PDB-5y2p: Crystal Structure of Bacillus sp. TB-90 Urate Oxidase Improved by...

ID or keywords:

Entry

Database: PDB / ID: 5y2p

Title

Crystal Structure of Bacillus sp. TB-90 Urate Oxidase Improved by Humidity Control at 89% 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 / 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 sp. (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.5 Å

Authors

Itoh, 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	Jul 26, 2017	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Aug 8, 2018	Provider: repository / Type: Initial release
Revision 1.1	Sep 2, 2020	Group: Derived calculations / Structure summary / Category: struct / struct_conn Item: _struct.title / _struct_conn.conn_type_id ..._struct.title / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Revision 1.2	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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PDBx/mmCIF format	5y2p.cif.gz	377.6 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	5y2p_validation.pdf.gz	474.1 KB	Display	wwPDB validaton report
Full document	5y2p_full_validation.pdf.gz	476 KB	Display
Data in XML	5y2p_validation.xml.gz	30.7 KB	Display
Data in CIF	5y2p_validation.cif.gz	46.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/y2/5y2p ftp://data.pdbj.org/pub/pdb/validation_reports/y2/5y2p	HTTPS FTP

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Related structure data

Related structure data	3wlvS S: Starting model for refinement
Similar structure data	3wlv-d 5y52-d 7cuc-1 7cmq-1 5yj2-d 5z27-1 7cuf-1 5z2b-1 1j2g-d 5yja-d Search similar-shape structures by Omokage search (details) 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

hetero molecules

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

1

A: Uric acid degradation bifunctional protein

B: Uric acid degradation bifunctional protein

hetero molecules

A: Uric acid degradation bifunctional protein

B: Uric acid degradation bifunctional protein

hetero molecules

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

Unit cell

Length a, b, c (Å)	71.095, 133.885, 145.797
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	23
Space group name H-M	I222

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Protein , 1 types, 2 molecules AB

#1: Protein	Uric acid degradation bifunctional protein Mass: 35714.102 Da / Num. of mol.: 2 / 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 (E. coli) / Strain (production host): DH5alpha References: UniProt: Q45697, factor-independent urate hydroxylase

#1: Protein

Uric acid degradation bifunctional protein

Mass: 35714.102 Da / Num. of mol.: 2 / 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 (E. coli) / Strain (production host): DH5alpha
References: UniProt: Q45697, factor-independent urate hydroxylase

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Non-polymers , 6 types, 692 molecules

#2: Chemical	ChemComp-AZA / 8-AZAXANTHINE Mass: 153.099 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₄H₃N₅O₂
#3: Chemical	ChemComp-OXY / OXYGEN MOLECULE Mass: 31.999 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: O₂
#4: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO₄
#5: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₂H₆O₂
#6: Chemical	ChemComp-K / POTASSIUM ION Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 680 / 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: 2.28 Å³/Da / Density % sol: 46.2 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.1 M Tris-HCl, 0.06 M K2SO4, 16% (w/v) PEG 8000

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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: ADSC QUANTUM 315 / Detector: CCD / Date: May 22, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.5→40.121 Å / Num. obs: 111066 / % possible obs: 99.9 % / Redundancy: 7.2 % / R_merge(I) obs: 0.077 / R_pim(I) all: 0.031 / Net I/σ(I): 34.5
Reflection shell	Resolution: 1.5→1.53 Å / Redundancy: 6.9 % / R_merge(I) obs: 0.895 / Mean I/σ(I) obs: 2.47 / Num. unique obs: 5500 / CC_1/2: 0.78 / R_pim(I) all: 0.367 / % possible all: 100

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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: 1.5→40.121 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.33

	R_factor	Num. reflection	% reflection
R_free	0.1769	5546	4.99 %
R_work	0.1574	-	-
obs	0.1584	111035	99.91 %

Solvent computation

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

Refine analyze

Luzzati coordinate error obs: 0.162 Å

Refinement step

Cycle: LAST / Resolution: 1.5→40.121 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4824	0	56	680	5560

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	5139
X-RAY DIFFRACTION	f_angle_d	1.091	6989
X-RAY DIFFRACTION	f_dihedral_angle_d	11.632	1857
X-RAY DIFFRACTION	f_chiral_restr	0.082	775
X-RAY DIFFRACTION	f_plane_restr	0.008	901

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 (%)
1.4999-1.5169	0.2887	178	0.245	3470	X-RAY DIFFRACTION	100
1.5169-1.5347	0.2642	183	0.2329	3473	X-RAY DIFFRACTION	100
1.5347-1.5535	0.2745	169	0.2247	3487	X-RAY DIFFRACTION	100
1.5535-1.5731	0.2346	177	0.2145	3513	X-RAY DIFFRACTION	100
1.5731-1.5938	0.2575	158	0.2078	3534	X-RAY DIFFRACTION	100
1.5938-1.6157	0.2267	191	0.2001	3498	X-RAY DIFFRACTION	100
1.6157-1.6387	0.2541	193	0.1877	3441	X-RAY DIFFRACTION	100
1.6387-1.6632	0.2069	173	0.1909	3480	X-RAY DIFFRACTION	100
1.6632-1.6892	0.2147	198	0.1796	3483	X-RAY DIFFRACTION	100
1.6892-1.7169	0.2011	177	0.1784	3522	X-RAY DIFFRACTION	100
1.7169-1.7465	0.2194	184	0.1767	3477	X-RAY DIFFRACTION	100
1.7465-1.7783	0.1962	200	0.1681	3493	X-RAY DIFFRACTION	100
1.7783-1.8125	0.2104	191	0.1721	3480	X-RAY DIFFRACTION	100
1.8125-1.8495	0.1825	171	0.1636	3512	X-RAY DIFFRACTION	100
1.8495-1.8897	0.1962	167	0.1667	3508	X-RAY DIFFRACTION	100
1.8897-1.9336	0.1991	178	0.1624	3495	X-RAY DIFFRACTION	100
1.9336-1.982	0.1764	168	0.1535	3533	X-RAY DIFFRACTION	100
1.982-2.0356	0.1688	190	0.1544	3498	X-RAY DIFFRACTION	100
2.0356-2.0955	0.1596	187	0.1512	3506	X-RAY DIFFRACTION	100
2.0955-2.1631	0.1687	191	0.1477	3515	X-RAY DIFFRACTION	100
2.1631-2.2404	0.1747	208	0.1397	3490	X-RAY DIFFRACTION	100
2.2404-2.3301	0.1774	211	0.1429	3493	X-RAY DIFFRACTION	100
2.3301-2.4361	0.1573	197	0.1456	3525	X-RAY DIFFRACTION	100
2.4361-2.5645	0.1728	189	0.1531	3531	X-RAY DIFFRACTION	100
2.5645-2.7252	0.1722	187	0.148	3517	X-RAY DIFFRACTION	100
2.7252-2.9355	0.1859	187	0.146	3552	X-RAY DIFFRACTION	100
2.9355-3.2308	0.1537	174	0.1492	3582	X-RAY DIFFRACTION	100
3.2308-3.6981	0.162	197	0.1443	3558	X-RAY DIFFRACTION	100
3.6981-4.6581	0.1371	181	0.1339	3609	X-RAY DIFFRACTION	100
4.6581-40.1353	0.1719	191	0.1705	3714	X-RAY DIFFRACTION	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	0.3433	0.1302	0.0999	1.1488	0.4615	2.2965	0.0203	0.0602	0.0692	-0.0581	0.0207	-0.1352	-0.1369	0.1869	-0.0496	0.1244	-0.0097	0.0167	0.1136	0.0243	0.1481	11.0997	18.9336	28.8683
2	0.312	-0.1642	-0.0714	0.5202	-0.05	0.5627	0.0178	0.0429	0.0896	-0.0363	0.0008	-0.1075	-0.1072	0.0699	-0.0127	0.1031	-0.0108	0.0107	0.0969	0.0073	0.1205	11.5662	11.9438	25.5357
3	0.5527	0.0339	-0.1829	2.6291	-0.9942	1.6881	0.0396	0.1004	0.0581	-0.1305	-0.0286	-0.1425	-0.0134	0.201	-0.0103	0.0762	0.007	0.028	0.1585	-0.0058	0.1317	19.3437	-1.6689	19.2656
4	1.7194	-0.356	-0.1857	0.276	-0.1159	1.5078	0.0332	0.113	-0.0929	-0.1622	-0.0743	0.0086	0.2886	0.0725	0.0205	0.1673	0.029	0.0044	0.0987	-0.0032	0.1128	10.904	-16.1442	27.2081
5	0.4016	-0.2238	-0.4042	0.4171	0.4337	1.79	-0.0084	-0.0529	0.004	0.0157	0.0239	-0.0777	0.0855	0.2777	-0.0202	0.0786	0.0306	0.0003	0.1448	0.0039	0.1175	20.008	-9.32	47.6075
6	1.7302	-0.2377	-0.9775	0.7857	0.2028	1.5136	-0.0395	-0.0728	-0.0544	0.1122	0.0269	-0.0815	0.1643	0.1756	0.0143	0.1043	0.0294	-0.004	0.1019	0.0003	0.1057	19.7402	-12.4124	49.8271
7	2.5345	-0.0331	-0.4676	1.1	0.1475	0.6029	0.0536	0.0138	0.0236	0.062	0.0017	-0.1197	0.0354	0.1598	-0.0294	0.0797	0.0185	-0.0293	0.1256	-0.0249	0.0704	16.558	-5.586	54.165
8	0.3593	-0.1254	0.029	0.8903	-0.5999	1.1934	0.0007	-0.0611	0.0739	0.0431	0.0512	-0.0145	-0.1459	0.1086	-0.059	0.1291	-0.0119	-0.0229	0.1203	-0.0416	0.131	11.4409	14.5921	55.5593
9	1.351	-0.2475	1.0698	0.755	-0.4516	1.5636	-0.0978	-0.0859	0.2118	0.0631	0.015	0.0069	-0.2095	0.0285	0.0901	0.1492	-0.0131	-0.0044	0.1025	-0.03	0.1287	8.996	16.9647	52.915

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 8 through 72 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 73 through 192 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 193 through 276 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 277 through 310 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 8 through 72 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 73 through 129 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 130 through 172 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 173 through 248 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 249 through 310 )

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