PDB-2oq2: Crystal structure of yeast PAPS reductase with PAP, a product complex

ID or keywords:

Entry

Database: PDB / ID: 2oq2

Title

Crystal structure of yeast PAPS reductase with PAP, a product complex

Components

Phosphoadenosine phosphosulfate reductase

Keywords

OXIDOREDUCTASE / sulfate reduction / PAPS reductase

Function / homology

Function and homology information

3'-phosphoadenylylselenate reductase activity / phosphoadenylyl-sulfate reductase (thioredoxin) / phosphoadenylyl-sulfate reductase (thioredoxin) activity / sulfate assimilation, phosphoadenylyl sulfate reduction by phosphoadenylyl-sulfate reductase (thioredoxin) / hydrogen sulfide biosynthetic process / glutathione biosynthetic process / cysteine biosynthetic process / methionine biosynthetic process / cytosol / cytoplasm
Similarity search - Function

Biological species

Saccharomyces cerevisiae (brewer's yeast)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 2.1 Å

Authors

Yu, Z. / Fisher, A.J.

Citation

Journal: Biochemistry / Year: 2008
Title: Crystal structure of Saccharomyces cerevisiae 3'-phosphoadenosine-5'-phosphosulfate reductase complexed with adenosine 3',5'-bisphosphate.
Authors: Yu, Z. / Lemongello, D. / Segel, I.H. / Fisher, A.J.

History

Deposition	Jan 31, 2007	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 15, 2008	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Oct 18, 2017	Group: Refinement description / Category: software
Revision 1.3	Dec 27, 2023	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2oq2.cif.gz	219.1 KB	Display	PDBx/mmCIF format
PDB format	pdb2oq2.ent.gz	175.2 KB	Display	PDB format
PDBx/mmJSON format	2oq2.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/oq/2oq2 ftp://data.pdbj.org/pub/pdb/validation_reports/oq/2oq2	HTTPS FTP

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Related structure data

Similar structure data	2go4-3 7ba2-1 1rc6-d 6bdr-2 4qaf-d 2hw1-1 2i5g-d 6pey-4 6ul7-1 6d79-d Search similar-shape structures by Omokage search (details) 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
Related items in Molecule of the Month	#116 - Aug 2009 Sulfotransferases similarity (1)

Deposited unit

A: Phosphoadenosine phosphosulfate reductase

B: Phosphoadenosine phosphosulfate reductase

C: Phosphoadenosine phosphosulfate reductase

D: Phosphoadenosine phosphosulfate reductase

hetero molecules

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

1

A: Phosphoadenosine phosphosulfate reductase

B: Phosphoadenosine phosphosulfate reductase

hetero molecules

defined by author&software
61.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Phosphoadenosine phosphosulfate reductase

D: Phosphoadenosine phosphosulfate reductase

hetero molecules

defined by author&software
61.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	49.418, 63.082, 323.960
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Details

The biological assembly is a dimer formed by chain A and B or C and D in the deposited coordinates.

#1: Protein	Phosphoadenosine phosphosulfate reductase / PAPS reductase / thioredoxin dependent / PAdoPS reductase / 3'- phosphoadenylylsulfate reductase Mass: 30420.291 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: CRY1 / Gene: MET16 / Plasmid: pTYB2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 Codon+ References: UniProt: P18408, phosphoadenylyl-sulfate reductase (thioredoxin)
#2: Chemical	ChemComp-A3P / ADENOSINE-3'-5'-DIPHOSPHATE Type: RNA linking / Mass: 427.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₀H₁₅N₅O₁₀P₂
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 333 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.07 Å³/Da / Density % sol: 40.7 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 30% w/v PEG 6000, 0.1 M HEPES pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction

ID	Mean temperature (K)	Crystal-ID
1	100	1
2	100	1
3		1
1,2		1

Diffraction source

Source	Site	Beamline	ID	Wavelength (Å)
SYNCHROTRON	SSRL	BL9-2	1	0.97944
SYNCHROTRON	SSRL	BL9-2	2	0.97879, 0.91838, 0.97931

Detector

Type	ID	Detector	Date	Details
ADSC QUANTUM 4	1	CCD	Aug 3, 2006	Si(1,1,1)
ADSC QUANTUM 315	2	CCD	Aug 3, 2006

Radiation

ID	Monochromator	Protocol	Monochromatic (M) / Laue (L)	Scattering type	Wavelength-ID
1	Si(1,1,1)	SINGLE WAVELENGTH	M	x-ray	1
2		MAD	M	x-ray	2

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.97944	1
2	0.97879	1
3	0.91838	1
4	0.97931	1

Reflection

D res high: 3.1 Å / D res low: 50 Å / Redundancy: 6.9 %

ID	Av σ(I) over netI	Number	R_merge(I) obs	Χ²	Num. obs	% possible obs
1	13.5	129139	0.066	1.02	18686	99.5
2	16	129670	0.062	1.19	18665	99.4
3	13.5	129271	0.069	1.08	18680	99.5

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	% possible obs (%)	ID	R_merge(I) obs	Chi squared	Redundancy
6.67	50	96.4	1	0.039	1.001	6.1
5.3	6.67	99.8	1	0.067	1.098	6.9
4.63	5.3	99.9	1	0.051	0.967	7
4.21	4.63	100	1	0.059	0.928	7.1
3.91	4.21	100	1	0.073	0.944	7.2
3.68	3.91	99.9	1	0.104	1.062	7.1
3.49	3.68	100	1	0.142	1.126	7.1
3.34	3.49	99.9	1	0.211	1.064	7.1
3.21	3.34	99.9	1	0.291	0.992	7
3.1	3.21	99.6	1	0.422	1.002	6.6
6.67	50	96.4	2	0.031	0.903	6.1
5.3	6.67	99.8	2	0.063	1.089	6.9
4.63	5.3	99.8	2	0.053	1.116	7
4.21	4.63	99.8	2	0.055	1.07	7
3.91	4.21	99.7	2	0.07	1.18	7.1
3.68	3.91	99.7	2	0.103	1.201	7.1
3.49	3.68	99.9	2	0.137	1.334	7.1
3.34	3.49	99.9	2	0.204	1.353	7.1
3.21	3.34	100	2	0.28	1.325	7.1
3.1	3.21	99.6	2	0.398	1.318	6.9
6.67	50	96.4	3	0.042	1.156	6.1
5.3	6.67	99.8	3	0.07	1.385	6.9
4.63	5.3	99.9	3	0.053	1.035	7
4.21	4.63	100	3	0.059	0.947	7.1
3.91	4.21	100	3	0.075	0.972	7.2
3.68	3.91	99.9	3	0.108	1.114	7.2
3.49	3.68	100	3	0.144	1.123	7.1
3.34	3.49	99.9	3	0.218	1.085	7.1
3.21	3.34	99.8	3	0.291	0.984	7
3.1	3.21	99	3	0.425	1	6.6

Reflection

Resolution: 2.05→107.833 Å / Num. all: 64994 / Num. obs: 62580 / % possible obs: 96.5 % / Observed criterion σ(I): 1 / Redundancy: 4.3 % / B_iso Wilson estimate: 30.9 Å² / R_merge(I) obs: 0.073 / R_sym value: 0.073 / Net I/σ(I): 7.2

Reflection shell

Resolution: 2.05→2.1 Å / Redundancy: 3 % / R_merge(I) obs: 0.373 / Mean I/σ(I) obs: 1.6 / Num. unique all: 3655 / R_sym value: 0.373 / % possible all: 78.2

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Phasing

Phasing

Method:

MAD

Phasing set

ID
1
2

Phasing MAD set

Clust-ID	Expt-ID	Set-ID	Wavelength (Å)	F double prime refined	F prime refined
1	2 wavelength	1	0.979	3.43	-10.73
1	2 wavelength	2	0.89	3.2	-1.4

Phasing MR

	Highest resolution	Lowest resolution
Rotation	2.2 Å	49.85 Å
Translation	2.2 Å	49.85 Å

Phasing dm

FOM : 0.71 / FOM acentric: 0.71 / FOM centric: 0.72 / Reflection: 18467 / Reflection acentric: 15478 / Reflection centric: 2989

Phasing dm shell

Resolution (Å)	FOM	FOM acentric	FOM centric	Reflection	Reflection acentric	Reflection centric
3.1-3.3	0.34	0.34	0.34	3282	2912	370
3.3-3.9	0.64	0.64	0.6	5471	4784	687
3.9-4.4	0.81	0.82	0.75	3119	2656	463
4.4-5.5	0.88	0.89	0.83	3149	2600	549
5.5-8.9	0.9	0.92	0.86	2562	1975	587
8.9-47.246	0.95	0.97	0.92	884	551	333

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
PHASER		phasing
SOLVE		phasing
RESOLVE	2.1	phasing
REFMAC		refinement
PDB_EXTRACT	2	data extraction
ADSC	Quantum	data collection
MOSFLM		data reduction
SCALA		data scaling

Refinement

Method to determine structure:

MAD / Resolution: 2.1→40 Å / Cor.coef. F_o:F_c: 0.95 / Cor.coef. F_o:F_c free: 0.921 / SU B: 10.125 / SU ML: 0.146 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.287 / ESU R Free: 0.215 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.246	2802	5.1 %	RANDOM
R_work	0.193	-	-	-
obs	0.196	55322	98.23 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 36.637 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	3.29 Å²	0 Å²	0 Å²
2-	-	-1.17 Å²	0 Å²
3-	-	-	-2.12 Å²

Refine analyze

	Free	Obs
Luzzati sigma a	0.216 Å	0.29 Å

Refinement step

Cycle: LAST / Resolution: 2.1→40 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8175	0	108	333	8616

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.022	8501
X-RAY DIFFRACTION	r_angle_refined_deg	1.178	1.958	11560
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.529	5	999
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.991	24.822	421
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.702	15	1421
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	22.089	15	30
X-RAY DIFFRACTION	r_chiral_restr	0.071	0.2	1247
X-RAY DIFFRACTION	r_gen_planes_refined	0.003	0.02	6461
X-RAY DIFFRACTION	r_nbd_refined	0.184	0.2	3831
X-RAY DIFFRACTION	r_nbtor_refined	0.301	0.2	5779
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.135	0.2	459
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.176	0.2	76
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.111	0.2	14
X-RAY DIFFRACTION	r_mcbond_it	0.373	1.5	5172
X-RAY DIFFRACTION	r_mcangle_it	0.643	2	8088
X-RAY DIFFRACTION	r_scbond_it	1.026	3	3891
X-RAY DIFFRACTION	r_scangle_it	1.606	4.5	3472

LS refinement shell

Resolution: 2.1→2.154 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.272	99	-
R_work	0.217	1995	-
obs	-	2094	84.81 %

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	4.4435	0.5707	0.4495	3.453	-1.2276	5.3204	0.0932	-0.0826	-0.2374	0.1137	0.0963	-0.1978	0.4463	0.287	-0.1895	0.0515	0.0107	-0.0216	-0.1573	-0.0617	-0.1965	23.2501	17.0512	54.3242
2	1.8216	0.1701	-1.4572	0.5934	-0.4514	5.0934	0.1785	-0.0323	0.4075	0.1435	0.1027	0.1625	-0.3761	-0.2731	-0.2812	-0.0595	-0.0302	0.0176	-0.1541	0.0303	-0.0602	16.9503	28.7361	36.0976
3	1.8557	-0.367	-2.2248	2.6004	2.0332	12.067	0.1183	-0.0242	-0.0265	0.0344	-0.1208	-0.3187	0.4806	0.8979	0.0025	-0.1209	0.0208	-0.0352	-0.0051	0.0094	-0.0378	34.7513	24.5158	27.6359
4	3.959	1.5354	0.7717	2.1778	0.7297	4.661	0.2347	0.1241	-0.2708	0.0776	0.0612	-0.148	0.7932	0.1504	-0.2959	0.0645	-0.0781	-0.0282	-0.1307	-0.0136	-0.1554	17.454	14.857	40.6418
5	4.1609	0.4698	-1.4812	5.0972	0.7229	4.6142	0.1582	-0.3844	-0.8369	0.1361	0.1096	-0.3214	1.0971	-0.116	-0.2678	0.1693	-0.0181	-0.0513	-0.0449	0.0832	0.0099	21.4916	14.2691	26.4944
6	2.2866	0.0989	-0.0911	4.5147	-0.6077	5.4196	0.0214	0.1143	0.1668	0.1143	0.2279	-0.1133	-0.2791	0.2407	-0.2493	0.0097	-0.025	0.0111	-0.1736	-0.0389	-0.1653	21.7196	24.2584	62.8062
7	3.0824	0.6164	2.13	3.3641	-1.2475	4.1936	0.3154	-0.3061	-0.4073	0.7559	0.2336	0.3384	0.1937	-0.4341	-0.549	0.2267	-0.0335	0.0346	-0.0859	0.0983	-0.0184	13.6118	12.0382	79.9315
8	3.5772	0.4411	1.7174	4.8753	-0.2085	8.6538	0.3427	-0.634	0.0626	1.5779	0.0212	-0.3383	-0.1604	0.2182	-0.3639	0.5899	-0.0508	-0.1359	0.0062	0.0102	-0.0369	28.906	18.4036	91.4048
9	2.4705	-0.115	-0.1129	4.5382	-1.473	3.5752	-0.0137	-0.2937	0.3513	0.9024	0.3753	0.5196	-0.6365	-0.2739	-0.3617	0.2404	0.0434	0.1314	-0.058	0.0202	-0.0628	13.3598	25.8932	74.7778
10	6.855	2.2526	-0.2252	2.4519	-1.17	1.6208	0.0975	0.3029	0.4508	1.1954	0.1474	0.0353	-0.9727	-0.5118	-0.2449	1.0978	0.0642	0.207	0.164	0.0322	0.0979	17.111	26.9856	88.898
11	3.218	1.2986	-0.2531	3.7029	0.1196	3.483	0.1337	-0.2263	0.0029	0.2014	-0.1292	0.2077	-0.1238	-0.2079	-0.0045	-0.2632	-0.0377	-0.0129	-0.1589	-0.0375	-0.2184	-8.6749	-8.0787	17.659
12	0.8687	-0.3911	0.2088	1.7646	0.1567	3.8818	0.03	-0.0114	0.2188	0.0771	-0.1128	-0.2862	-0.4237	0.39	0.0829	-0.2614	-0.0614	-0.0017	-0.1783	-0.0132	-0.1234	1.6523	2.8074	0.7617
13	2.6615	-0.5143	1.9205	2.1857	-0.6167	9.4512	0.1482	0.1778	-0.2247	-0.2781	-0.1014	0.1744	0.292	-0.0971	-0.0469	-0.2204	0.0615	-0.0074	-0.2158	-0.0312	-0.1483	-3.0691	-12.3181	-11.6717
14	1.6772	-1.1172	0.3125	4.1235	-1.78	2.9934	-0.0127	-0.0436	-0.0096	-0.0915	0.0552	0.5236	-0.2516	-0.4006	-0.0425	-0.1818	0.0169	-0.0223	-0.1393	-0.0695	-0.1351	-11.7983	1.0371	6.2498
15	3.7428	-1.9978	0.817	7.3549	0.8796	4.2754	0.0149	-0.2293	-0.3907	0.463	0.0924	0.9274	0.2061	-0.8052	-0.1073	-0.1242	0.0151	0.0071	-0.0205	-0.0449	-0.0413	-14.3329	-1.0067	-8.1937
16	3.7504	0.0587	-0.4504	5.5361	0.1113	4.0166	0.0546	-0.0268	-0.0298	-0.0265	-0.115	-0.0406	-0.1794	0.0683	0.0605	-0.2352	-0.0388	-0.0227	-0.1504	-0.028	-0.2781	-1.0904	-9.1469	25.8262
17	1.4553	1.2978	-1.2417	6.8262	-1.9328	6.0777	0.3852	-0.2585	0.2047	1.4462	-0.2388	1.1074	-0.6973	-0.9771	-0.1464	0.1622	-0.1182	0.2783	0.1255	-0.1264	0.0313	-12.3065	-6.0492	45.0696
18	3.8073	-0.56	5.6914	7.2443	-4.143	17.7769	0.4361	-0.516	-0.6679	1.5835	-0.3539	-0.1544	0.7456	-0.154	-0.0821	0.486	-0.3288	0.0946	0.1383	0.0255	0.0146	-5.952	-23.5203	51.108
19	1.6038	2.3226	0.7115	8.0641	2.0812	6.247	0.2183	-0.1611	-0.1118	0.8628	-0.2145	-0.2997	-0.2551	0.3184	-0.0038	0.0001	-0.1636	-0.0025	-0.061	-0.0272	-0.1986	1.1954	-4.1418	39.7395
20	6.5217	0.831	0.9587	7.2937	1.7252	8.7153	0.5004	-0.2699	-0.5952	1.9908	-0.7467	-1.2822	-0.23	0.4213	0.2463	0.788	-0.409	-0.1252	0.2688	0.0811	0.0001	3.2102	-7.6067	53.85

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	A	A	1 - 43	1 - 43
2	2	A	A	44 - 109	44 - 109
3	3	A	A	110 - 152	110 - 152
4	4	A	A	153 - 205	153 - 205
5	5	A	A	206 - 256	206 - 256
6	6	B	B	1 - 43	1 - 43
7	7	B	B	44 - 109	44 - 109
8	8	B	B	110 - 152	110 - 152
9	9	B	B	153 - 205	153 - 205
10	10	B	B	206 - 259	206 - 259
11	11	C	C	1 - 43	1 - 43
12	12	C	C	44 - 109	44 - 109
13	13	C	C	110 - 152	110 - 152
14	14	C	C	153 - 205	153 - 205
15	15	C	C	206 - 257	206 - 257
16	16	D	D	1 - 43	1 - 43
17	17	D	D	44 - 109	44 - 109
18	18	D	D	110 - 152	110 - 152
19	19	D	D	153 - 205	153 - 205
20	20	D	D	206 - 253	206 - 253

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Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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+About Yorodumi

-News

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

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

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

+Jul 12, 2017. Major update of PDB

-Yorodumi

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Movie

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Structure viewers

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Viewer log

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This page

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This web site

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Options

+
Open data

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Basic information

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Structure visualization

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Downloads & links

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Download

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Validation report

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Related structure data

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Links

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Assembly

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Components

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Experimental details

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Experiment

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Sample preparation

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Data collection

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Phasing

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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

+
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)

+
Jul 12, 2017. Major update of PDB

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Yorodumi