PDB-8a56: Coenzyme A-persulfide reductase (CoAPR) from Enterococcus faecalis

ID or keywords:

Entry

Database: PDB / ID: 8a56

Title

Coenzyme A-persulfide reductase (CoAPR) from Enterococcus faecalis

Components

Coenzyme A-persulfide reductase

Keywords

FLAVOPROTEIN / Hydrogen sulfide / coenzyme A / persulfide reductase

Function / homology

FLAVIN-ADENINE DINUCLEOTIDE / IODIDE ION / 3'-PHOSPHATE-ADENOSINE-5'-DIPHOSPHATE

Function and homology information

Biological species

Enterococcus faecalis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.05 Å

Authors

Costa, S.S. / Walsh, B.J. / Giedroc, D.P. / Brito, J.A.

Funding support

Portugal,

United States, 6items

Organization	Grant number	Country
Fundacao para a Ciencia e a Tecnologia	UIDB/04612/2020	Portugal
Fundacao para a Ciencia e a Tecnologia	UIDP/04612/2020	Portugal
Fundacao para a Ciencia e a Tecnologia	LA/P/0087/2020	Portugal
Fundacao para a Ciencia e a Tecnologia	Article 23 of Decree-Law No. 57/2017 of August 29	Portugal
National Institutes of Health/National Cancer Institute (NIH/NCI)	GM097225	United States
National Institutes of Health/National Cancer Institute (NIH/NCI)	GM118157	United States

Citation

Journal: Antioxidants / Year: 2022
Title: Metabolic and Structural Insights into Hydrogen Sulfide Mis-Regulation in Enterococcus faecalis.
Authors: Walsh, B.J.C. / Costa, S.S. / Edmonds, K.A. / Trinidad, J.C. / Issoglio, F.M. / Brito, J.A. / Giedroc, D.P.

History

Deposition	Jun 14, 2022	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Sep 14, 2022	Provider: repository / Type: Initial release
Revision 1.1	Jan 31, 2024	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	8a56.cif.gz	731.8 KB	Display	PDBx/mmCIF format
PDB format	pdb8a56.ent.gz	507.7 KB	Display	PDB format
PDBx/mmJSON format	8a56.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8a56_validation.pdf.gz	1.7 MB	Display	wwPDB validaton report
Full document	8a56_full_validation.pdf.gz	1.8 MB	Display
Data in XML	8a56_validation.xml.gz	39.2 KB	Display
Data in CIF	8a56_validation.cif.gz	55.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/a5/8a56 ftp://data.pdbj.org/pub/pdb/validation_reports/a5/8a56	HTTPS FTP

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Related structure data

Related structure data	3icsS S: Starting model for refinement
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Coenzyme A-persulfide reductase

B: Coenzyme A-persulfide reductase

hetero molecules

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

1

Idetical with deposited unit
defined by author
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	139.797, 194.809, 91.460
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	B-823- HOH

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Protein , 1 types, 2 molecules AB

#1: Protein	Coenzyme A-persulfide reductase Mass: 61950.367 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterococcus faecalis (bacteria) / Production host: Escherichia coli (E. coli)

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Non-polymers , 6 types, 258 molecules

#2: Chemical	ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₇H₃₃N₉O₁₅P₂ / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Chemical	ChemComp-IOD / IODIDE ION Mass: 126.904 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: I
#5: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₆O₂
#6: Chemical	ChemComp-PAP / 3'-PHOSPHATE-ADENOSINE-5'-DIPHOSPHATE Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₀H₁₆N₅O₁₃P₃ / Feature type: SUBJECT OF INVESTIGATION
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 244 / 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: 2.68 Å³/Da / Density % sol: 54.11 %
Crystal grow	Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 20 % (V/V) PEG 3350 0.1 M Bis.Tris Propane pH 7.5 0.2 M NaI

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8731 Å
Detector	Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 13, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.8731 Å / Relative weight: 1
Reflection	Resolution: 2.05→48.25 Å / Num. obs: 54207 / % possible obs: 92.5 % / Redundancy: 4.2 % / B_iso Wilson estimate: 30.57 Å² / CC_1/2: 0.996 / Net I/σ(I): 7.2
Reflection shell	Resolution: 2.05→2.26 Å / Redundancy: 3.5 % / R_merge(I) obs: 0.818 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 2710 / CC_1/2: 0.649 / R_pim(I) all: 0.457 / R_rim(I) all: 0.942 / % possible all: 65.3

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Processing

Software

Name	Version	Classification
autoPROC	1.0.5 (20201211)	data processing
XDS	Feb 5, 2021	data reduction
Aimless	0.7.4	data scaling
STARANISO	2.3.54	data scaling
PHASER		phasing
RESOLVE		model building
PHENIX	1.20rc4_4425	refinement
Coot	0.9.8	model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3ICS

3ics

Resolution: 2.05→48.25 Å / SU ML: 0.2348 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.4566
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2338	2673	4.93 %
R_work	0.1862	51515	-
obs	0.1886	54188	68.63 %

Solvent computation

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

Displacement parameters

B_iso mean: 37.97 Å²

Refinement step

Cycle: LAST / Resolution: 2.05→48.25 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8165	0	194	244	8603

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0026	8512
X-RAY DIFFRACTION	f_angle_d	0.5248	11581
X-RAY DIFFRACTION	f_chiral_restr	0.0457	1357
X-RAY DIFFRACTION	f_plane_restr	0.0043	1591
X-RAY DIFFRACTION	f_dihedral_angle_d	12.4082	3229

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 (%)
2.05-2.08	0.2711	2	0.2916	53	X-RAY DIFFRACTION	1.34
2.08-2.12	0.37	11	0.277	251	X-RAY DIFFRACTION	6.44
2.12-2.17	0.364	27	0.257	528	X-RAY DIFFRACTION	13.78
2.17-2.21	0.3569	46	0.2532	802	X-RAY DIFFRACTION	20.46
2.21-2.26	0.3152	56	0.2483	1109	X-RAY DIFFRACTION	28.39
2.26-2.32	0.2899	60	0.255	1501	X-RAY DIFFRACTION	37.9
2.32-2.38	0.3308	102	0.2477	2003	X-RAY DIFFRACTION	51.3
2.38-2.45	0.2863	121	0.2528	2691	X-RAY DIFFRACTION	68.02
2.45-2.53	0.2862	181	0.248	3252	X-RAY DIFFRACTION	83.41
2.53-2.62	0.3346	196	0.2415	3730	X-RAY DIFFRACTION	95.18
2.62-2.73	0.3082	190	0.238	3954	X-RAY DIFFRACTION	99.59
2.73-2.85	0.2584	237	0.2323	3900	X-RAY DIFFRACTION	99.73
2.85-3	0.2782	199	0.2214	3913	X-RAY DIFFRACTION	99.66
3-3.19	0.2805	182	0.2048	3946	X-RAY DIFFRACTION	99.49
3.19-3.44	0.2699	194	0.1914	3953	X-RAY DIFFRACTION	99.35
3.44-3.78	0.2066	213	0.159	3957	X-RAY DIFFRACTION	99.45
3.78-4.33	0.1722	219	0.1367	3948	X-RAY DIFFRACTION	99.47
4.33-5.45	0.1805	231	0.1347	3988	X-RAY DIFFRACTION	99.39
5.46-48.25	0.1998	206	0.1751	4036	X-RAY DIFFRACTION	96.69

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	0.719115549306	-0.34309947333	0.236994450274	0.928060898512	-0.280187571322	0.702372080273	0.00529261536362	0.144610681365	-0.0708472751304	-0.110227775472	-0.05308906556	0.0990899746022	0.0750259170974	-0.134387132318	0.0319067221285	0.178084101623	-0.0217832741604	0.0246951195647	0.229472083947	-0.0341494637298	0.155031326368	17.313280167	44.3358467201	59.1068753014
2	0.416148275917	0.109919776064	0.0420394767444	1.07459181525	0.0120096451451	0.0518285833322	-0.0538311906939	0.0104116323089	0.0498465535946	0.0710492346648	0.0254682638015	0.137450761931	-0.017126097803	-0.0302711088897	0.0556858994661	0.185234544674	-0.00588442204842	0.0399351491006	0.187298717347	0.000298275122936	0.152546295077	23.3871190741	63.1854939368	73.3604825406
3	2.12176029287	0.257524656956	0.794873225672	0.466210386905	-0.0910243350784	1.29683989309	-0.201917305287	0.410427079764	0.499909367322	-0.332088957622	0.0952615490719	0.258781346643	-0.0636513737034	0.139904491814	0.103235491342	0.325098798236	-0.00867681278792	-0.0737031640839	0.300736737424	0.0529131032696	0.514537854946	14.9396505592	93.381054094	66.565489434
4	0.615766200834	0.521393324155	0.177410358135	1.13199982769	-0.00776905390069	0.0870021844188	0.0502813946803	0.175979072272	0.141774769077	-0.143877875558	-0.071112419565	0.18044940899	-0.059347360328	-0.164779828986	-0.0261474820075	0.197828757191	0.0245077120331	-0.0224526254359	0.202389794358	-0.0105347188602	0.250671536676	40.111720348	94.5833610016	68.4725150473
5	0.905951150604	-0.305186582206	-0.547574641262	0.69624665541	0.123110460827	0.574668376805	-0.0339608907521	0.309314149648	0.116122882177	-0.310462077583	-0.0735909317827	0.342287379923	-0.028846382141	-0.154348227992	0.0432229874498	0.310402656473	0.0382534971114	-0.0249314055551	0.234345592311	0.0471902034626	0.34185994136	40.851125786	96.8299726194	61.9220676593
6	1.2456216321	0.275303976896	-0.388593065371	1.11972309661	-0.0794378325841	0.915626578013	-0.0068224546611	-0.0869902516457	0.199553474708	0.0773864796912	0.104912239799	-0.0422950696646	-0.235794185629	0.181170486159	-0.0909192496854	0.240425815476	-0.00357255169547	-0.0359680312134	0.243609434073	-0.0130020317458	0.216304289183	53.8287000238	100.179951388	72.7994669068
7	1.50043294025	0.115801196658	0.220285001167	2.26546723715	0.238077390554	1.12898757715	-0.00753003621381	0.129773366656	0.0857799315775	-0.191565587734	0.0379204120061	0.0829329147102	-0.206870286909	-0.240824229268	-0.0175530591699	0.29358038733	0.0304121227158	-0.0102044261709	0.244674092642	0.0262346261185	0.145579164276	57.2481836805	83.4080696818	52.140924537
8	1.02859767363	0.573214254042	-0.450606607075	2.31992569666	-0.793795175071	1.02681238584	-0.0356772073284	0.0627349368889	-0.188330998156	-0.0144020665018	-0.0945571943018	-0.176385513856	0.013408149492	0.0649604515284	0.0333729460514	0.271428396104	0.0074893774314	0.0273638831995	0.217737360525	0.013631025422	0.220662833522	59.8446046874	68.1232088309	57.2569001555
9	3.4674164341	-0.355058162838	-0.283564100544	1.83873747678	0.684475899929	1.62719884456	0.0686866514519	0.154179199774	-0.155035158922	-0.131320052421	0.0129727418294	-0.257987854821	-0.166635921638	0.168092339796	-0.00666559687557	0.25104672264	-0.0386582339266	0.0310550774152	0.257090553337	0.00597952573727	0.239282751869	70.580491925	80.528191816	54.3177734288
10	0.586311636516	0.0540085850443	0.120080307657	1.64032231654	0.633272321749	0.646770344396	-0.0502771938434	-0.115181002432	0.0180632622097	0.10018413648	0.0894603615174	0.0127582614477	0.0435788925037	0.0191446310288	-0.0055163318197	0.188862005807	0.0155731861891	-0.00631212752876	0.203167057291	-0.00532797589558	0.143891605278	47.0509222596	84.3431520058	78.7825292102
11	1.28441622062	0.189900103072	-0.271980883609	1.21567494109	-0.0416241902185	0.507443221507	-0.0846868807714	0.0125602468118	-0.114143330236	0.00946545275096	0.029503659139	-0.0352782790304	0.0791730586406	0.0313070139395	0.0734193068341	0.19578917926	-0.00812878214795	0.0121677763528	0.158144242683	0.0291434074729	0.146056389397	42.9120457034	57.5062712878	70.9211060435
12	1.80552112444	0.881579439868	-0.530458151841	2.47808501487	-0.146632654461	0.743531905155	-0.319354672691	0.266985533671	-0.628958213545	-0.455873619069	0.167334065543	-0.427973739116	0.147735106544	0.0284863582196	0.124621984883	0.308427555068	0.018445930746	0.116001087012	0.263150640247	-0.01233441645	0.418358614938	57.6830615049	37.2742498785	66.298910515
13	2.45722730033	1.95949688552	-1.00369514546	2.73038569402	-0.477984122682	0.601264332636	-0.148320302995	0.165698459883	-0.231942715496	-0.231793075829	0.0536003734917	-0.497790331264	-0.0205035691222	-0.16030602475	0.132833305474	0.297358206624	0.0359408554212	0.0513912971487	0.240556557594	0.0724238265717	0.29664072351	53.0903170664	43.028913302	68.0962808193
14	0.099985487276	0.258633734538	-0.026592490543	0.917705764618	-0.329278338889	0.286639851694	-0.0219692606137	0.011161658388	0.0217777533886	-0.0139867919864	-0.00373533072152	-0.0292076586349	-0.0537749249069	0.0206535290583	0.00134995012819	0.938080871814	0.194207582458	-0.0242042962446	1.16127062945	-0.090283216551	1.06072828048	67.7504018271	51.2995794779	59.6732726701

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 1 through 240 )	A	A	1 - 240	1 - 240
2	2	chain 'A' and (resid 241 through 462 )	A	A	241 - 462	241 - 462
3	3	chain 'A' and (resid 463 through 543 )	A	A	463 - 543	463 - 538
4	4	chain 'B' and (resid 1 through 48 )	B	I	1 - 48	1 - 48
5	5	chain 'B' and (resid 49 through 84 )	B	I	49 - 84	49 - 84
6	6	chain 'B' and (resid 85 through 124 )	B	I	85 - 124	85 - 124
7	7	chain 'B' and (resid 125 through 169 )	B	I	125 - 169	125 - 169
8	8	chain 'B' and (resid 170 through 211 )	B	I	170 - 211	170 - 211
9	9	chain 'B' and (resid 212 through 240 )	B	I	212 - 240	212 - 240
10	10	chain 'B' and (resid 241 through 331 )	B	I	241 - 331	241 - 331
11	11	chain 'B' and (resid 332 through 452 )	B	I	332 - 452	332 - 452
12	12	chain 'B' and (resid 453 through 510 )	B	I	453 - 510	453 - 504
13	13	chain 'B' and (resid 511 through 543 )	B	I	511 - 543	505 - 537
14	14	chain 'B' and (resid 544 through 545 )	B	I	544 - 545	538 - 539

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