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

ID or keywords:

Entry

Database: PDB / ID: 7cuf

Title

Crystal Structure of Urate Oxidase from Bacillus sp. TB-90 in the absence from Chloride Anion at 1.44 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: 1.46 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 22, 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	7cuf.cif.gz	450 KB	Display	PDBx/mmCIF format
PDB format	pdb7cuf.ent.gz	306.6 KB	Display	PDB format
PDBx/mmJSON format	7cuf.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7cuf_validation.pdf.gz	1.7 MB	Display	wwPDB validaton report
Full document	7cuf_full_validation.pdf.gz	1.7 MB	Display
Data in XML	7cuf_validation.xml.gz	30.7 KB	Display
Data in CIF	7cuf_validation.cif.gz	47.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/cu/7cuf ftp://data.pdbj.org/pub/pdb/validation_reports/cu/7cuf	HTTPS FTP

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Related structure data

Related structure data	7cucC 7cugC 3wlvS 7cmn C: citing same article (ref.) S: Starting model for refinement
Similar structure data	7cmq-1 3wlv-d 5ayj-d 5y2p-1 7cuc-1 7cug-1 5y52-d 5z27-1 5yj2-d 5z2b-1 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

72.6 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)	71.622, 133.850, 145.391
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, 711 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-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Chemical	ChemComp-MXE / 2-METHOXYETHANOL Mass: 76.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₃H₈O₂
#6: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO₄
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 698 / 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: 50.3 %
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: 1.46→50 Å / Num. obs: 120337 / % possible obs: 97.9 % / Redundancy: 16.4 % / B_iso Wilson estimate: 18.12 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.081 / R_rim(I) all: 0.085 / Net I/σ(I): 13.6
Reflection shell	Resolution: 1.46→1.47 Å / R_merge(I) obs: 0.534 / Mean I/σ(I) obs: 2 / Num. unique obs: 3561 / CC_1/2: 0.845 / R_rim(I) all: 0.574 / % possible all: 92.4

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3WLV

3wlv

Resolution: 1.46→40.14 Å / SU ML: 0.2035 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.0051
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2306	6017	5 %
R_work	0.1992	114309	-
obs	0.2007	120326	98.51 %

Solvent computation

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

Displacement parameters

B_iso mean: 22.15 Å²

Refinement step

Cycle: LAST / Resolution: 1.46→40.14 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4799	0	63	698	5560

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0096	5051
X-RAY DIFFRACTION	f_angle_d	1.0937	6853
X-RAY DIFFRACTION	f_chiral_restr	0.0841	760
X-RAY DIFFRACTION	f_plane_restr	0.0081	873
X-RAY DIFFRACTION	f_dihedral_angle_d	6.4794	683

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 (%)
1.46-1.47	0.3357	178	0.3175	3383	X-RAY DIFFRACTION	87.9
1.47-1.49	0.3437	192	0.3123	3642	X-RAY DIFFRACTION	94.92
1.49-1.51	0.3235	190	0.3015	3625	X-RAY DIFFRACTION	95.35
1.51-1.53	0.296	195	0.2794	3696	X-RAY DIFFRACTION	95.44
1.53-1.55	0.3077	195	0.2717	3706	X-RAY DIFFRACTION	96.61
1.55-1.57	0.2818	194	0.272	3681	X-RAY DIFFRACTION	95.96
1.57-1.59	0.3026	193	0.2718	3672	X-RAY DIFFRACTION	96.58
1.59-1.61	0.3105	197	0.2732	3745	X-RAY DIFFRACTION	97.38
1.61-1.64	0.2598	199	0.2644	3771	X-RAY DIFFRACTION	97.88
1.64-1.67	0.326	199	0.2767	3783	X-RAY DIFFRACTION	98.56
1.67-1.69	0.2779	201	0.2571	3817	X-RAY DIFFRACTION	99.41
1.69-1.73	0.2889	200	0.2595	3808	X-RAY DIFFRACTION	99.58
1.73-1.76	0.2828	202	0.2482	3841	X-RAY DIFFRACTION	99.8
1.76-1.79	0.2819	202	0.2447	3838	X-RAY DIFFRACTION	99.85
1.79-1.83	0.2757	202	0.2535	3828	X-RAY DIFFRACTION	99.98
1.83-1.88	0.2946	204	0.2445	3881	X-RAY DIFFRACTION	100
1.88-1.92	0.277	202	0.2383	3836	X-RAY DIFFRACTION	100
1.92-1.97	0.2555	203	0.2257	3849	X-RAY DIFFRACTION	100
1.97-2.03	0.252	202	0.2255	3849	X-RAY DIFFRACTION	100
2.03-2.1	0.2489	204	0.2161	3869	X-RAY DIFFRACTION	100
2.1-2.17	0.2301	204	0.2081	3874	X-RAY DIFFRACTION	100
2.17-2.26	0.2199	202	0.1969	3852	X-RAY DIFFRACTION	100
2.26-2.36	0.2537	204	0.1952	3861	X-RAY DIFFRACTION	100
2.36-2.49	0.2299	206	0.1972	3912	X-RAY DIFFRACTION	100
2.49-2.64	0.24	203	0.192	3874	X-RAY DIFFRACTION	100
2.64-2.85	0.2306	207	0.1872	3921	X-RAY DIFFRACTION	100
2.85-3.13	0.2039	204	0.1828	3883	X-RAY DIFFRACTION	100
3.13-3.59	0.1941	207	0.1615	3939	X-RAY DIFFRACTION	100
3.59-4.52	0.1799	209	0.1413	3966	X-RAY DIFFRACTION	99.98
4.52-40.14	0.1815	217	0.1663	4107	X-RAY DIFFRACTION	99.93

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	0.417909045161	-0.253676668811	-0.154790553762	0.65806178809	-0.0630202255513	0.866494158346	0.146256067273	0.110527251439	-0.105097283365	-0.150816912908	-0.0915505859983	0.0986999210061	0.0841616573576	-0.109240524792	-0.0516929341915	0.222728395954	0.00676341900934	-0.0548404320951	0.147912419893	-0.0316812951212	0.173969505525	-11.1725165264	-18.9991422608	-43.5530751924
2	0.986994589915	-0.210354907176	-0.0686508798849	1.35511828983	-0.639627158708	1.59745798323	0.126543375924	0.101333257679	-0.17335952856	-0.131987134241	-0.0903466726229	0.110979347013	0.16456339472	-0.0623095268955	-0.0470591265147	0.242635558295	0.00217521682207	-0.0648463098058	0.131721136289	-0.0298809433402	0.202371822622	-12.588608012	-24.4805387369	-43.4544278251
3	0.578131680446	-0.3021183005	-0.0257277563362	0.662456223442	0.194703699838	0.520473540148	0.108099875628	0.135908236097	-0.0490450489691	-0.0873229519172	-0.0507914855265	0.0374123314475	0.103214430892	-0.0462021305973	-0.0585849457482	0.202982646161	0.0346265257215	-0.0262262561134	0.154334004022	0.00216050934394	0.128404492036	-10.1413052054	-4.18091780092	-50.5104127046
4	0.455546139886	-0.0794524181389	0.106749800951	1.94860655754	0.694697179478	1.30003600272	0.125167282772	0.126568241715	-0.0316229531064	-0.220981154434	-0.118326647855	0.0690084318576	0.0183919879411	-0.109405363012	-0.00825273629213	0.202105342774	0.0708730705495	-0.0107671855122	0.221891937915	-0.00290227419926	0.169882667878	-19.3684728324	2.02253177313	-53.6193793264
5	2.24579886875	0.643784227123	0.439898181334	1.47413875449	0.476112435077	1.34193780705	0.0408437108561	0.139422757494	0.114615905841	-0.261069647461	-0.0644284231333	-0.0626265518502	-0.218504901571	0.0500451876882	0.0238640439845	0.213216254046	0.0726626376739	0.0219583530603	0.148643432081	0.0167492639679	0.147097993713	-10.7118207796	15.9956581014	-45.5619140231
6	0.523578147273	-0.294422037557	0.426877043086	0.223712181762	-0.375127062523	1.24678466345	0.0111273464478	-0.0744320982474	0.00330249276221	-0.00258299031388	0.0139687209973	-0.0292251221123	-0.0646950200798	-0.118603837056	-0.00899259110436	0.136841318858	0.00338058930186	-0.00372167639821	0.156556159161	-0.004474286581	0.131220309056	-15.8864547712	6.98916064025	-16.0295552438
7	1.05488939731	-0.0221529380537	0.944718676836	0.663085372213	-0.0702023761226	2.07431916407	-0.0166754182107	0.013430332861	0.0276641411416	-0.0781998847068	-0.0388919875562	0.0474103542431	-0.014776511629	-0.196464682438	-0.0199089833399	0.153357168784	0.040561394308	0.00364941249051	0.169578421018	0.00257602860143	0.150127302113	-25.6189126489	12.2574477182	-38.0674642034
8	0.954906945702	-0.455542310266	0.563783446797	1.23869277193	-0.506612055599	2.18599122824	0.0254103422506	-0.0520697207397	0.0161851637257	0.061703449094	-0.0010668345517	0.0547321595703	-0.0795275835945	-0.128946063348	-0.0300323429198	0.081849885095	0.00795332765356	0.0120461225015	0.1259402776	0.00437905145649	0.122304047064	-24.1257060926	13.2117237305	-25.5652510849
9	2.00588515521	0.315369130154	1.77184728774	0.915555392508	0.369575965596	2.67833195224	0.0468158263453	-0.26340273225	-0.00186387675677	0.323383297924	0.018798330221	-0.127771682576	-0.082026035045	-0.00312059210152	-0.0185708746746	0.248824720703	-0.0100836303871	-0.0436519117556	0.209126053122	0.00310810522201	0.183960321235	1.72247029037	10.102130972	-6.91852720581
10	0.152795133251	-0.155994892544	-0.0504509458135	0.497009619946	-0.120190930281	0.300023341305	0.0382600377836	-0.0125446042367	-0.0842148531127	-0.0124518388962	-0.0128369716047	0.0520670906094	0.0598472859703	-0.059158759007	-0.0225506100665	0.122648072863	-0.00643661651447	-0.0109520665996	0.130895287346	0.000312516103959	0.146168043316	-14.5554868981	-5.34139258023	-22.2334102715
11	0.834927297551	-0.425104242567	-0.1841317117	1.26635163433	0.621606669819	1.41532063936	0.0321048060573	-0.0819448926301	-0.079108553926	0.0334636273021	0.0229770899524	0.0376700619061	0.0991945896618	-0.0786611302677	-0.0463897572039	0.112183128689	-0.0267977392632	-0.00685496002488	0.139137417808	0.0360854168647	0.142082533606	-14.822413962	-12.4590700619	-15.5272884837
12	1.97729455627	1.17255136987	-0.0341356012771	1.4978436572	0.590942984032	3.29112145314	-0.00842283228065	-0.468160601395	-0.418143178981	0.249388229367	0.100763369993	-0.280249169504	0.53482315977	0.522094016437	-0.0335455457743	0.26565313947	0.0552021721035	-0.0291662951663	0.32027235969	0.0337897564928	0.262003104948	9.77128088436	-22.1039414627	-20.1712477517
13	1.74394991374	0.201410566814	-0.825292582559	0.550077400013	0.0719844192924	1.244927951	-0.0379943540981	0.103782066814	0.0576482760171	0.0295470742926	0.0201763083299	0.0434366612421	0.153769921895	-0.131723088057	0.0380504524511	0.168695400516	-0.0223136130756	-0.0167079943391	0.119573115685	-0.00439537845576	0.151238231199	-7.26067685526	-17.0718057527	-26.1210674362

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 119 )	A	A	73 - 119	66 - 112
3	3	chain 'A' and (resid 120 through 192 )	A	A	120 - 192	113 - 186
4	4	chain 'A' and (resid 193 through 276 )	A	A	193 - 276	187 - 271
5	5	chain 'A' and (resid 277 through 310 )	A	A	277 - 310	272 - 305
6	6	chain 'B' and (resid 8 through 43 )	B	J	8 - 43	1 - 36
7	7	chain 'B' and (resid 44 through 72 )	B	J	44 - 72	37 - 65
8	8	chain 'B' and (resid 73 through 119 )	B	J	73 - 119	66 - 113
9	9	chain 'B' and (resid 120 through 135 )	B	J	120 - 135	114 - 129
10	10	chain 'B' and (resid 136 through 192 )	B	J	136 - 192	130 - 189
11	11	chain 'B' and (resid 193 through 276 )	B	J	193 - 276	190 - 275
12	12	chain 'B' and (resid 277 through 292 )	B	J	277 - 292	276 - 291
13	13	chain 'B' and (resid 293 through 310 )	B	J	293 - 310	292 - 309

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Protein , 1 types, 2 molecules AB

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Non-polymers , 6 types, 711 molecules

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Details

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Sample preparation

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