PDB-6wy9: Tcur3481-Tcur3483 steroid ACAD G363A variant

ID or keywords:

Entry

Database: PDB / ID: 6wy9

Title

Tcur3481-Tcur3483 steroid ACAD G363A variant

Components

(Acyl-CoA dehydrogenase domain protein ...) x 2

Keywords

OXIDOREDUCTASE / Steroid degradation / Acyl-CoA acyl dehydrogenase / flavin

Function / homology

Function and homology information

oxidoreductase activity, acting on the CH-CH group of donors / acyl-CoA dehydrogenase activity / flavin adenine dinucleotide binding
Similarity search - Function

Biological species

Thermomonospora curvata (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2 Å

Authors

Kimber, M.S. / Stirling, A.J. / Seah, S.Y.K.

Funding support

Canada, 2items

Citation

Journal: Biochemistry / Year: 2020
Title: A Key Glycine in Bacterial Steroid-Degrading Acyl-CoA Dehydrogenases Allows Flavin-Ring Repositioning and Modulates Substrate Side Chain Specificity.
Authors: Stirling, A.J. / Gilbert, S.E. / Conner, M. / Mallette, E. / Kimber, M.S. / Seah, S.Y.K.

History

Deposition	May 12, 2020	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 28, 2020	Provider: repository / Type: Initial release
Revision 1.1	Nov 11, 2020	Group: 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 1.2	Oct 18, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6wy9.cif.gz	369.2 KB	Display	PDBx/mmCIF format
PDB format	pdb6wy9.ent.gz	249.4 KB	Display	PDB format
PDBx/mmJSON format	6wy9.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6wy9_validation.pdf.gz	792 KB	Display	wwPDB validaton report
Full document	6wy9_full_validation.pdf.gz	812.5 KB	Display
Data in XML	6wy9_validation.xml.gz	31.9 KB	Display
Data in CIF	6wy9_validation.cif.gz	44.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/wy/6wy9 ftp://data.pdbj.org/pub/pdb/validation_reports/wy/6wy9	HTTPS FTP

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Related structure data

Related structure data	6wy8SC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6wy8-d 4l1f-1 2eba-1 3swo-d 3oib-2 2vig-1 1rx0-d 4kto-d 5jsc-1 5lnx-1 Search similar-shape structures by Omokage search (details) 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

Deposited unit

A: Acyl-CoA dehydrogenase domain protein Tcur3483

B: Acyl-CoA dehydrogenase domain protein Tcur3481

hetero molecules

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

1

A: Acyl-CoA dehydrogenase domain protein Tcur3483

B: Acyl-CoA dehydrogenase domain protein Tcur3481

hetero molecules

A: Acyl-CoA dehydrogenase domain protein Tcur3483

B: Acyl-CoA dehydrogenase domain protein Tcur3481

hetero molecules

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

Unit cell

Length a, b, c (Å)	99.500, 123.200, 139.210
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	24
Space group name H-M	I2₁2₁2₁
Space group name Hall	I2b2c
Symmetry operation	#1: x,y,z #2: x,-y,-z+1/2 #3: -x+1/2,y,-z #4: -x,-y+1/2,z #5: x+1/2,y+1/2,z+1/2 #6: x+1/2,-y+1/2,-z+1 #7: -x+1,y+1/2,-z+1/2 #8: -x+1/2,-y+1,z+1/2

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Acyl-CoA dehydrogenase domain protein ... , 2 types, 2 molecules AB

#1: Protein	Acyl-CoA dehydrogenase domain protein Tcur3483 Mass: 44378.254 Da / Num. of mol.: 1 / Mutation: G363A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermomonospora curvata (strain ATCC 19995 / DSM 43183 / JCM 3096 / NBRC 15933 / NCIMB 10081 / Henssen B9) (bacteria) Strain: ATCC 19995 / DSM 43183 / JCM 3096 / NBRC 15933 / NCIMB 10081 / Henssen B9 Gene: Tcur_3483 / Production host: Escherichia coli (E. coli) / References: UniProt: D1AB78
#2: Protein	Acyl-CoA dehydrogenase domain protein Tcur3481 Mass: 38102.945 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermomonospora curvata (strain ATCC 19995 / DSM 43183 / JCM 3096 / NBRC 15933 / NCIMB 10081 / Henssen B9) (bacteria) Strain: ATCC 19995 / DSM 43183 / JCM 3096 / NBRC 15933 / NCIMB 10081 / Henssen B9 Gene: Tcur_3481 / Production host: Escherichia coli (E. coli) / References: UniProt: D1AB76

#1: Protein

Acyl-CoA dehydrogenase domain protein Tcur3483

Mass: 44378.254 Da / Num. of mol.: 1 / Mutation: G363A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Thermomonospora curvata (strain ATCC 19995 / DSM 43183 / JCM 3096 / NBRC 15933 / NCIMB 10081 / Henssen B9) (bacteria)
Strain: ATCC 19995 / DSM 43183 / JCM 3096 / NBRC 15933 / NCIMB 10081 / Henssen B9
Gene: Tcur_3483 / Production host:

Escherichia coli (E. coli) / References: UniProt: D1AB78

#2: Protein

Acyl-CoA dehydrogenase domain protein Tcur3481

Mass: 38102.945 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Thermomonospora curvata (strain ATCC 19995 / DSM 43183 / JCM 3096 / NBRC 15933 / NCIMB 10081 / Henssen B9) (bacteria)
Strain: ATCC 19995 / DSM 43183 / JCM 3096 / NBRC 15933 / NCIMB 10081 / Henssen B9
Gene: Tcur_3481 / Production host:

Escherichia coli (E. coli) / References: UniProt: D1AB76

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Non-polymers , 5 types, 219 molecules

#3: Chemical	ChemComp-FDA / DIHYDROFLAVINE-ADENINE DINUCLEOTIDE Mass: 787.566 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂₇H₃₅N₉O₁₅P₂ / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₀H₂₂O₆ / Comment: precipitant*YM
#5: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C₃H₈O₃
#6: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 202 / 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: 2.59 Å³/Da / Density % sol: 52.45 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 20% PEG 400, 100 mM CaCl2, 10% glycerol, 100 mM HEPES

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
Detector	Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jan 19, 2019
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97949 Å / Relative weight: 1
Reflection	Resolution: 2→49.02 Å / Num. obs: 57970 / % possible obs: 100 % / Redundancy: 8.1 % / B_iso Wilson estimate: 43.71 Å² / CC_1/2: 0.999 / R_rim(I) all: 0.071 / R_sym value: 0.066 / Net I/σ(I): 16.1
Reflection shell	Resolution: 2→2.05 Å / Mean I/σ(I) obs: 2.11 / Num. unique obs: 4216 / CC_1/2: 0.765 / R_sym value: 0.9 / % possible all: 100

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Processing

Software

Name	Version	Classification
PHENIX	1.15.2_3472	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 6WY8

6wy8

Resolution: 2→49.02 Å / SU ML: 0.2164 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.8065
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.202	2897	5 %
R_work	0.17	55060	-
obs	0.1716	57957	99.97 %

Solvent computation

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

Displacement parameters

B_iso mean: 56.81 Å²

Refinement step

Cycle: LAST / Resolution: 2→49.02 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5563	0	149	202	5914

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0136	5848
X-RAY DIFFRACTION	f_angle_d	1.1843	7948
X-RAY DIFFRACTION	f_chiral_restr	0.0717	886
X-RAY DIFFRACTION	f_plane_restr	0.0079	1020
X-RAY DIFFRACTION	f_dihedral_angle_d	18.4581	3386

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 (%)
2-2.03	0.3047	136	0.292	2588	X-RAY DIFFRACTION	99.93
2.03-2.07	0.2835	137	0.2436	2609	X-RAY DIFFRACTION	99.96
2.07-2.11	0.2393	135	0.2117	2569	X-RAY DIFFRACTION	99.96
2.11-2.15	0.2226	137	0.194	2613	X-RAY DIFFRACTION	100
2.15-2.19	0.2116	137	0.1812	2589	X-RAY DIFFRACTION	100
2.19-2.24	0.2099	136	0.1785	2585	X-RAY DIFFRACTION	100
2.24-2.29	0.2148	138	0.177	2623	X-RAY DIFFRACTION	99.93
2.29-2.35	0.2006	136	0.1737	2585	X-RAY DIFFRACTION	99.96
2.35-2.41	0.2135	137	0.1737	2595	X-RAY DIFFRACTION	100
2.41-2.48	0.1942	136	0.1759	2618	X-RAY DIFFRACTION	99.96
2.48-2.56	0.2246	136	0.1817	2585	X-RAY DIFFRACTION	100
2.56-2.65	0.2262	138	0.1763	2606	X-RAY DIFFRACTION	100
2.65-2.76	0.2387	138	0.1719	2624	X-RAY DIFFRACTION	100
2.76-2.88	0.2218	137	0.171	2606	X-RAY DIFFRACTION	100
2.88-3.04	0.1909	138	0.1731	2633	X-RAY DIFFRACTION	99.96
3.04-3.23	0.2179	138	0.1672	2620	X-RAY DIFFRACTION	100
3.23-3.48	0.1757	138	0.1624	2620	X-RAY DIFFRACTION	100
3.48-3.83	0.1916	141	0.1529	2664	X-RAY DIFFRACTION	100
3.83-4.38	0.1678	139	0.1512	2660	X-RAY DIFFRACTION	100
4.38-5.52	0.1983	142	0.1644	2681	X-RAY DIFFRACTION	99.96
5.52-49.02	0.2093	147	0.1801	2787	X-RAY DIFFRACTION	99.8

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	1.96727526677	0.636334689044	-1.2626960231	3.96090938279	3.93588532675	5.90327425181	0.352640356952	0.511677086948	-0.0870609531634	-0.0272034707317	-0.0977156719682	-0.293671337301	0.460413488618	-0.0123366394883	-0.216304714259	0.543485385676	0.223009436513	-0.04786170068	0.89114628557	-0.0263706730575	0.426216704471	-35.393705131	23.1753555879	-19.8709678056
2	3.77174677025	-0.0580048331141	0.00239301754094	1.17608613727	-1.19600334656	4.63314402084	-0.0295240538749	0.747287432068	0.005009827861	-0.0683954994792	0.0626895395142	0.203871470874	-0.368907835114	-1.50083138361	-0.0460198580128	0.455565022997	0.13458746985	-0.0838880303244	0.854700823707	-0.106547034566	0.399910416766	-29.4606931729	19.4684317799	-43.5585030122
3	1.05023106313	0.573181130139	-0.97551860192	0.719625735588	-0.624554699463	2.93506221645	0.0779628103566	0.134787422044	0.0494959466949	-0.0576220288821	0.0614754008804	0.253308674332	0.0274026721295	-0.555145905715	-0.166895309628	0.283032933932	0.0259409354442	-0.00268122599731	0.390606854473	-0.0109866621767	0.411219911826	-14.9494966324	27.8281510873	-19.017031299
4	6.15616318274	7.50565705233	5.73821944089	9.17492186475	6.83822899995	5.40885281196	-0.232906055722	1.39882868728	-1.23433406513	-0.113033072501	0.668825020689	-0.98563274324	0.283869855543	1.35406968159	-0.51386501099	0.55591564958	0.12494653241	0.0120442893085	0.695498747666	-0.00387954671574	0.494330499152	13.7585264155	-1.81833574466	-25.6038346395
5	8.1190113938	-0.109692473208	1.68750190977	0.486277190486	1.21073764055	4.2447545846	0.154887509215	-0.0431806302514	-0.746875550693	0.18710422211	-0.0665267538342	0.205314412144	0.564557981465	-0.130671074746	-0.0638630683398	0.647622946829	-0.0168768502886	-0.0390073272135	0.241199171133	-0.015939927304	0.467187631408	-3.48864365231	-6.15240958805	-21.4159146687
6	6.20274992509	1.2132519491	0.231242087439	3.10106078033	2.33699100651	4.70891406645	-0.0382052827396	-0.42990434061	0.0293134948972	0.192138066282	0.0099836793462	-0.678057023603	0.229441620537	0.469587530473	0.0382872590126	0.411427518759	0.100081100261	-0.0732416198622	0.3007325148	-0.0115494700583	0.395226478585	13.4714332613	-0.816055787971	-16.3249773556
7	4.6600142408	-2.30830743666	3.28546883584	4.70453529275	-2.43798817895	9.07407494129	-0.242650752164	-0.182131859386	-0.0709295379978	0.261201354401	0.0726348742434	-0.220747247721	0.235821696007	0.498820456178	0.290918522049	0.512194406114	0.083476558871	-0.0555171162315	0.340269571776	0.0199930884647	0.403718262099	7.54286230779	0.150326470684	-9.01572430908
8	6.43322387691	-2.67127345708	-1.80345071635	7.31887021614	1.57501205253	0.634487436478	-0.165413933232	-0.727388228109	-0.755265344188	0.565342513173	0.274516193014	-0.334778733149	0.737274631932	0.329158703183	-0.124189684278	0.793127673658	0.113435368473	-0.0956765439658	0.463512514834	0.105095316036	0.496898381507	8.93452207136	-8.01771399435	-3.4992362892
9	2.68263906615	0.125016075829	0.930217209728	3.24550431727	-0.286447992812	4.16035896456	0.000341842877841	-0.406509276864	-0.253210859086	0.629969615003	-0.0505323242599	-0.0209224372634	0.799643118913	-0.0850394186501	0.00711972890478	0.683843268663	-0.0148900623232	0.00152304565686	0.411651401827	0.0629864576717	0.392739466595	-1.95538942511	2.25048180594	3.74474634152
10	0.952526008978	-0.143335886848	0.230754042875	1.06333903185	-0.436188061994	2.05647020999	0.0597623466849	-0.0306469963412	-0.116608403561	0.0942343573271	-0.0155415586513	-0.0188088201823	0.268124500862	0.0949142235616	-0.0530646986884	0.387597225699	0.030024044731	-0.034803227401	0.293201714	-0.0285630006865	0.432294743889	0.712097238374	9.79127772394	-18.3029995595
11	6.54747163616	-3.7518340413	4.57823973805	5.29325148977	-4.49177872086	4.04655347513	-0.00557854139574	-0.398544849448	-0.173940001976	0.217919225318	-0.00122975592611	-0.322306293404	0.227600159968	0.110421643435	0.0746455434047	0.314405456287	0.0806657456352	-0.0241078591838	0.367912332675	-0.0350082002264	0.385655987548	11.9553754491	18.2116859545	-20.8826539127
12	1.28671651348	0.11258798605	1.50619580736	0.887391312523	0.162522961776	3.00831096724	0.0514115754267	-0.0530829446736	-0.109779005372	-0.0220447133037	-0.0344345871137	0.0689069882367	0.256244485387	-0.0625459290069	0.00909808797748	0.333568869653	0.0415912610301	0.00405050542404	0.307175092722	0.00355466655339	0.369903784399	-2.1170092853	14.7557339985	-22.3029438665
13	7.04387489962	6.38282952124	1.49673419582	8.60690641401	4.41807403093	3.88310345948	0.44071872302	-0.468688460471	-0.368874922809	0.457156614655	-0.164257502697	-0.241378831022	0.46541709432	-0.048830929149	-0.369921077791	0.354027529729	0.0297368451047	-0.0486474897045	0.31004611808	0.0480501292604	0.305125386551	7.45848539592	23.3148926099	-2.98060083616

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 6 through 94 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 95 through 242 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 243 through 384 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 5 through 23 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 24 through 49 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 50 through 81 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 82 through 100 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 101 through 122 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 123 through 191 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 192 through 259 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 260 through 294 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 295 through 342 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 343 through 364 )

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Acyl-CoA dehydrogenase domain protein ... , 2 types, 2 molecules AB

-
Non-polymers , 5 types, 219 molecules

-
Details

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

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About Yorodumi

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News

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Feb 9, 2022. New format data for meta-information of EMDB entries

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Aug 12, 2020. Covid-19 info

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Mar 5, 2020. Novel coronavirus structure data

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Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

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Jul 12, 2017. Major update of PDB

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-Related structure data

-Links

-Assembly

-Components

-Acyl-CoA dehydrogenase domain protein ... , 2 types, 2 molecules AB

-Non-polymers , 5 types, 219 molecules

-Details

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

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Acyl-CoA dehydrogenase domain protein ... , 2 types, 2 molecules AB

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Non-polymers , 5 types, 219 molecules

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