PDB-5yj2: Crystal structure of Bacillus sp. TB-90 urate oxidase without deh...

ID or keywords:

Entry

Database: PDB / ID: 5yj2

Title

Crystal structure of Bacillus sp. TB-90 urate oxidase without dehydration

Components

Uric acid degradation bifunctional protein

Keywords

OXIDOREDUCTASE / enzyme catalysis / oxidation / water square / dehydration / humid control / environmental adaptation

Function / homology

Function and homology information

2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline decarboxylase / 2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline decarboxylase activity / urate oxidase activity / factor-independent urate hydroxylase / urate catabolic process / allantoin metabolic process / purine nucleobase metabolic process / peroxisome
Similarity search - Function

Biological species

Bacillus sp. (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.71 Å

Authors

Hibi, T. / Itoh, T. / Nishiya, Y.

Citation

Journal: To Be Published
Title: Crystal structure of Bacillus sp. TB-90 urate oxidase without dehydration
Authors: Hibi, T. / Itoh, T. / Nishiya, Y.

History

Deposition	Oct 7, 2017	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Oct 10, 2018	Provider: repository / Type: Initial release
Revision 1.1	Dec 19, 2018	Group: Data collection / Experimental preparation / Structure summary Category: entity / exptl_crystal_grow Item: _entity.formula_weight / _exptl_crystal_grow.pdbx_details

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5yj2.cif.gz	703.3 KB	Display	PDBx/mmCIF format
PDB format	pdb5yj2.ent.gz	615.7 KB	Display	PDB format
PDBx/mmJSON format	5yj2.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5yj2_validation.pdf.gz	2.9 MB	Display	wwPDB validaton report
Full document	5yj2_full_validation.pdf.gz	2.9 MB	Display
Data in XML	5yj2_validation.xml.gz	56.7 KB	Display
Data in CIF	5yj2_validation.cif.gz	84.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/yj/5yj2 ftp://data.pdbj.org/pub/pdb/validation_reports/yj/5yj2	HTTPS FTP

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Related structure data

Related structure data	1j2g 3wlv 4xfp 5ayj 5y2p 5y52
Similar structure data	7cmq-1 3wlv-d 7cuc-1 5z27-1 5y2p-1 1j2g-d 5y52-d 5ayj-d 5z2b-1 4xfp-d 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	#117 - Sep 2009 Xanthine Oxidoreductase similarity (5) #263 - Nov 2021 Acetohydroxyacid Synthase similarity (1) #41 - May 2003 Hemoglobin similarity (1) #159 - Mar 2013 Erythrocruorin similarity (1) #186 - Jun 2015 Receptor for Advanced Glycation End Products similarity (1) #206 - Feb 2017 Globin Evolution similarity (1) #257 - May 2021 Fetal Hemoglobin similarity (1)

Deposited unit

A: Uric acid degradation bifunctional protein

B: Uric acid degradation bifunctional protein

C: Uric acid degradation bifunctional protein

D: Uric acid degradation bifunctional protein

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	133.073, 143.895, 70.231
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P2₁2₁2

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Protein , 1 types, 4 molecules ABCD

#1: Protein	Uric acid degradation bifunctional protein Mass: 35714.102 Da / Num. of mol.: 4 / Fragment: UNP RESIDUES 178-489 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus sp. (strain TB-90) (bacteria) / Strain: TB-90 / Gene: uao / Production host: Escherichia coli DH5[alpha] (bacteria) References: UniProt: Q45697, 2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline decarboxylase, factor-independent urate hydroxylase

#1: Protein

Uric acid degradation bifunctional protein

Mass: 35714.102 Da / Num. of mol.: 4 / Fragment: UNP RESIDUES 178-489
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Bacillus sp. (strain TB-90) (bacteria) / Strain: TB-90 / Gene: uao / Production host:

Escherichia coli DH5[alpha] (bacteria)
References: UniProt: Q45697, 2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline decarboxylase, factor-independent urate hydroxylase

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Non-polymers , 5 types, 1324 molecules

#2: Chemical	ChemComp-AZA / 8-AZAXANTHINE Mass: 153.099 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₄H₃N₅O₂ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-OXY / OXYGEN MOLECULE Mass: 31.999 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: O₂ / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-MXE / 2-METHOXYETHANOL Mass: 76.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₃H₈O₂
#5: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO₄
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1311 / 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: 2.17 Å³/Da / Density % sol: 47.74 %
Crystal grow	Temperature: 288 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 16% PEG 8000, 0.1 M Tris-HCl, 0.08 M K2SO4, 2 mM 8-azaxanthine

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
Detector	Type: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 14, 2012
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.71→50 Å / Num. obs: 147456 / % possible obs: 99.8 % / Redundancy: 6.7 % / B_iso Wilson estimate: 27.1 Å² / R_merge(I) obs: 0.102 / R_pim(I) all: 0.042 / R_rim(I) all: 0.107 / Χ²: 1.033 / Net I/σ(I): 15.8
Reflection shell	Resolution: 1.71→1.74 Å / Redundancy: 6.3 % / R_merge(I) obs: 0.76 / Mean I/σ(I) obs: 2.38 / Num. unique obs: 7291 / CC_1/2: 0.809 / R_pim(I) all: 0.397 / Χ²: 1.105 / % possible all: 99.9

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Processing

Software

Name	Version	Classification
PHENIX	(1.12_2829)	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.71→34.114 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 20.09

	R_factor	Num. reflection	% reflection
R_free	0.1902	14368	9.94 %
R_work	0.1626	-	-
obs	0.1653	144496	99 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Displacement parameters

B_iso mean: 22.4 Å²

Refine analyze

Luzzati coordinate error obs: 0.177 Å

Refinement step

Cycle: LAST / Resolution: 1.71→34.114 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9608	0	77	1311	10996

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.005	9974
X-RAY DIFFRACTION	f_angle_d	0.754	13552
X-RAY DIFFRACTION	f_dihedral_angle_d	9.473	5849
X-RAY DIFFRACTION	f_chiral_restr	0.051	1513
X-RAY DIFFRACTION	f_plane_restr	0.005	1724

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 (%)
1.7099-1.7294	0.2939	395	0.2381	3489	X-RAY DIFFRACTION	81
1.7294-1.7497	0.2563	511	0.2285	4338	X-RAY DIFFRACTION	100
1.7497-1.771	0.2558	448	0.2229	4332	X-RAY DIFFRACTION	100
1.771-1.7935	0.246	458	0.2109	4388	X-RAY DIFFRACTION	100
1.7935-1.8171	0.2481	447	0.2189	4301	X-RAY DIFFRACTION	100
1.8171-1.8419	0.2514	482	0.204	4350	X-RAY DIFFRACTION	100
1.8419-1.8683	0.2396	460	0.206	4340	X-RAY DIFFRACTION	100
1.8683-1.8961	0.2301	457	0.1979	4362	X-RAY DIFFRACTION	100
1.8961-1.9258	0.2218	483	0.1885	4314	X-RAY DIFFRACTION	100
1.9258-1.9573	0.2336	446	0.1867	4387	X-RAY DIFFRACTION	100
1.9573-1.9911	0.2189	472	0.1836	4330	X-RAY DIFFRACTION	100
1.9911-2.0273	0.2071	484	0.1821	4341	X-RAY DIFFRACTION	100
2.0273-2.0663	0.2078	524	0.1774	4268	X-RAY DIFFRACTION	99
2.0663-2.1084	0.1985	467	0.1709	4364	X-RAY DIFFRACTION	100
2.1084-2.1543	0.1869	474	0.1624	4320	X-RAY DIFFRACTION	99
2.1543-2.2044	0.1861	474	0.1545	4350	X-RAY DIFFRACTION	99
2.2044-2.2595	0.1871	447	0.1583	4399	X-RAY DIFFRACTION	100
2.2595-2.3206	0.1919	477	0.1564	4340	X-RAY DIFFRACTION	99
2.3206-2.3888	0.1893	467	0.1604	4380	X-RAY DIFFRACTION	100
2.3888-2.4659	0.2021	491	0.1632	4306	X-RAY DIFFRACTION	100
2.4659-2.554	0.2083	447	0.1596	4402	X-RAY DIFFRACTION	100
2.554-2.6563	0.1886	526	0.1599	4316	X-RAY DIFFRACTION	99
2.6563-2.7771	0.1982	515	0.1573	4334	X-RAY DIFFRACTION	99
2.7771-2.9234	0.1929	541	0.1606	4328	X-RAY DIFFRACTION	100
2.9234-3.1065	0.1943	532	0.1579	4320	X-RAY DIFFRACTION	99
3.1065-3.3462	0.1771	507	0.152	4428	X-RAY DIFFRACTION	100
3.3462-3.6825	0.156	474	0.1433	4431	X-RAY DIFFRACTION	100
3.6825-4.2146	0.1612	455	0.1321	4469	X-RAY DIFFRACTION	99
4.2146-5.3067	0.1314	448	0.1214	4542	X-RAY DIFFRACTION	100
5.3067-34.1212	0.1927	559	0.1906	4559	X-RAY DIFFRACTION	98

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	0.7718	0.1388	0.1482	3.0775	-0.5894	0.5761	-0.0434	0.0918	-0.0223	-0.2267	0.0359	0.1398	-0.0116	-0.0168	-0.0006	0.1233	0.0052	-0.0278	0.1306	0.0021	0.1035	-13.2038	32.4847	134.8605
2	0.4244	0.3548	-0.2103	1.6036	-1.4064	2.6146	-0.0399	0.0199	-0.0816	-0.0633	0	0.0283	0.04	-0.0506	0.0703	0.1315	0.0194	-0.0039	0.1265	-0.019	0.1618	-10.0375	19.4924	141.6783
3	0.5205	0.0446	0.0374	0.427	0.0695	0.0462	0.0174	0.059	-0.0036	-0.061	-0.0163	0.0144	-0.0231	0.0334	0.0013	0.1233	0.0085	-0.0003	0.1268	-0.0016	0.0908	5.8699	22.135	143.5275
4	1.3485	0.747	0.6754	0.9918	0.4999	0.9054	0.0091	0.0493	-0.0582	-0.0469	0.0106	-0.033	0.0119	0.0461	-0.0166	0.1406	0.0084	0.01	0.1313	-0.0071	0.1181	12.6472	14.8968	142.8778
5	1.0434	0.1185	-0.1867	1.5414	0.8517	1.8105	0.0045	-0.1045	-0.1005	0.1559	0.0384	-0.142	0.0419	0.2141	-0.0101	0.1207	-0.0024	-0.0097	0.1484	-0.0034	0.1642	19.8374	22.9941	158.1353
6	0.3774	0.408	0.1143	1.3997	0.033	0.0077	0.0088	-0.0431	-0.0031	0.1522	-0.0214	-0.0325	0.0038	-0.0093	0.0257	0.1589	0.0007	-0.0088	0.1422	0.0015	0.128	9.7354	24.8224	178.0824
7	1.6386	0.7141	0.2976	2.4374	0.3901	1.2442	0.0261	-0.0519	-0.0763	0.1309	-0.046	-0.1101	0.0325	0.018	0.0252	0.1367	-0.0093	-0.0243	0.1304	0.0058	0.1203	13.8015	25.2821	182.2945
8	0.5407	-0.0062	0.2258	0.3214	-0.287	-0.042	0.0128	-0.0415	-0.0683	0.0153	-0.0393	-0.0314	-0.0207	-0.0584	0.0318	0.1276	-0.0026	0.0001	0.1327	-0.0026	0.1144	-1.7952	18.9817	169.0963
9	0.8046	-0.3805	0.4439	0.9496	-0.5135	0.929	0.0023	-0.0341	-0.0276	0.0067	0.0183	0.0468	0.03	-0.07	-0.0239	0.1314	0.0011	0.0093	0.1312	-0.0006	0.122	-13.9048	17.9195	169.0675
10	0.8251	0.1153	-0.0451	1.0595	-0.1068	0.3001	0.0118	-0.073	0.099	0.114	-0.0023	-0.0235	-0.0876	-0.0183	-0.0073	0.1531	0.0212	0.0012	0.1478	-0.0149	0.1311	-17.8439	44.3968	169.1
11	1.1693	0.6227	0.2068	1.7766	-0.1231	0.5663	0.0133	-0.046	0.1225	0.0488	-0.0119	0.1263	-0.0692	-0.0272	0.0054	0.1213	0.0117	0.0168	0.1529	-0.0058	0.1183	-23.3066	43.9143	170.3923
12	0.5138	-0.0906	0.2031	0.3966	0.1481	0.0125	-0.0139	-0.0493	0.0676	0.0034	-0.0419	0.0059	-0.0494	0.0004	0.0619	0.1189	-0.0047	0.0051	0.1103	-0.0084	0.0991	-2.8778	50.0524	168.5957
13	2.2086	-0.462	0.1131	1.4115	0.0155	0.5695	-0.0448	-0.0924	0.1757	0.0745	-0.0098	0.0098	-0.1103	-0.0549	0.0579	0.177	0.0002	-0.0076	0.1431	-0.0198	0.1229	3.3183	53.48	177.4488
14	1.3058	-0.3753	-0.2427	1.3018	0.2522	1.6456	-0.0656	-0.0773	0.056	0.0165	0.0262	-0.157	-0.1529	0.1796	0.0241	0.1219	-0.0092	-0.0267	0.1279	-0.009	0.1336	16.9865	45.0401	168.9917
15	0.6429	0.0104	0.0794	1.1842	0.0103	0.1427	-0.0243	0.1029	0.0901	-0.1042	0.0029	0.0061	-0.0548	0.0267	0.0304	0.1345	-0.015	-0.0018	0.1366	0.0167	0.1076	20.0044	43.2516	147.0411
16	1.1426	-0.821	-0.6333	1.5599	0.3507	0.8897	0.0275	0.0274	0.1269	0.0015	-0.0143	-0.0906	-0.128	0.0252	-0.0191	0.1115	-0.0128	-0.016	0.128	0.0074	0.1166	21.5786	47.1722	150.3113
17	0.1936	0.0086	0.0711	0.3225	-0.0557	0.1795	-0.0078	0.0373	0.0238	-0.0479	-0.0234	0.021	-0.0211	0.0466	0.028	0.1325	0.0079	-0.001	0.1473	0.0087	0.1118	4.8543	46.5841	143.1322
18	1.2902	0.1547	-0.0733	1.1591	-0.2541	0.5917	-0.0423	0.0875	0.1298	-0.0435	0.0035	0.0511	-0.0484	0.0154	0.0393	0.1538	0.0001	-0.0176	0.1459	0.0111	0.1276	-4.4215	51.3611	141.0689
19	0.249	-0.538	0.034	1.524	-0.0356	0.0569	-0.0101	0.0086	-0.0331	-0.0951	0.0121	0.0208	0.0066	0.0048	0.0002	0.1608	-0.0057	-0.019	0.1422	-0.0002	0.1426	-6.5615	16.1119	142.1182

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'B' and (resid 44 through 91 )
2	X-RAY DIFFRACTION	2	chain 'B' and (resid 92 through 135 )
3	X-RAY DIFFRACTION	3	chain 'B' and (resid 136 through 192 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 193 through 276 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 277 through 310 )
6	X-RAY DIFFRACTION	6	chain 'C' and (resid 8 through 72 )
7	X-RAY DIFFRACTION	7	chain 'C' and (resid 73 through 119 )
8	X-RAY DIFFRACTION	8	chain 'C' and (resid 120 through 192 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 193 through 310 )
10	X-RAY DIFFRACTION	10	chain 'D' and (resid 8 through 72 )
11	X-RAY DIFFRACTION	11	chain 'D' and (resid 73 through 119 )
12	X-RAY DIFFRACTION	12	chain 'D' and (resid 120 through 192 )
13	X-RAY DIFFRACTION	13	chain 'D' and (resid 193 through 276 )
14	X-RAY DIFFRACTION	14	chain 'D' and (resid 277 through 310 )
15	X-RAY DIFFRACTION	15	chain 'A' and (resid 8 through 72 )
16	X-RAY DIFFRACTION	16	chain 'A' and (resid 73 through 135 )
17	X-RAY DIFFRACTION	17	chain 'A' and (resid 136 through 192 )
18	X-RAY DIFFRACTION	18	chain 'A' and (resid 193 through 310 )
19	X-RAY DIFFRACTION	19	chain 'B' and (resid 8 through 43 )

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