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

ID or keywords:

Entry

Database: PDB / ID: 6bur

Title

Crystal structures of cyanuric acid hydrolase from Moorella thermoacetica complexed with barbituric acid

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 ATCC 39073 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.18 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	Oct 4, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	6bur.cif.gz	558.1 KB	Display	PDBx/mmCIF format
PDB format	pdb6bur.ent.gz	462.5 KB	Display	PDB format
PDBx/mmJSON format	6bur.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

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

-
Related structure data

Related structure data	6bumC 6bunC 6buoC 6bupC 6buqC 6cwjC 6dhjC 4nq3S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6buq-d 6bun-d 6cwj-d 4bvs-1 6bum-d 4bvt-1 6buo-d 4bvq-1 1ea0-1 5hwe-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

-
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

155 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)	81.075, 89.121, 199.121
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 / Barbiturase Mass: 38484.652 Da / Num. of mol.: 4 Fragment: Q103A, E104A, K107A, L279I, K280R, F281S, E288D, L290M, A291D, K292R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Moorella thermoacetica ATCC 39073 (bacteria) Strain: ATCC 39073 / JCM 9320 / Gene: Moth_2120 / Production host: Escherichia coli (E. coli) / References: UniProt: Q2RGM7, cyanuric acid amidohydrolase
#2: Chemical	ChemComp-BR8 / BARBITURIC ACID Mass: 128.086 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₄H₄N₂O₃
#3: Chemical	ChemComp-MLI / MALONATE ION Mass: 102.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₂O₄
#4: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 406 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

Crystal	Density Matthews: 2.34 Å³/Da / Density % sol: 47.36 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 20%PEG3350, 100mM

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å
Detector	Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 6, 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: 2.18→89.12 Å / Num. obs: 75417 / % possible obs: 99.3 % / Redundancy: 4.4 % / CC_1/2: 0.999 / R_merge(I) obs: 0.122 / R_sym value: 0.101 / Net I/σ(I): 12.3
Reflection shell	Resolution: 2.18→2.22 Å / Redundancy: 4.6 % / R_merge(I) obs: 0.941 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 4434 / CC_1/2: 0.536 / % possible all: 99.9

-
Processing

Software

Name	Version	Classification
PHENIX	(1.13rc2_2981: ???)	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4NQ3

4nq3

Resolution: 2.18→39.723 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.49 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2117	3791	5.03 %
R_work	0.1632	-	-
obs	0.1656	75340	99.07 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.18→39.723 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10734	0	47	406	11187

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	10972
X-RAY DIFFRACTION	f_angle_d	0.747	14856
X-RAY DIFFRACTION	f_dihedral_angle_d	15.285	6723
X-RAY DIFFRACTION	f_chiral_restr	0.053	1749
X-RAY DIFFRACTION	f_plane_restr	0.004	1969

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 (%)
2.18-2.2076	0.3277	160	0.2627	2597	X-RAY DIFFRACTION	100
2.2076-2.2367	0.279	129	0.2596	2653	X-RAY DIFFRACTION	100
2.2367-2.2673	0.3097	119	0.2545	2652	X-RAY DIFFRACTION	99
2.2673-2.2997	0.276	139	0.2262	2615	X-RAY DIFFRACTION	100
2.2997-2.334	0.2736	153	0.2174	2624	X-RAY DIFFRACTION	100
2.334-2.3705	0.2741	137	0.1929	2631	X-RAY DIFFRACTION	100
2.3705-2.4093	0.247	148	0.1971	2623	X-RAY DIFFRACTION	99
2.4093-2.4509	0.2769	136	0.2072	2638	X-RAY DIFFRACTION	99
2.4509-2.4954	0.2443	141	0.1941	2587	X-RAY DIFFRACTION	99
2.4954-2.5434	0.2465	129	0.1835	2651	X-RAY DIFFRACTION	99
2.5434-2.5953	0.2425	146	0.1775	2617	X-RAY DIFFRACTION	100
2.5953-2.6517	0.2288	129	0.1692	2647	X-RAY DIFFRACTION	100
2.6517-2.7134	0.2296	154	0.1738	2647	X-RAY DIFFRACTION	100
2.7134-2.7813	0.2443	141	0.1727	2641	X-RAY DIFFRACTION	100
2.7813-2.8564	0.2384	144	0.1694	2653	X-RAY DIFFRACTION	100
2.8564-2.9405	0.2437	131	0.1728	2680	X-RAY DIFFRACTION	100
2.9405-3.0353	0.2154	159	0.1666	2624	X-RAY DIFFRACTION	100
3.0353-3.1438	0.231	139	0.164	2670	X-RAY DIFFRACTION	99
3.1438-3.2696	0.2321	126	0.156	2614	X-RAY DIFFRACTION	98
3.2696-3.4183	0.2023	148	0.1539	2667	X-RAY DIFFRACTION	100
3.4183-3.5984	0.1776	146	0.1543	2647	X-RAY DIFFRACTION	99
3.5984-3.8237	0.1856	144	0.1501	2673	X-RAY DIFFRACTION	99
3.8237-4.1187	0.1718	146	0.1418	2680	X-RAY DIFFRACTION	99
4.1187-4.5326	0.1898	166	0.1313	2654	X-RAY DIFFRACTION	98
4.5326-5.1873	0.1689	114	0.1381	2650	X-RAY DIFFRACTION	97
5.1873-6.5307	0.2158	139	0.161	2723	X-RAY DIFFRACTION	99
6.5307-39.7293	0.1932	128	0.1596	2791	X-RAY DIFFRACTION	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	1.6696	0.8185	-0.3409	1.7277	-0.2756	1.3973	0.0774	-0.303	0.0699	0.4192	-0.0248	-0.0729	0.0168	0.1222	-0.049	0.3748	0.0371	-0.0211	0.314	-0.0469	0.2885	95.9197	-2.0394	58.5894
2	2.1591	-0.5813	0.3314	2.4938	-0.4263	1.5841	-0.0268	-0.1158	0.1662	0.2099	0.0841	-0.3042	-0.1607	0.171	-0.0127	0.2642	-0.0263	-0.0214	0.2963	-0.0778	0.3398	106.0927	8.0036	50.8576
3	1.524	0.7297	-0.107	1.4549	-0.1526	4.5606	0.0322	-0.0289	-0.0265	-0.0384	0.0996	-0.3528	0.3015	0.378	-0.1074	0.2637	0.0532	-0.0027	0.2897	-0.0641	0.3788	109.2663	-7.2112	43.0477
4	2.7651	-1.1291	-1.0474	1.7907	0.4912	3.0867	0.0058	-0.1526	0.1844	0.2052	0.0505	0.2794	0.0418	-0.1376	-0.0746	0.267	-0.0392	-0.0025	0.2321	-0.0209	0.4042	70.665	3.8205	47.9569
5	3.1675	-1.5443	-0.0432	3.5465	0.6669	2.1971	-0.0847	0.1046	-0.2048	0.0251	-0.0439	0.4896	0.1807	-0.2163	0.1281	0.2714	-0.0539	-0.0173	0.2709	-0.011	0.3977	64.2117	-10.5078	35.4805
6	3.6292	-0.7689	-0.8639	1.6096	0.3327	2.4044	0.0038	0.3121	0.2611	-0.2716	-0.123	0.3747	-0.1625	-0.2104	0.0896	0.3283	0.0144	-0.1105	0.2848	0.0261	0.414	67.1978	5.9478	26.8664
7	3.3564	-0.2738	-1.7502	1.773	0.6373	2.9423	0.0163	0.6929	0.1884	-0.5562	0.15	-0.3935	-0.1607	0.3437	-0.1688	0.4923	-0.0629	0.1358	0.6603	-0.013	0.3805	111.2561	-8.1778	7.9573
8	1.4751	0.0403	-0.6566	1.6615	0.1872	1.8577	-0.0673	0.8727	-0.133	-0.4612	0.0604	-0.1497	0.3278	0.0031	0.0232	0.5555	0.0084	0.0993	0.7406	-0.1198	0.3212	105.9034	-21.6754	10.3885
9	4.1802	-1.6712	-0.0778	3.8607	0.0215	3.1645	-0.04	0.4843	0.0287	-0.43	0.0528	0.2342	-0.0415	-0.3117	-0.066	0.5067	-0.0893	0.0214	0.6631	-0.1081	0.2798	93.259	-20.6435	12.4628
10	2.9735	-0.865	0.3826	2.0026	0.6558	2.1696	0.1126	0.5769	-0.3021	-0.2787	-0.0209	-0.044	0.2131	-0.0389	-0.0373	0.362	-0.0114	0.0795	0.3937	-0.0821	0.3078	100.5128	-25.6457	18.8373
11	8.6903	2.7143	-2.5211	5.3466	-0.999	7.4193	-0.1469	-0.164	-0.9666	0.3416	-0.0522	-1.0869	0.5423	1.2168	0.1382	0.3599	0.0873	-0.0155	0.4463	-0.1179	0.4949	118.6621	-21.1916	28.4305
12	1.738	0.2495	-0.4073	1.9219	0.3217	2.0814	0.0203	0.3096	-0.2005	-0.1439	0.0812	-0.1856	0.0109	0.1893	-0.1131	0.2794	0.0046	0.0128	0.2982	-0.0553	0.252	102.3052	-16.2608	30.294
13	1.0203	-0.5755	-0.3691	1.5212	-0.3247	2.6438	0.1814	0.7842	0.6037	-0.7208	-0.0173	-0.3041	-0.4008	0.2163	0.0126	0.8102	-0.0164	0.1408	0.8523	0.3054	0.5831	95.5176	15.1982	3.7844
14	1.0681	0.2182	-0.7691	2.8453	0.0646	4.8555	-0.0452	0.7758	1.1581	-0.3934	0.0517	-1.1027	-0.3485	1.2121	-0.1066	0.8438	-0.1179	0.0609	0.9284	0.1275	0.9419	103.5336	21.6535	17.0387
15	1.8173	0.0445	0.2199	3.5615	-0.0992	3.3747	0.1462	0.294	0.8085	-0.1274	-0.0274	-0.5221	-0.9205	0.6462	-0.1491	0.7689	-0.1791	0.1227	0.666	0.1526	0.8215	97.7538	26.0287	20.9588
16	1.6948	-0.1859	-0.2109	2.2213	-0.1446	3.5139	0.1133	0.6028	0.6729	-0.5507	-0.0992	0.0106	-0.5309	-0.0839	-0.0465	0.5677	0.0412	-0.0027	0.4386	0.222	0.5592	81.578	19.0086	16.2012

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	( CHAIN A AND RESID 1:146 )	A	1 - 146
2	X-RAY DIFFRACTION	2	( CHAIN A AND RESID 147:266 )	A	147 - 266
3	X-RAY DIFFRACTION	3	( CHAIN A AND RESID 267:367 )	A	267 - 367
4	X-RAY DIFFRACTION	4	( CHAIN B AND RESID 0:92 )	B	0 - 92
5	X-RAY DIFFRACTION	5	( CHAIN B AND RESID 93:239 )	B	93 - 239
6	X-RAY DIFFRACTION	6	( CHAIN B AND RESID 240:367 )	B	240 - 367
7	X-RAY DIFFRACTION	7	( CHAIN C AND RESID 1:77 )	C	1 - 77
8	X-RAY DIFFRACTION	8	( CHAIN C AND RESID 78:146 )	C	78 - 146
9	X-RAY DIFFRACTION	9	( CHAIN C AND RESID 147:184 )	C	147 - 184
10	X-RAY DIFFRACTION	10	( CHAIN C AND RESID 185:266 )	C	185 - 266
11	X-RAY DIFFRACTION	11	( CHAIN C AND RESID 267:300 )	C	267 - 300
12	X-RAY DIFFRACTION	12	( CHAIN C AND RESID 301:367 )	C	301 - 367
13	X-RAY DIFFRACTION	13	( CHAIN D AND RESID 1:146 )	D	1 - 146
14	X-RAY DIFFRACTION	14	( CHAIN D AND RESID 147:184 )	D	147 - 184
15	X-RAY DIFFRACTION	15	( CHAIN D AND RESID 185:239 )	D	185 - 239
16	X-RAY DIFFRACTION	16	( CHAIN D AND RESID 240:367 )	D	240 - 367

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi