PDB-5yja: Crystal structure of highly active BTUO mutant P287G without dehy...

ID or keywords:

Entry

Database: PDB / ID: 5yja

Title

Crystal structure of highly active BTUO mutant P287G without dehydration

Components

Uric acid degradation bifunctional protein

Keywords

OXIDOREDUCTASE / protein engineering / enzyme / loop flexibility / entropy of activation

Function / homology

Function and homology information

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

Biological species

Bacillus sp. (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / Resolution: 1.65 Å

Authors

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

Citation

Journal: to be published
Title: Flexibility of a Distal Interface Loop Modulates Water Network in the Active Site of Bacillus sp. TB-90 Urate Oxidase
Authors: Hibi, T. / Itoh, T. / Nishiya, Y.

History

Deposition	Oct 9, 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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PDBx/mmCIF format	5yja.cif.gz	694.8 KB	Display	PDBx/mmCIF format
PDB format	pdb5yja.ent.gz	605.8 KB	Display	PDB format
PDBx/mmJSON format	5yja.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5yja_validation.pdf.gz	2.2 MB	Display	wwPDB validaton report
Full document	5yja_full_validation.pdf.gz	2.2 MB	Display
Data in XML	5yja_validation.xml.gz	56.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/yj/5yja ftp://data.pdbj.org/pub/pdb/validation_reports/yj/5yja	HTTPS FTP

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Related structure data

Related structure data	5z27C 5z2bC 7cmnC 7cmqC 1j2g 3wlv 4xfp 5ayj 5y2p 5y52 5yj2 C: citing same article (ref.)
Similar structure data	5z2b-1 4xfp-d 5y52-d 5z27-1 5y2p-1 3wlv-d 7cuc-1 5yj2-d 7cmq-1 5ayj-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

149 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)	133.017, 144.252, 70.272
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: 37067.594 Da / Num. of mol.: 4 / Fragment: UNP RESIDUES 172-494 / Mutation: deletion of 1-7 and 318-331 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: 37067.594 Da / Num. of mol.: 4 / Fragment: UNP RESIDUES 172-494 / Mutation: deletion of 1-7 and 318-331
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 , 6 types, 1093 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-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO₄
#5: Chemical	ChemComp-K / POTASSIUM ION Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#6: Chemical	ChemComp-MXE / 2-METHOXYETHANOL Mass: 76.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₈O₂
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1079 / 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: 2.26 Å³/Da / Density % sol: 45.08 %
Crystal grow	Temperature: 288 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 16% PEG 8000, 0.1 M Tris-HCl, 0.07 M K2SO4, 2 mM 8-azaxanthine

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
Detector	Type: RAYONIX MX-225 / Detector: CCD / Date: Nov 18, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.65→50 Å / Num. obs: 162624 / % possible obs: 99 % / Redundancy: 11.4 % / B_iso Wilson estimate: 26.9 Å² / R_merge(I) obs: 0.089 / R_pim(I) all: 0.027 / R_rim(I) all: 0.093 / Χ²: 1.041 / Net I/σ(I): 22.4
Reflection shell	Resolution: 1.65→1.68 Å / Redundancy: 10 % / R_merge(I) obs: 0.888 / Num. unique obs: 8061 / CC_1/2: 0.8 / R_pim(I) all: 0.285 / R_rim(I) all: 0.934 / Χ²: 1.032 / % possible all: 99.8

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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

Resolution: 1.65→39.683 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.36

	R_factor	Num. reflection	% reflection
R_free	0.1867	16293	10.02 %
R_work	0.1637	-	-
obs	0.1659	161351	99.8 %

Solvent computation

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

Refine analyze

Luzzati coordinate error obs: 0.172 Å

Refinement step

Cycle: LAST / Resolution: 1.65→39.683 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9414	0	74	1079	10567

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	9812
X-RAY DIFFRACTION	f_angle_d	0.944	13343
X-RAY DIFFRACTION	f_dihedral_angle_d	9.084	5730
X-RAY DIFFRACTION	f_chiral_restr	0.059	1490
X-RAY DIFFRACTION	f_plane_restr	0.007	1703

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 (%)
1.6492-1.668	0.2533	512	0.2263	4830	X-RAY DIFFRACTION	99
1.668-1.6876	0.2369	539	0.2077	4803	X-RAY DIFFRACTION	100
1.6876-1.7082	0.2507	560	0.2104	4857	X-RAY DIFFRACTION	100
1.7082-1.7298	0.2366	535	0.1998	4787	X-RAY DIFFRACTION	100
1.7298-1.7526	0.2354	548	0.1953	4844	X-RAY DIFFRACTION	100
1.7526-1.7766	0.2235	559	0.1852	4805	X-RAY DIFFRACTION	100
1.7766-1.802	0.215	539	0.1792	4867	X-RAY DIFFRACTION	100
1.802-1.8289	0.2066	551	0.1817	4819	X-RAY DIFFRACTION	100
1.8289-1.8574	0.2113	542	0.1795	4847	X-RAY DIFFRACTION	100
1.8574-1.8879	0.2098	509	0.1813	4857	X-RAY DIFFRACTION	100
1.8879-1.9204	0.2073	559	0.1729	4825	X-RAY DIFFRACTION	100
1.9204-1.9554	0.1979	535	0.1669	4894	X-RAY DIFFRACTION	100
1.9554-1.993	0.194	530	0.1696	4829	X-RAY DIFFRACTION	100
1.993-2.0336	0.201	542	0.1685	4858	X-RAY DIFFRACTION	100
2.0336-2.0779	0.1802	523	0.1546	4887	X-RAY DIFFRACTION	100
2.0779-2.1262	0.178	552	0.1526	4849	X-RAY DIFFRACTION	100
2.1262-2.1794	0.1704	565	0.1477	4833	X-RAY DIFFRACTION	100
2.1794-2.2383	0.163	521	0.1497	4879	X-RAY DIFFRACTION	100
2.2383-2.3041	0.1698	614	0.1477	4790	X-RAY DIFFRACTION	100
2.3041-2.3785	0.1795	569	0.1516	4832	X-RAY DIFFRACTION	100
2.3785-2.4635	0.1873	545	0.1515	4902	X-RAY DIFFRACTION	100
2.4635-2.5621	0.1758	528	0.1505	4882	X-RAY DIFFRACTION	100
2.5621-2.6787	0.1833	543	0.1489	4924	X-RAY DIFFRACTION	100
2.6787-2.8199	0.1844	506	0.1566	4928	X-RAY DIFFRACTION	100
2.8199-2.9965	0.2006	519	0.1657	4923	X-RAY DIFFRACTION	100
2.9965-3.2278	0.1815	595	0.1634	4884	X-RAY DIFFRACTION	100
3.2278-3.5524	0.1835	533	0.1576	4955	X-RAY DIFFRACTION	100
3.5524-4.066	0.1637	577	0.1539	4937	X-RAY DIFFRACTION	100
4.066-5.121	0.1489	513	0.1355	5052	X-RAY DIFFRACTION	100
5.121-39.6947	0.2175	530	0.2105	5152	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	1.3116	0.2867	-0.1436	1.3597	0.078	0.2153	-0.0343	-0.0746	-0.3368	0.1504	-0.0319	0.0003	0.1433	0.0253	0.0724	0.2032	0.0477	-0.0174	0.1725	0.0325	0.2291	15.9612	163.5994	26.4308
2	0.7881	0.0397	-0.1366	2.0903	0.1274	0.6432	-0.0112	-0.1487	-0.0269	0.1526	0.0095	-0.2249	0.0724	0.1272	0.0039	0.1265	0.0331	-0.0389	0.1971	0.0129	0.1577	25.3996	177.7815	30.51
3	1.1947	-0.1873	-0.2818	0.6499	-0.1441	0.2511	-0.0131	-0.0586	-0.1558	0.021	-0.0645	0.0216	0.1364	-0.0517	0.0581	0.1559	-0.01	-0.0291	0.115	0.0323	0.1504	5.1877	166.8468	28.558
4	1.3142	-0.1638	-0.2678	1.2044	-0.1652	0.6299	-0.0466	-0.1655	-0.2446	0.1145	0.0031	0.0756	0.1062	-0.0109	0.051	0.2268	-0.0056	-0.0084	0.166	0.036	0.1903	-2.7792	163.6825	35.2913
5	2.1203	-0.4804	0.8712	0.9628	-0.7824	2.1495	-0.1052	-0.2229	-0.106	0.149	0.0834	-0.0201	0.1714	-0.0785	-0.0618	0.2024	0.0014	-0.004	0.1692	0.0097	0.1421	-9.609	173.521	32.4451
6	0.7235	0.3602	-0.0858	1.4864	-0.0519	0.5375	0.0397	-0.0976	-0.0424	0.2258	-0.0222	0.1611	0.0972	-0.0887	-0.0242	0.1212	-0.0239	0.0205	0.1026	0.0048	0.0857	-10.1225	191.4898	39.1498
7	1.2327	0.1546	-0.0912	0.7006	0.1853	0.5191	-0.0135	-0.01	0.0873	0.0039	-0.0367	0.0344	0.0213	0.0278	0.0619	0.1031	-0.0021	-0.0015	0.0677	-0.0095	0.0703	0.3954	198.4118	29.0057
8	1.2986	-0.7635	-0.3676	1.4076	0.2209	0.4408	0.0303	-0.0707	0.061	0.0406	0.0222	-0.116	-0.0041	0.1617	-0.0302	0.0991	0.0047	-0.0186	0.1135	-0.0114	0.0841	14.0384	200.1979	32.2014
9	0.9532	-0.0354	-0.1037	0.7251	-0.291	0.4981	-0.0052	0.0426	0.0495	0.0031	0.0387	-0.1769	0.1224	0.4017	0.0247	0.1487	0.0307	-0.0153	0.1914	-0.0038	0.1689	19.5292	192.3712	20.2371
10	0.9803	-0.5961	-0.009	1.3566	-0.1441	0.5431	0.0393	-0.0258	0.0894	-0.1067	0.0018	-0.1026	0.0386	0.0533	-0.0321	0.0831	-0.0013	0.0069	0.065	0	0.0588	7.0515	201.7315	1.66
11	1.3339	-0.1135	-0.0956	1.4564	-0.1465	0.55	0.0392	0.1784	-0.1307	-0.2725	-0.0347	-0.1788	0.2085	0.0744	-0.0124	0.1823	0.0475	0.0222	0.1444	-0.017	0.1131	13.32	187.0245	-6.9998
12	1.2914	-0.1391	0.2586	0.7692	0.213	2.5295	-0.0694	-0.0227	0.1606	-0.0746	-0.0292	-0.0876	-0.2538	0.014	0.0636	0.103	0.0096	-0.0012	0.0599	0.0291	0.0895	7.8594	200.0595	6.781
13	0.6874	0.0031	0.0517	0.6817	0.0534	0.0042	0.0376	0.0579	-0.026	-0.0355	-0.0146	0.1526	0.0582	-0.1575	-0.0047	0.1132	-0.0196	-0.021	0.1607	0.0015	0.1061	-15.8779	192.7566	5.4146
14	1.2013	0.7126	-0.547	1.4914	-0.3388	0.9959	0.02	0.0435	0.0222	-0.0425	0.0131	0.0839	0.0477	-0.1668	-0.0282	0.0894	-0.0057	-0.0173	0.1031	0.0106	0.082	-12.0569	200.6756	2.3235
15	0.9149	0.7102	-0.509	1.682	-0.994	2.6979	0.0147	-0.0069	0.0874	-0.0265	0.0512	0.1286	0.1468	-0.3976	-0.1459	0.119	-0.0286	-0.0213	0.1829	0.0091	0.1622	-17.5559	191.2756	11.7437
16	1.4413	-0.3435	0.0754	1.4048	-0.098	0.443	0.0109	0.0667	-0.3722	-0.1146	-0.0029	0.0207	0.2084	-0.0109	-0.0007	0.2274	-0.0492	-0.0211	0.1759	-0.036	0.2464	-13.5126	162.4189	8.908
17	0.9202	-0.0387	-0.212	1.3869	0.0168	0.4579	-0.0062	0.1349	-0.0506	-0.096	0.0084	0.225	0.0532	-0.0715	0.0049	0.1189	-0.0389	-0.0312	0.1888	-0.0126	0.1632	-23.4954	176.5615	4.6683
18	1.9229	-0.0754	0.703	0.5316	0.1385	1.6723	0.031	0.0434	-0.1747	0.0506	-0.1134	0.1137	0.3363	0.0977	0.0288	0.1755	-0.0267	-0.0073	0.0708	-0.0569	0.1772	-11.0835	163.6996	12.4627
19	0.6781	-0.05	-0.347	0.8745	-0.0248	0.2976	0.0606	0.1642	-0.0359	-0.1174	-0.0651	-0.1683	0.0727	0.0698	0.0216	0.1856	0.0242	-0.0106	0.2075	-0.0095	0.172	7.7675	170.6162	-1.6189
20	1.1964	0.6554	-0.4965	1.5826	-0.1825	0.5116	0.0333	0.0045	-0.1813	-0.0233	-0.1004	-0.3186	0.1193	0.0993	0.0749	0.2404	0.0183	-0.0097	0.204	-0.014	0.2062	11.1686	169.2532	0.8917
21	1.8606	0.271	0.0501	1.5871	-0.0522	1.3529	0.066	0.2702	-0.4411	-0.1471	-0.09	0.0894	0.1887	-0.0904	0.0052	0.2394	0.0184	-0.0185	0.173	-0.0927	0.2534	-1.9039	158.2195	-0.2002
22	3.1628	1.7075	1.5171	1.9433	1.3141	2.0103	-0.1511	0.4499	-0.3466	-0.2303	0.1964	-0.1707	-0.0123	0.2409	-0.039	0.2096	0.0014	0.0159	0.217	-0.0326	0.1916	7.5345	165.4935	-1.0568
23	1.9901	1.047	0.7188	2.1115	0.9018	1.6222	-0.2818	0.3033	-0.1594	-0.3491	0.1818	0.0631	-0.0796	-0.0479	0.1045	0.1892	-0.0328	0.0108	0.1904	-0.0159	0.1614	9.9886	174.0007	1.1427

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 8 through 43 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 44 through 119 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 120 through 192 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 193 through 291 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 292 through 310 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 9 through 119 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 120 through 188 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 189 through 276 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 277 through 313 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 9 through 43 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 44 through 119 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 120 through 161 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 162 through 192 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 193 through 276 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 277 through 314 )
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 8 through 43 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 44 through 119 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 120 through 161 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 162 through 192 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 193 through 213 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 214 through 248 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 249 through 293 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 294 through 310 )

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-Yorodumi

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Movie

-
Structure viewers

+
Viewer log

-
This page

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This web site

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Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Protein , 1 types, 4 molecules ABCD

-
Non-polymers , 6 types, 1093 molecules

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
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

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Yorodumi