PDB-5y52: Crystal Structure of Highly Active BTUO Mutant P287G Improved by ...

ID or keywords:

Entry

Database: PDB / ID: 5y52

Title

Crystal Structure of Highly Active BTUO Mutant P287G Improved by Humidity Control at 83% RH

Components

Uric acid degradation bifunctional protein

Keywords

OXIDOREDUCTASE / Protein engineering / Oxidase / pH dependence / enzyme activation / flexibility / loop plasticity

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 /

MOLECULAR REPLACEMENT / Resolution: 1.63 Å

Authors

Itoh, T. / Kishimoto, T. / Nishiya, Y.

Citation

Journal: To Be Published
Title: Conformational Flexibility of Plastic Interface Loop Allows Entropic Adaptation of Urate Oxidase to Environmental pH
Authors: Hibi, T. / Itoh, T. / Fukada, H. / Kishimoto, T. / Nishiya, Y.

History

Deposition	Aug 7, 2017	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Aug 8, 2018	Provider: repository / Type: Initial release
Revision 1.1	Nov 22, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5y52.cif.gz	704.6 KB	Display	PDBx/mmCIF format
PDB format	pdb5y52.ent.gz	593 KB	Display	PDB format
PDBx/mmJSON format	5y52.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5y52_validation.pdf.gz	497 KB	Display	wwPDB validaton report
Full document	5y52_full_validation.pdf.gz	500 KB	Display
Data in XML	5y52_validation.xml.gz	56.4 KB	Display
Data in CIF	5y52_validation.cif.gz	85 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/y5/5y52 ftp://data.pdbj.org/pub/pdb/validation_reports/y5/5y52	HTTPS FTP

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Related structure data

Related structure data	3wlvS S: Starting model for refinement
Similar structure data	5z27-1 3wlv-d 5z2b-1 5y2p-1 5yja-d 7cmq-1 5yj2-d 7cuc-1 5ayj-d 7cuf-1 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

153 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)	132.963, 144.172, 71.063
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: 37869.586 Da / Num. of mol.: 4 / Fragment: UNP residues 172-502 / Mutation: P287G 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 DH5alpha (bacteria) / Strain (production host): DH5alpha References: UniProt: Q45697, 2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline decarboxylase, factor-independent urate hydroxylase

#1: Protein

Uric acid degradation bifunctional protein

Mass: 37869.586 Da / Num. of mol.: 4 / Fragment: UNP residues 172-502 / Mutation: P287G
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 DH5alpha (bacteria) / Strain (production host): DH5alpha
References: UniProt: Q45697, 2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline decarboxylase, factor-independent urate hydroxylase

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Non-polymers , 5 types, 1374 molecules

#2: Chemical	ChemComp-AZA / 8-AZAXANTHINE Mass: 153.099 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₄H₃N₅O₂
#3: Chemical	ChemComp-OXY / OXYGEN MOLECULE Mass: 31.999 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: O₂
#4: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO₄
#5: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C₂H₆O₂
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1353 / 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: 2.24 Å³/Da / Density % sol: 45.1 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.1M Tris-HCl, 16% PEG 8000, 0.08M K2SO4

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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: 1.63→50 Å / Num. obs: 163621 / % possible obs: 96 % / Redundancy: 4.3 % / B_iso Wilson estimate: 23.8 Å² / R_merge(I) obs: 0.119 / R_pim(I) all: 0.061 / Net I/σ(I): 8.5
Reflection shell	Resolution: 1.63→1.66 Å / Redundancy: 4.2 % / R_merge(I) obs: 0.585 / Mean I/σ(I) obs: 2.05 / Num. unique obs: 8264 / CC_1/2: 0.611 / R_pim(I) all: 0.31 / % possible all: 97.3

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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
Starting model: 3wlv

3wlv

Resolution: 1.63→37.756 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 21.48

	R_factor	Num. reflection	% reflection
R_free	0.2093	7787	4.78 %
R_work	0.1724	-	-
obs	0.1741	162938	95.58 %

Solvent computation

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

Displacement parameters

B_iso mean: 20.7 Å²

Refine analyze

Luzzati coordinate error obs: 0.196 Å

Refinement step

Cycle: LAST / Resolution: 1.63→37.756 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9428	0	106	1353	10887

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	9806
X-RAY DIFFRACTION	f_angle_d	1.005	13291
X-RAY DIFFRACTION	f_dihedral_angle_d	9.069	5732
X-RAY DIFFRACTION	f_chiral_restr	0.06	1472
X-RAY DIFFRACTION	f_plane_restr	0.007	1696

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 (%)
1.6299-1.6484	0.2741	281	0.2314	4979	X-RAY DIFFRACTION	93
1.6484-1.6678	0.2699	257	0.2332	5116	X-RAY DIFFRACTION	96
1.6678-1.6881	0.28	258	0.2206	5169	X-RAY DIFFRACTION	96
1.6881-1.7095	0.2575	272	0.2215	5192	X-RAY DIFFRACTION	97
1.7095-1.732	0.2705	259	0.2188	5175	X-RAY DIFFRACTION	96
1.732-1.7557	0.2626	240	0.2153	5233	X-RAY DIFFRACTION	98
1.7557-1.7808	0.2465	267	0.2122	5191	X-RAY DIFFRACTION	96
1.7808-1.8074	0.254	253	0.2203	5203	X-RAY DIFFRACTION	98
1.8074-1.8356	0.2706	251	0.2055	5200	X-RAY DIFFRACTION	97
1.8356-1.8657	0.238	247	0.1998	5206	X-RAY DIFFRACTION	97
1.8657-1.8979	0.2286	236	0.187	5267	X-RAY DIFFRACTION	98
1.8979-1.9324	0.212	247	0.1805	5227	X-RAY DIFFRACTION	97
1.9324-1.9695	0.2152	281	0.1804	5179	X-RAY DIFFRACTION	97
1.9695-2.0097	0.2359	275	0.1779	5229	X-RAY DIFFRACTION	97
2.0097-2.0534	0.2025	257	0.1728	5170	X-RAY DIFFRACTION	97
2.0534-2.1012	0.1986	269	0.166	5219	X-RAY DIFFRACTION	96
2.1012-2.1537	0.2057	279	0.1588	5194	X-RAY DIFFRACTION	96
2.1537-2.212	0.1766	258	0.158	5201	X-RAY DIFFRACTION	97
2.212-2.277	0.18	270	0.1558	5202	X-RAY DIFFRACTION	97
2.277-2.3505	0.1924	271	0.1493	5178	X-RAY DIFFRACTION	96
2.3505-2.4345	0.1747	263	0.1486	5214	X-RAY DIFFRACTION	96
2.4345-2.532	0.1986	270	0.156	5161	X-RAY DIFFRACTION	96
2.532-2.6472	0.2139	233	0.161	5240	X-RAY DIFFRACTION	96
2.6472-2.7867	0.2211	240	0.1648	5165	X-RAY DIFFRACTION	95
2.7867-2.9612	0.2088	239	0.1639	5185	X-RAY DIFFRACTION	94
2.9612-3.1898	0.1975	266	0.1639	5137	X-RAY DIFFRACTION	95
3.1898-3.5106	0.2075	277	0.1616	5108	X-RAY DIFFRACTION	94
3.5106-4.0181	0.1816	264	0.1524	5127	X-RAY DIFFRACTION	93
4.0181-5.0604	0.1651	258	0.1412	5071	X-RAY DIFFRACTION	91
5.0604-37.7657	0.2446	249	0.2157	5013	X-RAY DIFFRACTION	87

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	0.572	-0.0331	0.1502	0.7035	0.187	0.1971	0.0912	0.0678	-0.0999	-0.113	-0.071	-0.0577	0.436	-0.2993	0.0371	0.4217	-0.1614	-0.0257	0.1332	-0.0171	0.1346	-14.054	19.0369	-26.7267
2	0.9355	0.2567	-0.1694	2.1545	-0.2641	0.7048	0.0083	0.067	0.0684	-0.042	0.0094	0.0977	0.1565	-0.2765	-0.052	0.1272	-0.073	-0.0271	0.2192	0.0094	0.1087	-24.1848	40.8115	-32.0826
3	0.9344	-0.1398	-0.1619	1.1793	0.0145	0.2034	0.0198	0.0318	-0.0544	-0.0203	-0.0386	0.0674	0.2484	-0.2259	0.0137	0.221	-0.1252	-0.031	0.2306	-0.0024	0.1258	-23.9383	28.3217	-30.1922
4	0.6808	0.1689	-0.247	0.3102	0.1933	0.4277	-0.0221	0.0566	-0.0332	-0.0175	-0.0468	0.019	0.36	-0.0492	0.0344	0.2815	-0.0404	-0.0169	0.1062	-0.0008	0.1245	-3.5997	22.0373	-28.4861
5	1.062	0.4326	-0.2366	1.2373	-0.103	0.8431	0.0154	0.1001	-0.1466	0.0124	-0.033	0.0067	0.4044	-0.0913	0.0088	0.3471	-0.0163	-0.0177	0.1276	-0.0236	0.1017	2.7932	18.5829	-35.1371
6	3.3956	2.8732	1.1408	3.7093	1.3921	0.7537	-0.0246	0.1862	-0.1942	-0.0897	0.0517	-0.1551	0.4929	-0.0425	-0.051	0.427	-0.0224	-0.01	0.1174	-0.0369	0.1381	5.617	16.614	-41.4075
7	0.8586	0.3575	-0.2512	1.3355	0.2205	0.6506	-0.0831	0.0944	0.0766	-0.1661	-0.0013	-0.0526	0.3625	0.0078	0.0042	0.2709	0.0098	-0.0133	0.1075	-0.0071	0.0801	8.4198	26.098	-33.8498
8	0.3786	-0.5511	-0.1576	1.5289	0.1749	0.3022	0.0398	0.0151	0.087	-0.109	-0.0325	0.0053	0.0218	-0.0038	-0.0008	0.0673	0.0139	-0.001	0.1018	0.0005	0.1127	7.1833	56.1923	-33.6552
9	0.9596	0.0983	-0.0982	2.1477	0.3659	0.9935	-0.0072	0.0602	0.0185	-0.1875	0.0092	-0.0451	0.1676	0.045	-0.0042	0.1136	0.0354	0.0063	0.1061	0.0039	0.0709	14.394	39.9988	-41.0193
10	2.4175	-0.7684	-1.4748	2.173	0.9981	3.1442	0.035	0.0772	0.1747	-0.2054	0.0534	-0.1267	0.0761	0.1087	-0.0505	0.0716	0.0275	-0.009	0.0892	0.0125	0.0829	11.085	45.8184	-44.5011
11	0.4093	-0.0663	-0.0243	0.3303	-0.0586	0.4941	0.02	-0.0158	0.0898	-0.0139	-0.0052	-0.0284	0.1109	-0.0201	-0.0056	0.0472	-0.0008	-0.0002	0.1118	0.0002	0.1246	-2.17	53.1534	-28.887
12	1.0511	0.4164	-0.3808	1.1014	-0.0798	0.9901	0.061	0.0374	0.066	-0.0467	-0.0148	0.0234	0.0123	-0.1126	-0.0477	0.0488	0.0085	-0.0087	0.1292	0.024	0.1256	-12.4135	57.0937	-32.0342
13	0.6012	0.0496	-0.2099	0.9507	-0.6523	2.0517	-0.0031	0.0444	0.0295	-0.0537	0.0292	0.0278	0.2507	-0.2447	-0.0437	0.0473	-0.0364	-0.0221	0.1413	0.0072	0.1399	-15.3802	49.2054	-26.4109
14	0.488	0.3915	-0.157	1.4665	-0.3045	0.549	0.0254	-0.0633	0.0147	0.1712	-0.0307	-0.0257	0.0962	-0.048	-0.0015	0.1044	-0.0282	0.0035	0.1132	0.0026	0.0853	-8.7387	46.8686	2.0241
15	1.4921	0.5296	-0.2274	1.987	-0.4448	1.194	0.01	-0.0716	0.0558	0.1151	-0.0064	0.1428	0.1068	-0.13	-0.0067	0.0901	-0.035	0.0113	0.1113	-0.0006	0.0859	-12.7572	46.362	6.2252
16	0.4732	0.0091	-0.0127	0.379	0.0306	0.4497	0.0297	0.0083	0.0758	0.0322	-0.0162	0.0191	0.1229	-0.0161	-0.0129	0.0596	-0.0031	-0.0055	0.1035	0.0002	0.1186	2.5561	53.141	-6.5028
17	1.1564	-0.5073	-0.4034	1.0406	0.0385	0.951	0.0641	-0.0382	0.1039	0.0367	-0.0264	-0.0777	0.0125	0.0988	-0.0536	0.0544	-0.0077	-0.0141	0.1095	-0.0149	0.1232	12.9358	57.4333	-3.7205
18	0.3665	0.019	0.0937	0.7263	0.4462	1.7784	0.0057	-0.006	0.0196	0.0236	0.0133	-0.0307	0.216	0.1996	-0.0293	0.0627	0.0314	-0.0217	0.1307	-0.0047	0.1164	16.1467	49.5202	-9.743
19	0.5043	0.1046	0.0365	1.1544	-0.1608	0.6111	0.0363	-0.0747	-0.0806	-0.0001	-0.0329	-0.0859	0.3116	0.1062	0.0024	0.2396	0.0726	-0.0297	0.1425	0.0139	0.1281	19.5551	28.8306	-6.7742
20	0.5882	0.5247	-0.2363	1.5776	-0.0893	0.4357	0.0264	-0.0826	-0.0609	-0.0157	-0.0493	-0.1104	0.3337	0.1874	0.0202	0.2333	0.0978	-0.0213	0.1819	0.0124	0.1389	25.9197	27.3982	-6.9287
21	1.3677	0.4511	0.5441	0.8915	0.4006	0.9452	-0.0297	-0.1484	-0.0283	-0.0884	-0.0781	0.009	0.2878	0.0433	0.0899	0.2957	0.0438	-0.0097	0.1097	0.0312	0.0809	16.5687	25.1659	-10.3764
22	0.922	0.223	0.2954	0.5182	0.1851	0.8161	0.0722	-0.1279	-0.0369	0.0016	-0.0542	-0.1059	0.3785	-0.0035	-0.0253	0.3211	0.0625	-0.0341	0.1182	0.0335	0.1271	14.65	22.0786	-6.894
23	0.8743	-0.0656	-0.4101	0.5796	0.0988	0.6141	-0.0317	-0.0679	-0.1193	0.0917	-0.0076	0.028	0.3393	-0.0141	0.0444	0.338	-0.0584	-0.0087	0.1251	0.0254	0.118	-5.1061	19.8042	0.7696
24	0.6084	-0.2926	-0.2745	1.3935	-0.1666	0.5288	-0.029	-0.1465	0.0152	0.1237	0.009	0.038	0.356	-0.1384	-0.0115	0.2666	-0.0612	-0.0076	0.1177	0.0229	0.0992	-7.0976	25.871	-1.6994

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 72 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 73 through 119 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 120 through 192 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 193 through 248 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 249 through 263 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 264 through 310 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 8 through 43 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 44 through 91 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 92 through 119 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 120 through 192 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 193 through 263 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 264 through 310 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 8 through 72 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 73 through 119 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 120 through 192 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 193 through 263 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 264 through 310 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 8 through 72 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 73 through 106 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 107 through 129 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 130 through 172 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 173 through 263 )
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 264 through 310 )

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+About Yorodumi

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

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-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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Open data

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Validation report

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Related structure data

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Assembly

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Components

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Protein , 1 types, 4 molecules ABCD

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Non-polymers , 5 types, 1374 molecules

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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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Processing

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About Yorodumi

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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

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

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Yorodumi