PDB-7f2v: Urate oxidase from Thermobispora bispora in apo form

ID or keywords:

Entry

Database: PDB / ID: 7f2v

Title

Urate oxidase from Thermobispora bispora in apo form

Components

Uricase

Keywords

OXIDOREDUCTASE / uricase / urate oxidase

Function / homology

factor-independent urate hydroxylase / Uricase / Uricase / urate oxidase activity / urate catabolic process / purine nucleobase metabolic process / Uricase

Function and homology information

Biological species

Thermobispora bispora (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.6 Å

Authors

Chiu, Y.C. / Hsu, T.S. / Huang, C.Y. / Hsu, C.H.

Funding support

Taiwan, 4items

Organization	Grant number	Country
Ministry of Science and Technology (MoST, Taiwan)	109-2113-M- 002-003	Taiwan
Ministry of Science and Technology (MoST, Taiwan)	109-2628-B-002-037	Taiwan
Ministry of Science and Technology (MoST, Taiwan)	108-2113-M-002-011	Taiwan
Ministry of Science and Technology (MoST, Taiwan)	108-2628-B-002-013	Taiwan

Citation

Journal: Int.J.Biol.Macromol. / Year: 2021
Title: Structural and biochemical insights into a hyperthermostable urate oxidase from Thermobispora bispora for hyperuricemia and gout therapy.
Authors: Chiu, Y.C. / Hsu, T.S. / Huang, C.Y. / Hsu, C.H.

History

Deposition	Jun 14, 2021	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	May 4, 2022	Provider: repository / Type: Initial release
Revision 1.1	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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PDBx/mmCIF format	7f2v.cif.gz	261.8 KB	Display	PDBx/mmCIF format
PDB format	pdb7f2v.ent.gz	209.5 KB	Display	PDB format
PDBx/mmJSON format	7f2v.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	7f2v_validation.pdf.gz	447.4 KB	Display	wwPDB validaton report
Full document	7f2v_full_validation.pdf.gz	447.9 KB	Display
Data in XML	7f2v_validation.xml.gz	30.4 KB	Display
Data in CIF	7f2v_validation.cif.gz	47.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/f2/7f2v ftp://data.pdbj.org/pub/pdb/validation_reports/f2/7f2v	HTTPS FTP

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Related structure data

Related structure data	7f2wC 6oe8S 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	#117 - Sep 2009 Xanthine Oxidoreductase similarity (3)

Deposited unit

A: Uricase

B: Uricase

hetero molecules

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

1

A: Uricase

B: Uricase

hetero molecules

A: Uricase

B: Uricase

hetero molecules

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

Unit cell

Length a, b, c (Å)	137.466, 78.051, 65.720
Angle α, β, γ (deg.)	90.000, 116.350, 90.000
Int Tables number	5
Space group name H-M	C121
Symmetry operation	#1: x,y,z #2: -x,y,-z #3: x+1/2,y+1/2,z #4: -x+1/2,y+1/2,-z

#1: Protein	Uricase / Urate oxidase Mass: 34140.188 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermobispora bispora (strain ATCC 19993 / DSM 43833 / CBS 139.67 / JCM 10125 / NBRC 14880 / R51) (bacteria) Strain: ATCC 19993 / DSM 43833 / CBS 139.67 / JCM 10125 / NBRC 14880 / R51 Gene: Tbis_2592 / Production host: Escherichia coli (E. coli) References: UniProt: D6Y599, factor-independent urate hydroxylase
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO₄
#3: Chemical	ChemComp-DMS / DIMETHYL SULFOXIDE Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₆OS / Comment: DMSO, precipitant*YM
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 807 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.38 Å³/Da / Density % sol: 48.39 %
Crystal grow	Temperature: 283 K / Method: vapor diffusion, sitting drop / Details: Bis-Tris, lithium sulfate monohydrate, PEG3350

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 0.99984 Å
Detector	Type: RAYONIX MX300-HS / Detector: CCD / Date: Feb 22, 2019
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.99984 Å / Relative weight: 1
Reflection	Resolution: 1.6→24.18 Å / Num. obs: 81042 / % possible obs: 99.9 % / Redundancy: 4.2 % / B_iso Wilson estimate: 12.72 Å² / CC_1/2: 0.935 / Net I/σ(I): 5.1
Reflection shell	Resolution: 1.6→1.65 Å / Num. unique obs: 7321 / CC_1/2: 0.735

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Processing

Software

Name	Version	Classification
PHENIX	1.17.1_3660	refinement
PDB_EXTRACT	3.25	data extraction
HKL-2000		data scaling
HKL-2000		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 6OE8

6oe8

Resolution: 1.6→24.18 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 19.77 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1978	1915	2.49 %
R_work	0.1671	74873	-
obs	0.1679	76788	93.34 %

Solvent computation

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

Displacement parameters

B_iso max: 64.25 Å² / B_iso mean: 17.3847 Å² / B_iso min: 4.66 Å²

Refinement step

Cycle: final / Resolution: 1.6→24.18 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4770	0	18	807	5595
B_iso mean	-	-	29.8	29.1	-
Num. residues	-	-	-	-	600

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / Total num. of bins used: 14

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.6-1.64	0.2597	109	0.2302	4133	4242	72
1.64-1.68	0.2762	127	0.2186	4773	4900	84
1.68-1.73	0.2226	122	0.2036	5082	5204	89
1.73-1.79	0.2216	144	0.1905	5135	5279	91
1.79-1.85	0.2325	127	0.1896	5261	5388	92
1.85-1.93	0.236	140	0.1859	5400	5540	94
1.93-2.01	0.2327	141	0.1744	5427	5568	95
2.01-2.12	0.1998	136	0.1647	5597	5733	97
2.12-2.25	0.1928	142	0.1611	5565	5707	98
2.25-2.43	0.1756	147	0.1654	5583	5730	98
2.43-2.67	0.2098	138	0.1703	5638	5776	99
2.67-3.06	0.2113	141	0.1731	5716	5857	99
3.06-3.85	0.1722	151	0.1497	5752	5903	100
3.85-24.18	0.1619	150	0.1438	5811	5961	99

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	0.0173	0.0147	-0.0008	0.0161	0.012	0.0208	-0.0144	-0.0102	0.0017	0.0787	0.025	-0.0107	0.0131	0.0478	0.0153	0.1055	0.0194	-0.0319	0.1297	0.0064	0.0618	17.1032	-50.5452	20.1405
2	0.0164	-0.013	0.0059	0.024	-0.0116	0.0118	-0.029	-0.0636	-0.0621	0.0508	0.0251	0.017	0.0544	-0.0176	-0.0039	0.1002	-0.0156	0.0111	0.0719	0.013	0.0553	-8.0614	-56.4337	18.4635
3	0.0058	0.0044	0.0033	-0.002	-0.0027	0.002	-0.0036	-0.0148	-0.0296	0.0526	0.0053	0.0368	0.0779	-0.017	-0.001	0.1345	0.0216	-0.0084	0.0966	0.0086	0.0511	3.8553	-58.9207	23.0616
4	0.0256	-0.0164	-0.0108	0.0319	0.0029	0.0454	-0.0113	-0.0429	0.0009	0.0851	0.0179	-0.0267	0.0801	0.0524	-0.0206	0.0971	0.0015	-0.0116	0.0954	-0.0064	0.0823	8.1192	-48.8675	17.0722
5	0.0032	-0.0085	-0.0031	0.0044	0.0053	0.0059	-0.0419	-0.0444	-0.0367	0.0118	-0.0252	-0.0097	0.0463	0.0284	-0.0054	0.0861	0.0103	-0.0298	0.1109	-0.0216	0.0687	15.7572	-37.5989	17.6913
6	0.0513	-0.0416	-0.0299	0.032	0.0313	0.0197	-0.0516	0.0413	-0.0758	0.002	-0.0358	0.0093	0.0227	-0.0132	-0.0041	0.1441	-0.0105	-0.0002	0.0741	0.0046	0.0769	-1.9452	-65.1549	7.7711
7	0.1169	0.0463	0.0217	0.0923	0.0492	0.0536	0.017	-0.0869	0.1391	0.0543	0.0555	-0.0017	-0.0444	0.1083	0.0458	0.0602	-0.0154	-0.0017	0.0608	-0.013	0.0894	14.3981	-22.787	10.5819
8	0.0093	0.0032	-0.0008	0.0202	0.0009	0.0159	0.0054	-0.1035	0.0975	0.0543	0.0704	-0.0328	-0.0326	0.0296	0.0352	0.0776	-0.0036	-0.013	0.0921	-0.0274	0.0832	13.8918	-20.8764	17.0682
9	0.0253	-0.0014	-0.0046	0.0067	0.0055	0.0051	-0.0129	-0.0503	0.0202	0.0591	-0.0297	0.0131	0.0124	-0.0476	-0.0081	0.1283	-0.0053	0.0243	0.12	0.012	0.0564	-1.4328	-42.3111	27.4902
10	0.0188	-0.0352	-0.0574	0.0205	0.0427	0.0485	0.011	-0.0753	0.0772	-0.0155	0.0372	0.063	-0.014	-0.0053	0.0745	0.0845	-0.0306	-0.004	0.0563	-0.0266	0.0949	3.1276	-19.0514	16.2506
11	0.015	-0.0014	-0.0136	0.0047	-0.0006	0.025	-0.0233	0.1064	0.036	0.0426	0.0376	0.0667	0.0565	-0.0557	0.0111	0.0102	-0.0094	-0.0028	0.1406	0.0177	0.0869	-26.413	-26.54	-1.2114
12	0.0555	-0.0277	-0.0375	0.0296	-0.0053	0.0341	0.0188	-0.0332	0.0471	0.0538	0.0195	0.0224	-0.0546	-0.041	0.0352	0.0706	0.0052	0.0137	0.0692	-0.0063	0.1008	-13.2808	-19.9145	15.5097
13	0.0312	0.0173	-0.0308	0.026	-0.023	0.0195	0.0358	0.0177	0.0309	0.0277	0.0155	0.0371	0.0033	-0.0588	0.0296	0.065	-0.0183	-0.0045	0.0841	-0.0046	0.0942	-18.4698	-28.2956	4.1076
14	0.007	0.0059	-0.0092	0.0119	0.0045	0.0392	-0.0022	0.0083	-0.0088	-0.0344	-0.0259	0.0291	-0.0347	-0.0808	-0.0366	0.0439	-0.0325	0.0067	0.0986	-0.0018	0.0997	-23.6063	-39.5458	-1.5363
15	-0.0004	0.0002	0.0057	0.0248	-0.0394	0.0298	0.0237	0.0234	-0.0124	-0.0232	-0.0748	-0.0246	-0.1044	0.0498	-0.0032	0.0684	-0.0023	0.01	0.0518	-0.0129	0.1052	-4.9455	-12.0063	6.3125
16	0.0736	0.0469	-0.0221	0.0468	0.0322	0.0552	0.0012	0.0154	-0.0357	0.037	0.0289	0.0224	0.1312	-0.0751	0.0759	0.1031	-0.013	-0.0095	0.0686	-0.0155	0.0774	-17.2171	-54.3245	-4.8993
17	0.0085	-0.0091	-0.0007	0.0061	0.0037	0.0038	0.0368	-0.0669	-0.0216	-0.0167	0.024	0.0518	0.0179	-0.0274	0.0022	0.0837	-0.0292	-0.0056	0.1147	0.0035	0.0992	-24.969	-51.3167	-1.1268
18	0.072	0.032	0.0082	0.0312	0.0116	0.0529	0.004	-0.0479	-0.0358	0.0489	0.0114	0.0039	0.0482	-0.0335	0.0229	0.1043	-0.0158	0.0215	0.086	-0.0021	0.0912	-20.3134	-50.3465	6.6992
19	0.0197	-0.0075	-0.0084	0.0212	-0.009	0.0108	-0.0328	-0.0928	-0.0246	0.0969	0.0633	-0.0176	0.101	-0.0245	-0.0011	0.1103	-0.0399	-0.0039	0.0458	-0.0117	0.0794	-14.6812	-58.0411	7.4951

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'B' and (resid 151 through 180 )	B	151 - 180
2	X-RAY DIFFRACTION	2	chain 'B' and (resid 181 through 215 )	B	181 - 215
3	X-RAY DIFFRACTION	3	chain 'B' and (resid 216 through 235 )	B	216 - 235
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 236 through 259 )	B	236 - 259
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 260 through 275 )	B	260 - 275
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 276 through 301 )	B	276 - 301
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 2 through 56 )	A	2 - 56
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 57 through 103 )	A	57 - 103
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 104 through 119 )	A	104 - 119
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 120 through 150 )	A	120 - 150
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 151 through 180 )	A	151 - 180
12	X-RAY DIFFRACTION	12	chain 'A' and (resid 181 through 235 )	A	181 - 235
13	X-RAY DIFFRACTION	13	chain 'A' and (resid 236 through 259 )	A	236 - 259
14	X-RAY DIFFRACTION	14	chain 'A' and (resid 260 through 275 )	A	260 - 275
15	X-RAY DIFFRACTION	15	chain 'A' and (resid 276 through 301 )	A	276 - 301
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 2 through 56 )	B	2 - 56
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 57 through 75 )	B	57 - 75
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 76 through 119 )	B	76 - 119
19	X-RAY DIFFRACTION	19	chain 'B' and (resid 120 through 150 )	B	120 - 150

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