PDB-4xfp: Crystal Structure of Highly Active Mutant of Bacillus sp. TB-90 U...

ID or keywords:

Entry

Database: PDB / ID: 4xfp

Title

Crystal Structure of Highly Active Mutant of Bacillus sp. TB-90 Urate Oxidase

Components

Urate oxidase

Keywords

OXIDOREDUCTASE / enzyme / protein engineering / flexible loop

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
Similarity search - Function

Biological species

Bacillus TB-90 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.66 Å

Authors

Hibi, T. / Hayashi, Y. / Kawamura, A. / Itoh, T.

Citation

Journal: To be published
Title: Glycine Substitution of Surface Proline 287 Involves Entropic Enhancement of Bacillus sp. TB-90 Uricase Activity
Authors: Hibi, T. / Hayashi, Y. / Kawamura, A. / Itoh, T. / Fukada, H. / Kishimoto, T. / Nishiya, Y.

History

Deposition	Dec 28, 2014	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Jan 13, 2016	Provider: repository / Type: Initial release
Revision 1.1	Feb 5, 2020	Group: Data collection / Derived calculations Category: diffrn_source / pdbx_prerelease_seq / pdbx_struct_oper_list Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2	Nov 8, 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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Validation report

Summary document	4xfp_validation.pdf.gz	476.7 KB	Display	wwPDB validaton report
Full document	4xfp_full_validation.pdf.gz	479.6 KB	Display
Data in XML	4xfp_validation.xml.gz	53.4 KB	Display
Data in CIF	4xfp_validation.cif.gz	78.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/xf/4xfp ftp://data.pdbj.org/pub/pdb/validation_reports/xf/4xfp	HTTPS FTP

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Related structure data

Related structure data	3wlvS 1j2g S: Starting model for refinement
Similar structure data	5z27-1 5yja-d 5z2b-1 5yj2-d 5y52-d 3wlv-d 5y2p-1 7cuc-1 5ayj-d 1j2g-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)

Deposited unit

A: Urate oxidase

B: Urate oxidase

C: Urate oxidase

D: Urate oxidase

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	134.135, 145.195, 71.141
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	18
Space group name H-M	P2₁2₁2

Details

biological unit is the same as asym.

#1: Protein	Urate oxidase Mass: 36235.684 Da / Num. of mol.: 4 / Fragment: UNP residues 178-494 / Mutation: P287G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus TB-90 (bacteria) / Strain: TB-90 / Gene: uao / Production host: Escherichia coli DH5alpha (bacteria) / Strain (production host): DH5alpha References: UniProt: Q45697, factor-independent urate hydroxylase
#2: Chemical	ChemComp-AZA / 8-AZAXANTHINE Mass: 153.099 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₄H₃N₅O₂
#3: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO₄
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1125 / 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: 2.43 Å³/Da / Density % sol: 49.4 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 15% PEG 8000, 0.1M TRIS-HCl, 0.07M K2SO4,

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

SPring-8

/ Beamline: BL26B2 / Wavelength: 1 Å

Detector

Type: RAYONIX MX-225 / Detector: CCD / Date: Nov 27, 2014

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→30 Å / Num. obs: 157977 / % possible obs: 94.3 % / Redundancy: 6 % / B_iso Wilson estimate: 19.03 Å² / R_merge(I) obs: 0.074 / R_pim(I) all: 0.031 / R_rim(I) all: 0.08 / Χ²: 1.664 / Net I/av σ(I): 29.423 / Net I/σ(I): 9.9 / Num. measured all: 944905

Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	CC_1/2	R_pim(I) all	R_rim(I) all	Χ²	% possible all
1.65-1.68	6.1	0.816	7556	0.783	0.342	0.887	0.744	91.6
1.68-1.71	6.1	0.709	7593	0.821	0.298	0.771	0.758	91.3
1.71-1.74	6	0.627	7645	0.854	0.263	0.682	0.784	91.8
1.74-1.78	6	0.479	7626	0.905	0.201	0.521	0.812	92.1
1.78-1.82	6	0.424	7680	0.917	0.178	0.461	0.84	92.5
1.82-1.86	6	0.345	7644	0.942	0.144	0.375	0.882	92.5
1.86-1.9	5.9	0.299	7729	0.958	0.126	0.326	0.95	92.7
1.9-1.96	5.9	0.227	7680	0.968	0.095	0.247	1.06	92.5
1.96-2.01	5.9	0.198	7702	0.978	0.083	0.215	1.12	92.6
2.01-2.08	5.8	0.169	7790	0.982	0.071	0.184	1.282	93
2.08-2.15	5.7	0.142	7765	0.987	0.06	0.154	1.357	93.3
2.15-2.24	5.6	0.123	7810	0.989	0.052	0.134	1.471	93.6
2.24-2.34	5.6	0.115	7791	0.99	0.049	0.125	1.496	93.4
2.34-2.46	5.6	0.1	7825	0.991	0.043	0.109	1.613	93.2
2.46-2.62	5.5	0.092	7872	0.993	0.039	0.1	1.872	94.1
2.62-2.82	5.5	0.089	8105	0.992	0.039	0.097	2.832	96.6
2.82-3.1	5.6	0.088	8379	0.993	0.038	0.096	4.133	99
3.1-3.55	6.4	0.066	8459	0.996	0.028	0.072	3.829	99.9
3.55-4.47	7.2	0.042	8559	0.999	0.017	0.046	2.635	100
4.47-30	7.1	0.034	8767	0.999	0.014	0.037	1.887	99.1

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Processing

Software

Name	Version	Classification
PHENIX	1.9-1692	refinement
SCALEPACK		data reduction
PHASER	2.5.6	phasing
PDB_EXTRACT	3.15	data extraction
HKL-2000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3WLV

3wlv

Resolution: 1.66→29.818 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 18.25 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1841	7662	4.95 %	Random selection
R_work	0.1558	147073	-	-
obs	0.1571	154735	94.26 %	-

Solvent computation

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

Displacement parameters

B_iso max: 80.9 Å² / B_iso mean: 25.001 Å² / B_iso min: 10.48 Å²

Refinement step

Cycle: final / Resolution: 1.66→29.818 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9368	0	70	1125	10563
B_iso mean	-	-	22.56	33.14	-
Num. residues	-	-	-	-	1175

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	9859
X-RAY DIFFRACTION	f_angle_d	1.03	13428
X-RAY DIFFRACTION	f_chiral_restr	0.041	1499
X-RAY DIFFRACTION	f_plane_restr	0.005	1726
X-RAY DIFFRACTION	f_dihedral_angle_d	11.455	3543

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.66-1.6789	0.2603	253	0.2213	4730	4983	92
1.6789-1.6986	0.2401	256	0.2127	4676	4932	91
1.6986-1.7193	0.2516	253	0.2177	4731	4984	92
1.7193-1.7411	0.2586	242	0.2075	4760	5002	92
1.7411-1.764	0.2387	254	0.1903	4707	4961	92
1.764-1.7882	0.2115	270	0.1755	4721	4991	92
1.7882-1.8137	0.2177	274	0.1809	4757	5031	92
1.8137-1.8408	0.227	232	0.1744	4757	4989	92
1.8408-1.8695	0.1981	259	0.1742	4737	4996	92
1.8695-1.9002	0.2112	274	0.1721	4775	5049	93
1.9002-1.9329	0.216	249	0.1709	4766	5015	92
1.9329-1.9681	0.2226	249	0.1659	4794	5043	93
1.9681-2.0059	0.1911	265	0.1633	4759	5024	93
2.0059-2.0469	0.2109	238	0.1611	4849	5087	93
2.0469-2.0913	0.1962	248	0.1578	4800	5048	93
2.0913-2.14	0.1928	256	0.1496	4859	5115	94
2.14-2.1935	0.1754	270	0.1497	4778	5048	93
2.1935-2.2528	0.1586	233	0.1482	4875	5108	93
2.2528-2.319	0.1967	245	0.1542	4846	5091	93
2.319-2.3939	0.197	231	0.1516	4842	5073	93
2.3939-2.4794	0.2057	253	0.1536	4867	5120	93
2.4794-2.5786	0.1874	248	0.1587	4879	5127	94
2.5786-2.6959	0.2142	213	0.1581	5025	5238	96
2.6959-2.8379	0.1744	241	0.1622	5084	5325	97
2.8379-3.0156	0.1953	259	0.1649	5141	5400	99
3.0156-3.2481	0.1828	323	0.1577	5192	5515	100
3.2481-3.5745	0.1677	281	0.1518	5231	5512	100
3.5745-4.0906	0.1509	267	0.1356	5313	5580	100
4.0906-5.1494	0.1249	267	0.1144	5359	5626	100
5.1494-29.8228	0.1908	259	0.1701	5463	5722	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	1.0567	-0.5233	0.2126	2.4584	-0.3434	0.8146	0.0157	0.0756	-0.0557	-0.0732	-0.0061	0.0783	0.1231	-0.0753	-0.0142	0.1382	-0.0366	-0.0082	0.1867	0.0074	0.1444	113.7169	28.1043	77.3289
2	4.7426	-2.627	2.002	1.9659	1.8929	1.9573	-0.0687	0.006	-0.4318	0.0053	-0.1059	-0.269	0.735	0.0926	0.2618	0.2927	0.0041	0.0283	0.1897	0.0001	0.1924	128.1102	10.5544	96.0099
3	0.94	0.2436	-0.2886	0.7075	0.0236	0.4946	-0.0006	0.1153	-0.0096	-0.0921	-0.0248	0.0873	0.0723	-0.0721	0.0246	0.1412	0.006	-0.0122	0.1176	-0.0107	0.1006	131.4367	25.547	74.0627
4	2.146	0.9811	0.2433	1.8572	0.2806	0.5112	-0.033	0.1219	-0.1095	-0.1193	0.0166	-0.0314	0.1077	-0.0214	0.0206	0.1808	0.0125	0.0113	0.1473	-0.0014	0.0857	139.6134	21.3555	71.1385
5	0.8582	-1.2991	-0.4218	3.4027	0.1534	0.2826	0.0222	-0.019	0.1041	-0.0778	-0.0363	-0.1483	-0.0092	0.0217	0.0197	0.1258	0.0016	0.0001	0.1441	0.0047	0.1429	141.5094	56.9812	73.243
6	1.535	0.4685	0.2425	3.6396	1.2664	1.4871	-0.0244	0.1938	-0.0592	-0.3254	0.0025	-0.0101	0.087	-0.0582	0.0239	0.1629	0.0075	0.0158	0.1452	0.0227	0.0681	146.9456	34.9325	63.7026
7	3.0071	-1.0007	-0.5497	4.0539	0.4949	1.9726	-0.0021	0.0811	0.1031	-0.2458	-0.0087	-0.1372	0.0354	0.0977	0.0146	0.0952	0.0072	0.0102	0.115	0.0081	0.0759	147.7745	47.0589	64.9436
8	3.3034	3.6976	3.3643	9.4736	2.1509	1.9889	-0.0844	-0.2107	0.5297	-0.2037	-0.0939	0.0839	-0.4097	-0.0894	0.0659	0.1665	0.0061	0.0262	0.2208	-0.0697	0.2997	144.3916	65.2936	90.2722
9	0.9938	-0.1676	-0.2194	0.5266	-0.1103	0.3295	0.0026	0.0831	0.014	-0.07	-0.0169	-0.0244	0.0546	-0.0567	0.0012	0.1335	-0.0069	-0.0122	0.1318	0.0129	0.1152	129.3814	50.0571	74.3329
10	0.5189	0.9039	-0.6755	1.6126	-1.4098	1.8967	0.011	-0.1464	-0.064	0.1064	-0.128	-0.0095	-0.0231	0.0552	0.148	0.1284	-0.0181	-0.0219	0.1594	-0.0046	0.1501	116.7909	50.4306	81.1079
11	6.858	0.6604	3.0863	7.9453	4.5109	7.166	0.1523	0.8694	0.1581	-0.8785	0.1705	-0.6064	-0.3876	0.3998	-0.2999	0.2244	0.026	0.076	0.2089	0.0244	0.1948	135.9253	62.0096	62.5142
12	4.1844	2.8179	-2.9683	3.0955	-1.0104	2.9592	0.0688	0.0528	0.0717	-0.0337	0.0413	0.1596	-0.1058	-0.1981	-0.114	0.1123	0.024	-0.0184	0.1333	0.0306	0.1532	118.6974	59.9137	76.053
13	0.5012	0.5356	-0.572	1.5093	-1.3358	2.4417	-0.033	0.0599	0.0308	-0.0636	0.0736	0.0387	0.128	-0.2224	-0.0493	0.1321	-0.0047	-0.0142	0.1908	0.0193	0.1866	119.1203	49.2388	79.4839
14	0.5822	0.6142	-0.1027	2.9929	-0.4558	0.3403	-0.0034	-0.0599	0.0074	0.2646	0.0453	0.0744	0.0171	-0.0419	-0.0341	0.1393	0.005	0.0219	0.1328	-0.0037	0.0765	125.342	47.0421	109.0394
15	1.3563	0.4735	0.0716	4.7421	-0.7482	1.2078	-0.019	-0.0399	0.075	0.1753	0.0138	0.0492	-0.0174	-0.1079	0.0071	0.1266	-0.0087	0.0254	0.1393	-0.0007	0.1078	119.7438	48.3724	112.2711
16	1.183	0.2471	-0.0361	1.1449	-0.6942	2.095	-0.0136	-0.0325	0.1162	0.1714	-0.0114	0.0497	-0.0876	0.0218	0.0566	0.1227	-0.0082	0.0003	0.0837	-0.0255	0.1205	127.733	52.3862	105.3662
17	0.1041	-0.5033	0.0828	1.1094	0.0323	0.2407	0.068	0.0413	0.0406	-0.0268	-0.0921	-0.2686	0.0422	0.1167	0.0343	0.13	0.0054	-0.0314	0.1818	0.0033	0.2279	155.7245	50.2455	95.4752
18	4.1724	-0.5616	-2.3905	1.4947	0.2082	2.6773	0.1447	-0.2423	0.1239	0.1664	-0.0215	-0.1094	-0.111	0.1521	-0.1468	0.1382	-0.0206	-0.0375	0.1015	-0.0244	0.1389	144.9125	60.9721	106.0438
19	0.5086	-0.5002	-0.5776	1.3486	0.8955	2.2624	-0.0364	-0.0828	0.0308	0.1051	0.0424	-0.0799	0.1209	0.2467	-0.0354	0.1318	-0.0034	-0.0373	0.1794	-0.0094	0.1906	150.0587	49.5928	98.173
20	0.7342	0.1085	-0.0323	1.9127	0.1353	0.5334	-0.0067	-0.0747	-0.0487	0.1723	-0.0059	-0.1371	0.1003	0.0549	0.0079	0.1499	0.0307	-0.0299	0.1565	0.0108	0.1548	153.7745	28.7013	100.1076
21	1.6395	0.9193	-0.4075	3.3984	0.5145	1.0948	-0.0019	-0.0634	0.0413	0.2544	-0.0093	-0.3173	0.1107	0.1365	0.0012	0.1216	0.0278	-0.0528	0.1643	0.0092	0.1544	159.3654	29.5883	101.6168
22	1.0568	-0.2542	-0.3017	0.5179	-0.2067	0.2505	-0.0323	-0.0651	-0.0293	0.0594	-0.022	-0.0273	0.1233	0.0038	0.0771	0.1667	-0.0134	-0.0153	0.117	0.0139	0.1091	139.3827	22.7331	99.5428
23	3.5487	-1.1548	-0.091	1.7456	-0.1698	0.4233	-0.0239	-0.161	-0.1946	0.1208	0.0088	0.0207	0.1325	0.0198	0.0182	0.2127	-0.0108	0.001	0.137	0.0114	0.079	132.3302	18.3132	107.8635
24	1.4894	-1.2892	0.2527	2.3416	-0.5121	0.7913	-0.1631	-0.1906	0.0188	0.2143	0.1087	-0.0467	0.0063	-0.0749	0.0441	0.166	-0.0237	0.0175	0.1542	0.0222	0.0771	127.5086	26.3912	105.355

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 8 through 119 )	A
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 120 through 135 )	A
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 136 through 192 )	A
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 193 through 310 )	A
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 8 through 43 )	B
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 44 through 72 )	B
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 73 through 119 )	B
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 120 through 135 )	B
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 136 through 192 )	B
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 193 through 213 )	B
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 214 through 229 )	B
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 230 through 263 )	B
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 264 through 310 )	B
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 8 through 72 )	C
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 73 through 106 )	C
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 107 through 172 )	C
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 173 through 213 )	C
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 214 through 263 )	C
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 264 through 310 )	C
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 8 through 72 )	D
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 73 through 119 )	D
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 120 through 192 )	D
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 193 through 263 )	D
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 264 through 310 )	D

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