	1	A-506- HOH
2	1	B-401- HOH

#1: Protein	Carbonyl Reductase / S-reductase Mass: 30204.873 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Candida parapsilosis (yeast) / Gene: DQ675534 / Production host: Escherichia coli (E. coli) References: UniProt: B2KJ46, Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor
#2: Protein	(S)-specific carbonyl reductase / Stereospecific carbonyl reductase 2 Mass: 30108.854 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Candida parapsilosis (yeast) / Gene: scr2, scrII / Production host: Escherichia coli (E. coli) / References: UniProt: D5G304
#3: Chemical	ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE Mass: 745.421 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₁H₃₀N₇O₁₇P₃ / Feature type: SUBJECT OF INVESTIGATION
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 243 / Source method: isolated from a natural source / Formula: H₂O
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: 2.12 Å³/Da / Density % sol: 41.93 %
Crystal grow	Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 1 M MES, 30% PEG 300, pH 6.5

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9793 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 26, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9793 Å / Relative weight: 1
Reflection	Resolution: 1.74→34.19 Å / Num. obs: 100531 / % possible obs: 98.5 % / Redundancy: 10.9 % / B_iso Wilson estimate: 23.53 Å² / CC_1/2: 0.99 / Net I/σ(I): 11
Reflection shell	Resolution: 1.74→1.76 Å / Num. unique obs: 3906 / CC_1/2: 0.97

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Processing

Software

Name	Version	Classification
PHENIX	1.18.2_3874	refinement
iMOSFLM		data reduction
SCALA		data scaling
REFMAC		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3CTM

3ctm

Resolution: 1.74→34.19 Å / SU ML: 0.1374 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.3748
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2066	3854	3.83 %
R_work	0.1661	96677	-
obs	0.1677	100531	98.94 %

Solvent computation

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

Displacement parameters

B_iso mean: 38.18 Å²

Refinement step

Cycle: LAST / Resolution: 1.74→34.19 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4705	0	96	243	5044

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0119	4961
X-RAY DIFFRACTION	f_angle_d	2.0938	6862
X-RAY DIFFRACTION	f_chiral_restr	0.0831	767
X-RAY DIFFRACTION	f_plane_restr	0.009	892
X-RAY DIFFRACTION	f_dihedral_angle_d	8.8847	728

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 (%)
1.74-1.76	0.2605	110	0.2373	2731	X-RAY DIFFRACTION	77.81
1.76-1.78	0.2609	128	0.2373	3493	X-RAY DIFFRACTION	99.78
1.78-1.81	0.28	153	0.2188	3461	X-RAY DIFFRACTION	99.78
1.81-1.83	0.2465	141	0.2127	3444	X-RAY DIFFRACTION	99.67
1.83-1.86	0.2386	121	0.2035	3522	X-RAY DIFFRACTION	99.48
1.86-1.88	0.245	150	0.201	3443	X-RAY DIFFRACTION	99.78
1.88-1.91	0.2229	149	0.2095	3507	X-RAY DIFFRACTION	99.92
1.91-1.94	0.2891	125	0.194	3452	X-RAY DIFFRACTION	99.75
1.94-1.98	0.2632	147	0.197	3510	X-RAY DIFFRACTION	100
1.98-2.01	0.2524	129	0.181	3479	X-RAY DIFFRACTION	99.75
2.01-2.05	0.1958	143	0.1804	3494	X-RAY DIFFRACTION	99.75
2.05-2.09	0.21	134	0.1781	3493	X-RAY DIFFRACTION	99.97
2.1-2.14	0.2212	121	0.1809	3440	X-RAY DIFFRACTION	99.86
2.14-2.19	0.2298	148	0.1721	3506	X-RAY DIFFRACTION	100
2.19-2.25	0.2004	157	0.1694	3505	X-RAY DIFFRACTION	99.7
2.25-2.31	0.2274	129	0.1738	3476	X-RAY DIFFRACTION	99.94
2.31-2.37	0.195	145	0.1815	3465	X-RAY DIFFRACTION	99.92
2.37-2.45	0.2427	150	0.174	3471	X-RAY DIFFRACTION	99.89
2.45-2.54	0.2326	140	0.1745	3506	X-RAY DIFFRACTION	100
2.54-2.64	0.2325	136	0.1682	3448	X-RAY DIFFRACTION	99.94
2.64-2.76	0.2077	144	0.1752	3493	X-RAY DIFFRACTION	99.73
2.76-2.9	0.2077	136	0.1784	3551	X-RAY DIFFRACTION	99.95
2.9-3.09	0.2254	141	0.1733	3426	X-RAY DIFFRACTION	99.94
3.09-3.32	0.1832	145	0.1553	3494	X-RAY DIFFRACTION	99.97
3.33-3.66	0.1761	117	0.1466	3507	X-RAY DIFFRACTION	99.83
3.66-4.19	0.1758	138	0.14	3504	X-RAY DIFFRACTION	99.86
4.19-5.27	0.165	147	0.1369	3452	X-RAY DIFFRACTION	99.67
5.27-34.19	0.2138	130	0.162	3404	X-RAY DIFFRACTION	97.01

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	1.70172720847	1.6473377524	0.962327348943	5.28773905541	-0.430398648759	1.04937154994	0.183132937578	-0.255831190608	0.702054757056	0.1709090453	-0.104301873871	0.452866490941	-0.0755571862137	-0.197277387952	-0.127662660977	0.194471084141	0.0339528238253	0.0613293387506	0.231516114052	-0.067504247989	0.450873890581	-8.33062542246	14.4549706433	4.31192976714
2	0.681751456215	0.306362158106	-0.28802350994	0.781287653551	0.502953440861	0.738745927329	-0.00098432343821	-0.477279394011	0.622428350195	0.257454559829	0.0568373253774	-0.0220669263437	-0.228047942276	0.0211448358215	0.0369721677649	0.317029002314	-0.0277405937029	0.0229946865115	0.403635349814	-0.333977405318	0.664894257113	16.8475017975	24.7797105453	17.7455525987
3	0.0313783169177	0.128488612909	-0.0273467441585	1.33301206231	-0.257220971771	0.0509796373831	0.0504232016166	-0.402203984535	0.492103935358	0.279294150893	-0.0492012434594	-0.106832888002	-0.0867326954964	-0.0477683795674	-0.0430389987245	0.419448870341	-0.0650461905191	-0.0274994835042	0.647284397065	-0.461432871552	0.764675476296	18.3602272827	26.8360016707	25.8702649326
4	0.404060894746	-1.23502811499	-0.249217982868	5.9129266971	1.21130834594	0.620212508997	-0.0969459030577	-0.19151380097	0.0994440225161	0.737989829727	0.119051936881	0.103854009676	-0.11372805083	-0.0666820214444	0.209783274503	0.392452719025	-0.0321879635569	0.0660933454042	0.885932397219	-0.409296592576	0.510061156094	7.9926633367	18.8129614329	30.3040284335
5	2.73585951952	-1.4866608306	-1.52437850763	3.45969450956	1.35157238107	0.95267563301	-0.126271713162	-1.20985576884	0.177675322166	0.417385215037	0.196690389643	-0.32660238594	0.117954604138	0.11691854857	-0.0946184394352	0.270158386627	-0.0670761316186	-0.0738301740619	0.594898252003	-0.0662284556877	0.286684493629	23.0747652559	2.4297990173	22.179445266
6	3.9923740278	-2.16270591258	0.151476482764	2.6250380507	-0.650316131995	1.87848559597	-0.207927192446	-0.827783159866	0.222140042865	0.42928267877	0.128179987049	0.0856451537439	-0.089953191304	0.00987353317376	0.0829024779501	0.273530875294	-0.0656247108524	0.0398352188997	0.550028590368	-0.218519421221	0.291730753231	7.72335401679	10.7019174529	22.7088547269
7	3.12874377792	-0.697474974303	-0.146383643345	0.656379132203	-0.150550146977	0.387925788607	0.0828284305077	-0.429466033917	0.312538931597	0.0443463954869	-0.0861675390899	-0.0578215578348	-0.022836212291	-0.0901366466183	0.00253395591006	0.191790070695	-0.0227484444472	0.00933035116659	0.224150146379	-0.0820349109247	0.200067573283	15.6360492624	5.48591887825	11.9780382052
8	0.132245782949	0.215555717543	-0.509737212698	2.79385418194	0.375411424287	2.55068269763	-0.178418421651	-1.14803457781	0.558776240889	0.478599291684	0.229078411536	-0.701898559062	0.139285636657	0.576472138571	-0.0312889622147	0.299340796971	0.0280837208301	-0.0600204296315	0.431750744083	-0.157947949057	0.389575346488	24.8697100435	11.7529814763	12.7636000249
9	3.49270696085	-2.91982600764	-1.7117904677	4.44901650808	1.07288648156	0.901507664382	0.0250616429167	-0.400881212146	0.686427369082	0.0858375275759	0.0498332952443	-0.263368697723	-0.111114484146	0.0740463529407	-0.0887590168238	0.192838910336	-0.0228312076612	-0.0155186695873	0.169974959421	-0.0737131451317	0.339927365612	29.1173534147	13.9291883967	5.96038362019
10	2.3974033971	0.972761209459	0.543599068218	0.749088946101	-0.426090559864	1.30138472864	0.043340664077	-0.19967034718	0.329955283427	-0.0910260412937	0.0402927343027	0.0172108572918	-0.0305767879061	-0.00134859983602	-0.0805147850201	0.198774941343	-0.0143263175695	-0.00253879969254	0.0969052461737	-0.0160252086463	0.258411314055	14.6370421803	12.7861555971	2.97865749495
11	0.984333867957	-0.710048835609	0.161480393671	1.46595279462	-0.109273609732	0.419015467524	0.0591610616024	0.268943244771	0.86574400116	-0.0877442191959	0.00820563527408	-0.174122617843	-0.133033143991	0.0393155530355	0.0364465054454	0.247771779708	-0.00442564333587	0.0643578400322	0.260097911366	0.16005197341	0.611593977641	22.2189035936	22.6969910119	-8.48847032406
12	0.192513930307	0.251867498611	-0.0183731661444	2.73648088766	0.659137233564	0.198458217436	-0.0460532072677	0.511459388859	0.618194361739	-0.33929018055	-0.143607547166	0.176218847225	-0.273938984722	0.14072584659	0.107804262706	0.445430073893	0.0870655846907	0.0313481795845	0.59542640602	0.411184368133	0.778234932764	14.7662517134	28.5882606968	-22.5845085792
13	1.86133382241	0.677181498954	-0.954759191136	2.97599603982	-0.346629090784	0.75393660656	0.0659013442941	0.847899156313	0.373303692589	-0.231909795329	-0.0550225632439	0.112917955574	-0.0497639569536	-0.0961356838438	-0.00480720380024	0.225393346481	0.0703292933226	-0.0111343361359	0.414782356438	0.130711251948	0.2682640328	11.2624387097	9.07356684122	-17.4711299309
14	2.62040953424	0.463900641872	-0.962047407634	1.42537500828	0.121491745587	0.602979078246	0.0757029584593	0.317266086402	0.640314017744	-0.072734687581	-0.0382171208631	0.177709571184	-0.0629803647594	-0.118301254733	-0.0254615883812	0.196886311136	0.0301567078321	-0.00779028552447	0.187652849257	0.0643308536891	0.278560724885	8.64825541658	13.2313529649	-5.77648156058

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

ID	Refine TLS-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	chain 'A' and (resid 0 through 26 )	A	A	0 - 26	1 - 27
2	2	chain 'A' and (resid 27 through 70 )	A	A	27 - 70	28 - 71
3	3	chain 'A' and (resid 71 through 94 )	A	A	71 - 94	72 - 96
4	4	chain 'A' and (resid 95 through 109 )	A	A	95 - 109	97 - 111
5	5	chain 'A' and (resid 110 through 141 )	A	A	110 - 141	112 - 146
6	6	chain 'A' and (resid 142 through 162 )	A	A	142 - 162	147 - 172
7	7	chain 'A' and (resid 163 through 207 )	A	A	163 - 207	173 - 225
8	8	chain 'A' and (resid 208 through 228 )	A	A	208 - 228	226 - 253
9	9	chain 'A' and (resid 229 through 258 )	A	A	229 - 258	254 - 285
10	10	chain 'A' and (resid 259 through 279 )	A	A	259 - 279	286 - 312
11	11	chain 'B' and (resid 0 through 70 )	B	B	0 - 70	1 - 71
12	12	chain 'B' and (resid 71 through 109 )	B	B	71 - 109	72 - 111
13	13	chain 'B' and (resid 110 through 189 )	B	B	110 - 189	112 - 205
14	14	chain 'B' and (resid 190 through 279 )	B	B	190 - 279	206 - 312

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