PDB-7cug: Crystal Structure of Urate Oxidase from Bacillus sp. TB-90 in the...

ID or keywords:

Entry

Database: PDB / ID: 7cug

Title

Crystal Structure of Urate Oxidase from Bacillus sp. TB-90 in the absence from Chloride Anion at 1.62 A resolution

Components

Uric acid degradation bifunctional protein

Keywords

OXIDOREDUCTASE / catalytic mechanism / water structure / enzyme kinetics / enzyme structure / conformational flexibility / quasi-stable water molecule

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: 1.62 Å

Authors

Hibi, T. / Itoh, T.

Citation

Journal: J.Biochem. / Year: 2021
Title: Identification of quasi-stable water molecules near the Thr73-Lys13 catalytic diad of Bacillus sp. TB-90 urate oxidase by X-ray crystallography with controlled humidity.
Authors: Hibi, T. / Itoh, T.

History

Deposition	Aug 23, 2020	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Nov 25, 2020	Provider: repository / Type: Initial release
Revision 1.1	Feb 17, 2021	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2	Nov 29, 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	7cug.cif.gz	448.6 KB	Display	PDBx/mmCIF format
PDB format	pdb7cug.ent.gz	305 KB	Display	PDB format
PDBx/mmJSON format	7cug.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7cug_validation.pdf.gz	1.5 MB	Display	wwPDB validaton report
Full document	7cug_full_validation.pdf.gz	1.5 MB	Display
Data in XML	7cug_validation.xml.gz	29.8 KB	Display
Data in CIF	7cug_validation.cif.gz	45.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/cu/7cug ftp://data.pdbj.org/pub/pdb/validation_reports/cu/7cug	HTTPS FTP

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Related structure data

Related structure data	7cucC 7cufC 3wlvS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	7cuf-1 7cmn-1 7cmq-1 3wlv-d 7cuc-1 5y2p-1 5z2b-1 1j2g-d 5lsr-1 5y52-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

72.5 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)	71.657, 133.715, 145.279
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	23
Space group name H-M	I222
Space group name Hall	I22
Symmetry operation	#1: x,y,z #2: x,-y,-z #3: -x,y,-z #4: -x,-y,z #5: x+1/2,y+1/2,z+1/2 #6: x+1/2,-y+1/2,-z+1/2 #7: -x+1/2,y+1/2,-z+1/2 #8: -x+1/2,-y+1/2,z+1/2

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Protein , 1 types, 2 molecules AB

#1: Protein	Uric acid degradation bifunctional protein / Urate oxidase Mass: 35823.301 Da / Num. of mol.: 2 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, factor-independent urate hydroxylase

#1: Protein

Uric acid degradation bifunctional protein / Urate oxidase

Mass: 35823.301 Da / Num. of mol.: 2
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, factor-independent urate hydroxylase

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Non-polymers , 6 types, 644 molecules

#2: Chemical	ChemComp-AZA / 8-AZAXANTHINE Mass: 153.099 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₄H₃N₅O₂ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-OXY / OXYGEN MOLECULE Mass: 31.999 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: O₂ / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-MXE / 2-METHOXYETHANOL Mass: 76.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₃H₈O₂
#5: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO₄
#6: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 633 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	Y

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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: 50.2 %
Crystal grow	Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8.3 Details: 16%(w/v) PEG 8000, 0.1M Tris/H2SO4, pH 8.3, 0.09 M K2SO4, 2mM 8-azaxanthine

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
Detector	Type: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Jan 22, 2020
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.62→50 Å / Num. obs: 87767 / % possible obs: 98.4 % / Redundancy: 12.9 % / B_iso Wilson estimate: 17.61 Å² / CC_1/2: 0.993 / R_merge(I) obs: 0.138 / R_rim(I) all: 0.372 / Net I/σ(I): 8.1
Reflection shell	Resolution: 1.62→1.72 Å / R_merge(I) obs: 0.372 / Mean I/σ(I) obs: 2 / Num. unique obs: 2227 / CC_1/2: 0.879 / R_rim(I) all: 0.413 / % possible all: 91.9

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Processing

Software

Name	Version	Classification
PHASER		phasing
PHENIX	1.18.2_3874	refinement
XDS		data reduction
XDS		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3WLV

3wlv

Resolution: 1.62→42.61 Å / SU ML: 0.2318 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 26.5022
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2562	4389	5 %
R_work	0.2188	83338	-
obs	0.2207	87727	98.61 %

Solvent computation

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

Displacement parameters

B_iso mean: 22.82 Å²

Refine analyze

Luzzati coordinate error obs: 0.257 Å

Refinement step

Cycle: LAST / Resolution: 1.62→42.61 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4803	0	57	633	5493

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0125	5025
X-RAY DIFFRACTION	f_angle_d	0.9891	6817
X-RAY DIFFRACTION	f_chiral_restr	0.0612	755
X-RAY DIFFRACTION	f_plane_restr	0.0088	871
X-RAY DIFFRACTION	f_dihedral_angle_d	6.0139	681

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 (%)
1.62-1.64	0.371	112	0.3113	2115	X-RAY DIFFRACTION	75.24
1.64-1.66	0.3147	140	0.2924	2671	X-RAY DIFFRACTION	97.06
1.66-1.68	0.2791	143	0.2714	2706	X-RAY DIFFRACTION	97.24
1.68-1.7	0.2897	143	0.2653	2726	X-RAY DIFFRACTION	97.39
1.7-1.72	0.2952	144	0.2661	2733	X-RAY DIFFRACTION	97.46
1.72-1.74	0.2953	143	0.2643	2723	X-RAY DIFFRACTION	98.15
1.74-1.77	0.2901	143	0.2585	2719	X-RAY DIFFRACTION	98.49
1.77-1.79	0.3015	148	0.2659	2792	X-RAY DIFFRACTION	99.09
1.79-1.82	0.3245	146	0.2987	2781	X-RAY DIFFRACTION	99.36
1.82-1.85	0.3546	146	0.2871	2779	X-RAY DIFFRACTION	99.86
1.85-1.88	0.343	148	0.2853	2813	X-RAY DIFFRACTION	99.9
1.88-1.92	0.2945	147	0.269	2781	X-RAY DIFFRACTION	99.97
1.92-1.96	0.299	146	0.2555	2787	X-RAY DIFFRACTION	100
1.96-2	0.2534	149	0.254	2818	X-RAY DIFFRACTION	100
2-2.04	0.3089	147	0.2525	2794	X-RAY DIFFRACTION	100
2.04-2.09	0.3085	147	0.2573	2807	X-RAY DIFFRACTION	100
2.09-2.14	0.2837	148	0.2491	2802	X-RAY DIFFRACTION	100
2.14-2.2	0.3164	148	0.2431	2817	X-RAY DIFFRACTION	100
2.2-2.26	0.3165	147	0.2396	2792	X-RAY DIFFRACTION	100
2.26-2.33	0.2928	149	0.2431	2832	X-RAY DIFFRACTION	100
2.33-2.42	0.2625	147	0.225	2795	X-RAY DIFFRACTION	100
2.42-2.51	0.2901	150	0.2262	2837	X-RAY DIFFRACTION	100
2.51-2.63	0.2714	148	0.2231	2812	X-RAY DIFFRACTION	100
2.63-2.77	0.252	149	0.2223	2843	X-RAY DIFFRACTION	100
2.77-2.94	0.2641	148	0.2098	2804	X-RAY DIFFRACTION	100
2.94-3.17	0.2421	151	0.2029	2867	X-RAY DIFFRACTION	100
3.17-3.49	0.2232	149	0.1802	2843	X-RAY DIFFRACTION	100
3.49-3.99	0.1914	151	0.1715	2872	X-RAY DIFFRACTION	100
3.99-5.02	0.1657	153	0.1469	2899	X-RAY DIFFRACTION	100
5.03-42.61	0.2121	159	0.1976	2978	X-RAY DIFFRACTION	98.9

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	0.603608208307	-0.297331687532	-0.093781502493	0.714743663756	-0.0170872484662	0.653805500455	0.201976086567	0.164286913109	-0.0685914418597	-0.259430674909	-0.122302596024	0.0917890595548	0.0765483392646	-0.0650729146654	-0.0893373120064	0.256808322747	0.0536190643913	-0.0704021178301	0.15683261177	-0.0412966106356	0.165759309837	-11.2553433314	-18.7495930576	-43.9662248391
2	0.987736723835	0.574584534771	-0.249322395987	1.03358715471	-0.275350366151	0.506141340638	0.1833206688	0.167096140178	-0.143604182595	0.0498362141628	-0.0897528971207	0.0346889570312	-0.0185364820614	-0.0339427189011	-0.0718085737472	0.265756937536	0.0696779523293	-0.0781089143632	0.170249940499	-0.0360221437936	0.1973491798	-8.74166848448	-20.9346068542	-46.9959384604
3	0.558601519699	-0.30805381455	-0.0400571130292	0.488977452685	0.339089375369	0.429680625022	0.164286507533	0.14455799565	-0.0462056494279	-0.0331028772532	-0.0833553563113	0.0221581518901	0.0349350819469	-0.0603279269157	-0.0792306864644	0.220666734278	0.0716274448227	-0.0316609170911	0.167788387368	-0.00468355310931	0.146400818314	-14.3836042778	-3.62364577647	-47.6751967246
4	0.580409295561	-0.125572173993	0.170520067713	1.30121874976	0.423793509368	0.940037396309	0.134520627558	0.165945460024	-0.0328167027661	-0.215997096703	-0.108703297376	-0.00126592956138	0.0445421482732	-0.0407644965566	-0.0254960410818	0.251956824635	0.118586786049	-0.00952032230858	0.250384877125	-0.00475747516429	0.168108049584	-19.4663882715	1.90332014761	-53.6093617692
5	2.19022343984	0.614220605595	0.209572579575	1.50446659945	0.484749086405	0.785337682701	-0.037125008145	0.199208681548	0.188925441148	-0.277547271832	0.00517862474951	-0.030276947052	-0.149600577247	-0.0271595481544	0.0145008320953	0.221481127298	0.0694804868754	0.0246010177141	0.192597175799	0.0327584738274	0.166730530435	-10.7139849853	16.0206192933	-45.6138074272
6	0.442562749074	-0.255668530639	0.462460191157	0.540177562932	-0.448812441962	1.13145178091	0.0324992822909	-0.0180225371494	0.042670439133	-0.0490083021037	-0.0302910956529	-0.0196715222462	0.0140527392423	-0.116862124892	-0.00415261568452	0.122326064184	0.0206699179941	0.0117245766757	0.157758483055	0.00196303160191	0.138874576849	-19.8538121555	9.14027399724	-25.0251196767
7	1.07338441927	-0.474115705409	0.449212850934	1.17645863053	-0.334688242551	1.6763204477	0.0518509246194	-0.0333330913138	0.016128286302	0.00470273040181	-0.0618161849021	0.0362559063737	-0.0141844028512	-0.0757524438245	0.0138173979947	0.0916550638037	0.0102240858347	-0.00141619945239	0.125889554866	0.00860282587068	0.13358296148	-24.1948484533	13.205131521	-25.5547577717
8	4.84617679527	0.386357364751	3.6951134629	1.13870314448	-0.096530985335	5.23797461248	0.101809001839	-0.389209665915	0.12292424574	0.213177831186	-0.0537531596876	-0.128189714837	-0.0732456331275	-0.104869789442	-0.0284587974784	0.212585825606	0.00664191650236	-0.0310975956379	0.182062361322	-0.0053936938056	0.195763642428	1.7341989885	10.0987641454	-6.92588326264
9	1.48179094499	0.0786850336039	0.027102097874	0.448238055448	0.0556288188941	0.234108091574	-0.0362299530889	0.208240501209	0.0254364320565	0.0722506686216	0.0229820477505	0.0371870428836	-0.0389140655528	-0.013290464131	0.0199997601367	0.138316070288	-0.00118041490396	0.0154675750767	0.146606309303	0.00625010462483	0.126279359452	-17.561004357	6.5008797526	-21.4005227104
10	0.187975356007	0.18116075397	0.144967413664	0.183657909497	0.256668189037	0.480288847275	0.073961951565	-0.0265823398545	-0.0946841875391	-0.00202991012644	0.033735990163	-0.114905213764	0.123974644083	0.0266749712642	-0.103646658089	0.169847183785	-0.00427239016312	-0.0252977372845	0.129465996218	0.0229090210776	0.177475454525	-10.3707809502	-17.4527052688	-22.95114571
11	2.36538463902	0.870877443418	0.344600133796	2.64707172788	0.0573358577709	1.92925705231	0.189959072051	-0.28197750219	0.124301423296	0.0805855324333	-0.164270670094	0.349100336815	-0.220591204731	-0.474337920169	-0.0255209648217	0.157501333728	0.0308910793818	0.0170184034559	0.266511990563	0.0242673096272	0.186590578665	-26.5533942521	1.76183162697	-10.4442982136
12	1.11725962371	-0.635770711307	-0.285496303779	1.03331814623	0.676388398242	0.939944205871	-0.0274491825367	-0.074812361907	-0.132923592606	0.156406278732	-0.01275463494	0.0965318458015	0.160918619543	-0.0284668619077	0.0407016811923	0.140043137555	-0.0187724609024	0.0116876209961	0.138435574124	0.0306602244769	0.153387864012	-14.7426934103	-14.4567552767	-14.0391913703
13	1.59002884244	0.608309461374	-0.808372382868	0.791486789848	0.201896473433	1.45885384434	-0.102894973329	-0.0522027920194	-0.074153956783	0.0701298125355	0.0451897534223	-0.0727145395885	0.335221406911	0.120436220502	0.032321948293	0.207194645046	0.0145893282003	-0.0140307253926	0.115252167345	0.00214473820234	0.122350454148	-0.280981889832	-19.1563704043	-23.7161084302

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

ID	Refine TLS-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	chain 'A' and (resid 8 through 72 )	A	A	8 - 72	1 - 65
2	2	chain 'A' and (resid 73 through 132 )	A	A	73 - 132	66 - 125
3	3	chain 'A' and (resid 133 through 192 )	A	A	133 - 192	126 - 186
4	4	chain 'A' and (resid 193 through 276 )	A	A	193 - 276	187 - 270
5	5	chain 'A' and (resid 277 through 310 )	A	A	277 - 310	271 - 304
6	6	chain 'B' and (resid 8 through 72 )	B	I	8 - 72	1 - 65
7	7	chain 'B' and (resid 73 through 119 )	B	I	73 - 119	66 - 113
8	8	chain 'B' and (resid 120 through 135 )	B	I	120 - 135	114 - 129
9	9	chain 'B' and (resid 136 through 161 )	B	I	136 - 161	130 - 157
10	10	chain 'B' and (resid 162 through 213 )	B	I	162 - 213	158 - 210
11	11	chain 'B' and (resid 214 through 229 )	B	I	214 - 229	211 - 226
12	12	chain 'B' and (resid 230 through 276 )	B	I	230 - 276	227 - 274
13	13	chain 'B' and (resid 277 through 310 )	B	I	277 - 310	275 - 308

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Protein , 1 types, 2 molecules AB

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Non-polymers , 6 types, 644 molecules

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Details

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Sample preparation

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