PDB-6buo: Crystal structures of cyanuric acid hydrolase from Moorella therm...

ID or keywords:

Entry

Database: PDB / ID: 6buo

Title

Crystal structures of cyanuric acid hydrolase from Moorella thermoacetica

Components

Cyanuric acid amidohydrolase

Keywords

HYDROLASE / Cyanuric acid hydrolase

Function / homology

Function and homology information

cyanuric acid amidohydrolase /

cyanuric acid amidohydrolase activity / atrazine catabolic process /

metal ion binding
Similarity search - Function

Biological species

Moorella thermoacetica (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.85 Å

Authors

Shi, K. / Aihara, H.

Funding support

United States, 2items

Organization	Grant number	Country
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	GM095558	United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	GM118047	United States

Citation

Journal: Plos One / Year: 2019
Title: Crystal structures of Moorella thermoacetica cyanuric acid hydrolase reveal conformational flexibility and asymmetry important for catalysis.
Authors: Shi, K. / Cho, S. / Aukema, K.G. / Lee, T. / Bera, A.K. / Seffernick, J.L. / Wackett, L.P. / Aihara, H.

History

Deposition	Dec 11, 2017	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 12, 2019	Provider: repository / Type: Initial release
Revision 1.1	Dec 25, 2019	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2	Jan 1, 2020	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3	Sep 22, 2021	Group: Data collection / Database references / Derived calculations Category: database_2 / reflns_shell / struct_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _reflns_shell.d_res_high / _reflns_shell.d_res_low / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_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
Revision 1.4	Oct 4, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6buo.cif.gz	806.7 KB	Display	PDBx/mmCIF format
PDB format	pdb6buo.ent.gz	682.9 KB	Display	PDB format
PDBx/mmJSON format	6buo.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/bu/6buo ftp://data.pdbj.org/pub/pdb/validation_reports/bu/6buo	HTTPS FTP

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Related structure data

Related structure data	6bumC 6bunC 6bupC 6buqC 6burC 6cwjC 6dhjC 4nq3S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6bun-d 6cwj-d 4bvr-1 4bvt-1 6bum-d 4bvq-1 4bvs-1 6buq-d 6bur-d 6bup-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

Deposited unit

A: Cyanuric acid amidohydrolase

B: Cyanuric acid amidohydrolase

C: Cyanuric acid amidohydrolase

D: Cyanuric acid amidohydrolase

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	81.450, 88.822, 202.847
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Cyanuric acid amidohydrolase / / CAH Mass: 38484.652 Da / Num. of mol.: 4 Mutation: Q103A,Q104A,K107A,L279I,K280R,F281S,Q288D,L290M,A291D,K292R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Moorella thermoacetica (strain ATCC 39073 / JCM 9320) (bacteria) Strain: ATCC 39073 / JCM 9320 / Gene: Moth_2120 / Production host: Escherichia coli (E. coli) / References: UniProt: Q2RGM7, cyanuric acid amidohydrolase
#2: Chemical	ChemComp-MLI / MALONATE ION / Malonic acid Mass: 102.046 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₃H₂O₄
#3: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Chemical	... ChemComp-PDO / 1,3-PROPANDIOL / 1,3-Propanediol Mass: 76.094 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C₃H₈O₂
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 959 / 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: 2.38 Å³/Da / Density % sol: 48.35 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 20%PEG3350, 100mM CaCl2

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å
Detector	Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 10, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.979 Å / Relative weight: 1
Reflection	Resolution: 1.85→29.953 Å / Num. obs: 248749 / % possible obs: 100 % / Redundancy: 7.1 % / CC_1/2: 0.996 / R_merge(I) obs: 0.124 / Net I/σ(I): 17.6
Reflection shell	Resolution: 1.62→1.85 Å / Redundancy: 3.7 % / R_merge(I) obs: 1.915 / Num. unique obs: 9034 / CC_1/2: 0.123 / % possible all: 62

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Processing

Software

Name	Version	Classification
PHENIX	(1.15.2_3472: ???)	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4NQ3

4nq3

Resolution: 1.85→29.953 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.93

	R_factor	Num. reflection	% reflection
R_free	0.1764	12142	5.04 %
R_work	0.1495	-	-
obs	0.1509	240847	99.27 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.85→29.953 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10734	0	152	959	11845

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	11080
X-RAY DIFFRACTION	f_angle_d	0.686	14939
X-RAY DIFFRACTION	f_dihedral_angle_d	19.363	4122
X-RAY DIFFRACTION	f_chiral_restr	0.066	1750
X-RAY DIFFRACTION	f_plane_restr	0.004	1970

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 (%)
1.85-1.871	0.3085	382	0.322	7610	X-RAY DIFFRACTION	99
1.871-1.893	0.3369	421	0.3067	7544	X-RAY DIFFRACTION	98
1.893-1.9161	0.3142	439	0.2856	7582	X-RAY DIFFRACTION	99
1.9161-1.9404	0.3013	391	0.271	7545	X-RAY DIFFRACTION	98
1.9404-1.9659	0.2726	399	0.2627	7491	X-RAY DIFFRACTION	99
1.9659-1.9928	0.2763	437	0.249	7516	X-RAY DIFFRACTION	98
1.9928-2.0213	0.2786	429	0.2425	7510	X-RAY DIFFRACTION	98
2.0213-2.0514	0.2575	399	0.2531	7601	X-RAY DIFFRACTION	99
2.0514-2.0835	0.2804	412	0.2514	7570	X-RAY DIFFRACTION	98
2.0835-2.1176	0.2292	392	0.1895	7553	X-RAY DIFFRACTION	99
2.1176-2.1541	0.208	389	0.1581	7650	X-RAY DIFFRACTION	99
2.1541-2.1933	0.1827	396	0.1521	7585	X-RAY DIFFRACTION	99
2.1933-2.2355	0.176	442	0.1461	7659	X-RAY DIFFRACTION	100
2.2355-2.2811	0.1911	374	0.144	7668	X-RAY DIFFRACTION	100
2.2811-2.3307	0.1725	415	0.1367	7668	X-RAY DIFFRACTION	100
2.3307-2.3849	0.1713	414	0.1318	7646	X-RAY DIFFRACTION	100
2.3849-2.4445	0.1654	393	0.1292	7643	X-RAY DIFFRACTION	100
2.4445-2.5105	0.1562	379	0.1332	7708	X-RAY DIFFRACTION	100
2.5105-2.5844	0.1728	426	0.1274	7612	X-RAY DIFFRACTION	100
2.5844-2.6677	0.1529	371	0.1199	7713	X-RAY DIFFRACTION	100
2.6677-2.763	0.1642	403	0.1197	7686	X-RAY DIFFRACTION	100
2.763-2.8736	0.1525	365	0.1271	7727	X-RAY DIFFRACTION	100
2.8736-3.0042	0.1699	396	0.127	7633	X-RAY DIFFRACTION	100
3.0042-3.1625	0.1628	456	0.1277	7672	X-RAY DIFFRACTION	100
3.1625-3.3604	0.1637	385	0.132	7641	X-RAY DIFFRACTION	100
3.3604-3.6194	0.1505	416	0.1341	7664	X-RAY DIFFRACTION	100
3.6194-3.9829	0.144	369	0.1312	7712	X-RAY DIFFRACTION	100
3.9829-4.5575	0.1349	416	0.1228	7676	X-RAY DIFFRACTION	100
4.5575-5.7354	0.1538	389	0.1351	7644	X-RAY DIFFRACTION	99
5.7354-29.957	0.1787	447	0.167	7576	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	1.3409	0.0141	-0.1977	1.1806	0.2365	1.6102	-0.0044	-0.23	0.0339	0.201	0.0277	0.0077	-0.0321	-0.0201	-0.0281	0.2107	0.005	-0.0035	0.2069	0.0045	0.1916	27.0841	5.0095	58.8129
2	1.6618	-1.949	-0.4759	6.0733	1.8389	0.6943	-0.2374	-0.1555	-0.2298	0.3128	0.0892	0.1725	0.2838	-0.0017	0.1854	0.2164	-0.0097	0.0192	0.2277	0.0708	0.2472	18.4874	-15.7262	56.1548
3	1.306	-0.2487	-0.2328	1.1981	0.0897	0.8181	-0.0217	-0.0314	-0.2003	0.0703	-0.0043	0.1457	0.1001	-0.0999	0.0439	0.1909	-0.0158	0.008	0.2074	0.0258	0.2402	15.8788	-9.043	49.631
4	0.7713	0.1298	-0.3243	0.6947	-0.0619	2.09	0.022	-0.0094	0.0685	0.0224	0.0429	0.1306	-0.1471	-0.1779	-0.0416	0.1604	0.0166	-0.0035	0.1855	0.0262	0.2096	13.292	6.3656	41.8883
5	4.3783	-1.6162	0.1181	2.1866	-0.6528	3.0932	0.0037	-0.2426	-0.1721	0.132	0.0191	-0.1976	0.1175	0.3262	-0.0364	0.2117	0.013	-0.0048	0.1874	0.0191	0.2539	56.3882	-11.5712	51.4529
6	3.2939	-0.9632	1.621	1.2265	-0.5983	2.255	-0.0846	-0.2359	-0.0585	0.1411	0.0657	-0.1272	-0.0584	-0.0883	0.0144	0.2065	-0.0141	-0.0085	0.1664	0.0138	0.2239	47.8363	-1.9546	49.4105
7	1.6202	0.3649	1.5558	2.2386	1.7576	8.3739	-0.1133	-0.1442	0.0206	0.1434	0.0449	-0.063	-0.4383	0.1101	0.0492	0.1794	0.0099	-0.0008	0.1955	0.0037	0.2202	50.318	-0.7293	48.8856
8	5.8924	-2.8075	-0.0979	1.9573	-0.6172	1.1576	-0.1562	-0.4123	-0.2925	0.1042	0.1192	-0.5515	-0.0368	0.3255	0.0213	0.1571	-0.0128	-0.0142	0.2791	0.0137	0.3021	67.2591	-6.1332	47.7244
9	0.9339	-1.4096	-0.0925	4.5253	-0.5352	1.9205	-0.0314	-0.0236	0.2867	0.0185	-0.0082	-0.3036	-0.2882	0.26	0.0579	0.2771	-0.0887	0.0066	0.2721	-0.02	0.2907	59.8085	15.2512	41.0869
10	1.2838	-0.0998	-0.1319	1.2531	0.1789	1.0078	0.0343	0.0675	0.1301	-0.0756	-0.0247	-0.1425	-0.2171	0.1718	-0.0056	0.2246	-0.0454	0.0308	0.2231	0.0109	0.2418	57.5167	8.2943	34.4031
11	2.6809	1.079	1.2076	2.5189	-2.6089	5.2858	0.0798	0.2167	-0.5543	-0.3271	-0.0958	-0.5048	0.6353	0.4455	0.0507	0.2529	0.0441	0.0236	0.2605	-0.0598	0.3851	62.8909	-14.4339	30.6521
12	1.6054	-0.0475	0.4718	0.5791	-0.1666	0.6519	0.028	0.1528	-0.0978	-0.1106	-0.0079	-0.0743	0.0067	0.1048	-0.0163	0.2181	0.0026	0.036	0.226	-0.0257	0.2327	50.5158	-3.4915	26.0692
13	1.6104	-0.6993	0.7673	1.3925	-0.5184	1.6134	0.0704	0.3304	0.0276	-0.2896	-0.0188	0.1379	-0.0266	-0.1847	-0.064	0.2365	0	-0.045	0.3034	0.0296	0.168	13.5032	11.0817	8.1588
14	1.4051	-0.1845	-0.2507	0.8414	-0.031	1.2457	0.0176	0.2162	0.2302	-0.1712	0.0098	-0.0702	-0.2512	0.0676	-0.0239	0.3101	-0.0273	0.006	0.2555	0.0565	0.2269	27.6825	23.7762	15.1509
15	2.4748	0.9644	1.6598	3.0957	0.349	4.0648	-0.0676	-0.1568	0.1973	0.0903	-0.0268	0.4338	-0.1497	-0.6992	0.0667	0.2585	0.0528	0.0043	0.3464	0.0707	0.2809	5.438	20.418	26.729
16	0.6766	-0.1454	0.2377	0.857	-0.3861	1.3293	0.0159	0.0548	0.0687	-0.0466	0.0339	0.0326	-0.0982	-0.0737	-0.0505	0.1922	0.015	0.0031	0.1835	0.0199	0.1894	21.6748	15.2964	30.0209
17	1.1568	-0.2546	0.1187	1.3092	0.0147	2.0612	0.1994	0.5672	-0.2502	-0.5194	-0.0917	0.1307	0.2772	-0.0049	-0.0176	0.4147	0.0446	-0.0479	0.3999	-0.1149	0.2101	31.9608	-9.0564	2.7376
18	1.9415	0.1988	-0.2841	2.0131	-0.2464	2.0522	0.1345	0.2765	-0.6135	-0.2227	-0.0501	0.4471	0.6254	-0.4431	-0.0146	0.5902	-0.0703	-0.1476	0.4642	-0.1115	0.6246	25.6819	-24.4279	14.2747
19	1.3466	-0.4149	0.5083	1.5761	-0.6473	3.0498	0.2283	0.3845	-0.3673	-0.4881	-0.1039	0.0666	0.5221	0.2575	-0.0384	0.3476	0.0614	-0.0235	0.2503	-0.1186	0.3094	43.313	-19.5435	17.3535

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 118 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 119 through 146 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 147 through 266 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 267 through 367 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 0 through 30 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 31 through 67 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 68 through 92 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 93 through 118 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 119 through 146 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 147 through 266 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 267 through 300 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 301 through 367 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 0 through 118 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 119 through 266 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 267 through 300 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 301 through 367 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 1 through 92 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 93 through 239 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 240 through 367 )

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