PDB-3iwv: Crystal structure of Y116T mutant of 5-HYDROXYISOURATE HYDROLASE (TRP)

ID or keywords:

Entry

Database: PDB / ID: 3iwv

Title

Crystal structure of Y116T mutant of 5-HYDROXYISOURATE HYDROLASE (TRP)

Components

5-hydroxyisourate hydrolase

Keywords

HYDROLASE / Transthyretin / molecular evolution / uric acid degradation / thyroid hormones / Peroxisome / Purine metabolism

Function / homology

Function and homology information

hydroxyisourate hydrolase / hydroxyisourate hydrolase activity / urate catabolic process / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides / purine nucleobase metabolic process / peroxisome
Similarity search - Function

Biological species

Danio rerio (zebrafish)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.68 Å

Authors

Cendron, L. / Ramazzina, I. / Berni, R. / Percudani, R. / Zanotti, G.

Citation

Journal: J.Mol.Biol. / Year: 2011
Title: Probing the evolution of hydroxyisourate hydrolase into transthyretin through active-site redesign.
Authors: Cendron, L. / Ramazzina, I. / Percudani, R. / Rasore, C. / Zanotti, G. / Berni, R.

History

Deposition	Sep 3, 2009	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Sep 1, 2010	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Jan 1, 2020	Group: Database references / Category: citation / struct_ref_seq_dif Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _struct_ref_seq_dif.details
Revision 1.3	Nov 1, 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 / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	3iwv.cif.gz	110 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	3iwv_validation.pdf.gz	457.6 KB	Display	wwPDB validaton report
Full document	3iwv_full_validation.pdf.gz	466.4 KB	Display
Data in XML	3iwv_validation.xml.gz	21.9 KB	Display
Data in CIF	3iwv_validation.cif.gz	31.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/iw/3iwv ftp://data.pdbj.org/pub/pdb/validation_reports/iw/3iwv	HTTPS FTP

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Related structure data

Related structure data	3iwuC 3q1eC 2h1xS 2h6u S: Starting model for refinement C: citing same article (ref.)
Similar structure data	3efe-d 3iwu-1 3q1e-d 2h1x-d 2h6u-2 5ttr-1 4grh-d 1etb-2 2h6u-1 1soq-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	#189 - Sep 2015 Amyloids similarity (7) #37 - Jan 2003 Serum Albumin similarity (7)

Deposited unit

A: 5-hydroxyisourate hydrolase

B: 5-hydroxyisourate hydrolase

C: 5-hydroxyisourate hydrolase

D: 5-hydroxyisourate hydrolase

61.8 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)	45.920, 103.690, 52.630
Angle α, β, γ (deg.)	90.00, 108.81, 90.00
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
3	1	C
4	1	D

NCS domain segments:

Ens-ID: 1 / Refine code: 5

Dom-ID	Component-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	SER	SER	ASP	ASP	A	A	7 - 33	26 - 52
2	1	SER	SER	ASP	ASP	B	B	7 - 33	26 - 52
3	1	SER	SER	ASP	ASP	C	C	7 - 33	26 - 52
4	1	SER	SER	ASP	ASP	D	D	7 - 33	26 - 52
1	2	THR	THR	PRO	PRO	A	A	44 - 54	63 - 73
2	2	THR	THR	PRO	PRO	B	B	44 - 54	63 - 73
3	2	THR	THR	PRO	PRO	C	C	44 - 54	63 - 73
4	2	THR	THR	PRO	PRO	D	D	44 - 54	63 - 73
1	3	PHE	PHE	THR	THR	A	A	62 - 115	81 - 134
2	3	PHE	PHE	THR	THR	B	B	62 - 115	81 - 134
3	3	PHE	PHE	THR	THR	C	C	62 - 115	81 - 134
4	3	PHE	PHE	THR	THR	D	D	62 - 115	81 - 134

#1: Protein	5-hydroxyisourate hydrolase / HIU hydrolase / HIUHase / Transthyretin-related protein Mass: 15441.656 Da / Num. of mol.: 4 / Mutation: Y116T Source method: isolated from a genetically manipulated source Source: (gene. exp.) Danio rerio (zebrafish) / Gene: urah / Plasmid: pET28b-HIUase / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q06S87, hydroxyisourate hydrolase
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 269 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

5-hydroxyisourate hydrolase / HIU hydrolase / HIUHase / Transthyretin-related protein

Mass: 15441.656 Da / Num. of mol.: 4 / Mutation: Y116T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Danio rerio (zebrafish) / Gene: urah / Plasmid: pET28b-HIUase / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q06S87, hydroxyisourate hydrolase

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 269 / 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: 1.92 Å³/Da / Density % sol: 35.94 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion / pH: 7.5 Details: 0.1M HEPES, 20% PEG10,000, pH7.5, VAPOR DIFFUSION, temperature 277K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.979 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 25, 2009
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.979 Å / Relative weight: 1
Reflection	Resolution: 1.68→44.91 Å / Num. all: 43900 / Num. obs: 43900 / % possible obs: 83.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / R_merge(I) obs: 0.052 / Net I/σ(I): 9.7
Reflection shell	Resolution: 1.68→1.77 Å / Redundancy: 3.5 % / R_merge(I) obs: 0.49 / Mean I/σ(I) obs: 1.8 / Num. unique all: 5810 / % possible all: 75.9

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Processing

Software

Name	Version	Classification
ADSC	Quantum	data collection
MOLREP		phasing
REFMAC	5.5.0072	refinement
MOSFLM		data reduction
SCALA		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2H1X

2h1x

Resolution: 1.68→25.44 Å / Cor.coef. F_o:F_c: 0.965 / Cor.coef. F_o:F_c free: 0.94 / SU B: 9.155 / SU ML: 0.124 / Cross valid method: THROUGHOUT / ESU R: 0.143 / ESU R Free: 0.145 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.25962	2250	5.1 %	RANDOM
R_work	0.20293	-	-	-
obs	0.20578	41609	83.11 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 20.493 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	4.83 Å²	0 Å²	3.67 Å²
2-	-	-3.39 Å²	0 Å²
3-	-	-	0.93 Å²

Refinement step

Cycle: LAST / Resolution: 1.68→25.44 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3616	0	0	269	3885

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.023	0.022	3712
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	2.088	1.947	5073
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.602	5	457
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	30.417	22.895	152
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.859	15	572
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	28.79	15	20
X-RAY DIFFRACTION	r_chiral_restr	0.144	0.2	588
X-RAY DIFFRACTION	r_gen_planes_refined	0.011	0.021	2804
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	1.094	1.5	2293
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	1.777	2	3744
X-RAY DIFFRACTION	r_scbond_it	3	3	1419
X-RAY DIFFRACTION	r_scangle_it	4.262	4.5	1329
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
A	368	medium positional	0.15	0.5
B	368	medium positional	0.15	0.5
C	368	medium positional	0.17	0.5
D	368	medium positional	0.16	0.5
A	362	loose positional	0.39	5
B	362	loose positional	0.38	5
C	362	loose positional	0.39	5
D	362	loose positional	0.42	5
A	368	medium thermal	1.3	2
B	368	medium thermal	1.12	2
C	368	medium thermal	1.9	2
D	368	medium thermal	1.48	2
A	362	loose thermal	1.74	10
B	362	loose thermal	1.56	10
C	362	loose thermal	1.93	10
D	362	loose thermal	1.71	10

LS refinement shell

Resolution: 1.683→1.727 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.451	145	-
R_work	0.439	2737	-
obs	-	2737	73.95 %

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	0.5513	0.8074	0.0685	2.1484	-0.1295	0.8939	-0.0848	0.1936	-0.0116	-0.1809	0.0721	-0.0115	-0.0128	0.0359	0.0126	0.1429	0.0096	-0.0055	0.1493	-0.0002	0.1274	0.557	11.599	12.597
2	2.1653	0.9205	1.6661	0.7938	0.5372	1.4218	-0.1118	-0.0192	0.1708	-0.0356	-0.0095	0.0237	-0.1981	-0.0076	0.1212	0.1832	0.003	0.0069	0.1821	0.001	0.1842	10.578	23.965	20.065
3	4.6417	1.2372	1.5	2.0445	0.6512	1.6698	-0.19	0.2556	0.3137	-0.1439	0.1313	-0.0803	-0.2417	0.2125	0.0587	0.2451	0.0116	0.0131	0.2267	0.0088	0.208	10.87	16.968	8.904
4	12.366	0.8909	-0.1621	1.8856	-0.5158	2.3959	0.0352	0.134	-0.0128	-0.0801	0.02	-0.0717	-0.037	0.0166	-0.0552	0.1933	0	-0.0045	0.1389	-0.003	0.1612	12.39	19.047	20.886
5	2.0774	-0.5207	0.1332	1.3393	-0.0714	1.262	-0.0008	0.0762	0.1191	-0.0654	-0.0021	0.1282	-0.0325	-0.1281	0.0028	0.1503	-0.0011	0.0003	0.1212	-0.0005	0.1206	-2.95	14.947	21.251
6	2.9276	1.2559	-0.8531	1.5906	-0.2593	1.6252	-0.0157	0.1537	-0.0763	-0.1159	0.0064	-0.2216	-0.0277	0.1511	0.0093	0.1839	0.0099	-0.0187	0.1448	0.0038	0.1458	7.659	8.163	18.098
7	2.4067	-0.8853	-2.4495	1.6296	1.5611	3.3422	-0.1547	-0.2155	-0.0692	0.2082	0.081	0.1194	0.1076	0.0608	0.0736	0.1795	0.0082	-0.0135	0.1806	0.0178	0.1533	1.913	1.483	37.252
8	1.2155	-2.2012	0.2231	4.2617	-0.455	0.4096	-0.1011	-0.0947	0.0586	0.226	0.0832	-0.0456	-0.0732	-0.0287	0.018	0.1728	-0.0093	-0.0047	0.1906	0.0004	0.1802	2.353	16.069	39.514
9	6.3169	-0.6236	-0.9899	5.6777	1.9745	6.6962	-0.0453	-0.0915	-0.1549	0.1203	0.0143	0.1078	0.0884	-0.0672	0.031	0.2252	-0.0137	-0.0024	0.2214	0.0167	0.2059	2.774	1.113	43.996
10	1.8791	0.4403	-1.0839	1.4593	-1.0072	3.9313	-0.0286	-0.4105	-0.1696	0.4226	0.012	0.2196	0.0431	-0.1019	0.0166	0.2293	0.0112	0.0065	0.195	0.0003	0.2142	-7.226	15.857	41.166
11	1.5942	-0.2902	-0.2183	1.6728	-0.1079	1.5411	-0.046	-0.1306	-0.024	0.0902	0.0217	-0.0573	0.028	0.0624	0.0243	0.1866	-0.0144	-0.0172	0.1342	-0.0083	0.1251	4.881	9.722	33.296
12	3.4964	-0.0985	-1.6614	2.4645	0.0437	3.3154	-0.0252	-0.014	-0.0169	0.0558	0.0143	0.0764	0.0083	-0.0858	0.0109	0.1554	-0.0045	-0.0236	0.1159	-0.0008	0.1167	2.487	3.835	29.699
13	0.8678	0.2853	-0.0078	1.2491	0.2336	1.1864	-0.0184	0.1267	0.0028	-0.082	0.038	-0.0082	-0.0026	0.0783	-0.0197	0.1399	0.0126	0.0093	0.1475	0.0063	0.1492	7.448	-9.131	9.977
14	1.1719	-0.1191	0.6598	1.0619	0.5104	1.2686	0.0156	0.1	-0.2968	-0.0662	0.0181	0.1158	0.1915	-0.1342	-0.0337	0.2699	-0.0139	0.0207	0.2591	-0.0216	0.23	1.156	-19.298	4.953
15	3.8249	3.0154	3.6152	2.4853	2.6817	5.3725	-0.0649	0.156	0.0018	-0.1105	0.0273	0.0169	-0.0866	0.0395	0.0376	0.2105	0.011	0.0147	0.2058	0.0014	0.2124	8.223	-7.099	2.411
16	1.8739	0.0835	0.7119	2.1744	-1.0849	4.6907	-0.0177	0.3517	0.1436	-0.3662	-0.0097	-0.1101	-0.0291	0.1991	0.0274	0.187	0.0013	0.001	0.1785	-0.0099	0.2004	-3.72	-13.218	1.761
17	1.0395	-0.2928	-0.1822	1.5571	-0.3448	1.3633	0.0381	-0.0263	-0.0918	0.0662	-0.0099	-0.1693	0.0742	0.2099	-0.0282	0.1427	-0.0001	0.012	0.1303	-0.006	0.1346	7.678	-14.179	18.31
18	1.4895	0.2288	0.6246	1.7757	-0.1101	3.393	-0.0167	0.1655	0.0821	-0.1811	-0.0114	0.1554	-0.0822	-0.0907	0.028	0.1377	0.0009	0.0295	0.1396	-0.0113	0.1698	0.868	-4.667	12.391
19	2.4925	-1.9294	1.6414	5.179	-2.8128	3.3565	-0.0539	-0.2619	-0.2159	0.4219	0.1482	0.0956	-0.0874	-0.0834	-0.0944	0.1561	-0.0087	0.007	0.1829	-0.022	0.1709	-7.118	-8.803	32.126
20	1.4423	-0.6014	0.1346	2.6711	-0.1463	1.0119	0.0563	0.0793	-0.1712	-0.1034	-0.0592	0.0002	0.1248	0.0683	0.003	0.1634	-0.0233	-0.0075	0.1993	0.0052	0.1481	-6.352	-20.136	25.739
21	2.3483	-1.1451	-0.5314	0.8207	0.2797	0.24	-0.1367	-0.3161	-0.1082	0.3036	0.1246	0.0731	0.0294	-0.0299	0.0122	0.244	0.0039	0.002	0.2165	0.0053	0.1981	-6.837	-18.694	33.994
22	5.9077	-3.2047	1.0204	6.6173	-1.2215	2.7794	0.0963	0.1758	-0.199	-0.2616	-0.0561	0.2257	0.1365	-0.0975	-0.0401	0.1393	-0.0177	0.0156	0.1576	0.0001	0.125	-12.711	-11.59	20.513
23	1.9816	0.0697	0.4415	0.9264	-0.0165	1.609	-0.026	-0.0074	0.0021	0.0004	0.0562	0.1328	-0.091	-0.1421	-0.0302	0.1466	-0.0162	0.0096	0.1365	-0.0108	0.1374	-7.124	-11.587	19.263
24	1.3477	-0.7206	0.4103	2.9337	-1.5652	3.0998	-0.0179	-0.1995	-0.1325	0.2235	0.0178	-0.1557	0.0673	0.12	0.0001	0.1373	-0.0175	0.0135	0.1526	-0.0192	0.1667	-0.705	-9.703	29.031

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	7 - 29
2	X-RAY DIFFRACTION	2	A	30 - 48
3	X-RAY DIFFRACTION	3	A	49 - 62
4	X-RAY DIFFRACTION	4	A	63 - 70
5	X-RAY DIFFRACTION	5	A	71 - 95
6	X-RAY DIFFRACTION	6	A	96 - 119
7	X-RAY DIFFRACTION	7	B	6 - 19
8	X-RAY DIFFRACTION	8	B	20 - 47
9	X-RAY DIFFRACTION	9	B	48 - 55
10	X-RAY DIFFRACTION	10	B	56 - 69
11	X-RAY DIFFRACTION	11	B	70 - 102
12	X-RAY DIFFRACTION	12	B	103 - 119
13	X-RAY DIFFRACTION	13	C	6 - 33
14	X-RAY DIFFRACTION	14	C	34 - 48
15	X-RAY DIFFRACTION	15	C	49 - 59
16	X-RAY DIFFRACTION	16	C	60 - 69
17	X-RAY DIFFRACTION	17	C	70 - 95
18	X-RAY DIFFRACTION	18	C	96 - 119
19	X-RAY DIFFRACTION	19	D	6 - 17
20	X-RAY DIFFRACTION	20	D	18 - 42
21	X-RAY DIFFRACTION	21	D	43 - 68
22	X-RAY DIFFRACTION	22	D	69 - 78
23	X-RAY DIFFRACTION	23	D	79 - 95
24	X-RAY DIFFRACTION	24	D	96 - 119

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