PDB-8c7e: Serendipitous cyanase structure from Serratia-like contamination

ID or keywords:

Entry

Database: PDB / ID: 8c7e

Title

Serendipitous cyanase structure from Serratia-like contamination

Components

Cyanate hydratase

Keywords

LYASE / contaminant / enzyme

Function / homology

Function and homology information

cyanate metabolic process / cyanase / cyanate hydratase activity / DNA binding
Similarity search - Function

Biological species

unidentified (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.8 Å

Authors

Bloch, Y. / Skladanowska, K. / Savvides, S.N.

Funding support

Belgium, 1items

Citation

Journal: To Be Published
Title: Serendipitous cyanase structure from Serratia-like contamination.
Authors: Bloch, Y. / Skladanowska, K. / Savvides, S.N.

History

Deposition	Jan 14, 2023	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Feb 22, 2023	Provider: repository / Type: Initial release
Revision 1.1	Jun 19, 2024	Group: Data collection / Category: chem_comp_atom / chem_comp_bond

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8c7e.cif.gz	1.1 MB	Display	PDBx/mmCIF format
PDB format	pdb8c7e.ent.gz	949.1 KB	Display	PDB format
PDBx/mmJSON format	8c7e.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8c7e_validation.pdf.gz	535.1 KB	Display	wwPDB validaton report
Full document	8c7e_full_validation.pdf.gz	557.2 KB	Display
Data in XML	8c7e_validation.xml.gz	96.8 KB	Display
Data in CIF	8c7e_validation.cif.gz	129.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/c7/8c7e ftp://data.pdbj.org/pub/pdb/validation_reports/c7/8c7e	HTTPS FTP

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Related structure data

Similar structure data	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	#112 - Apr 2009 Oct and Sox Transcription Factors similarity (1) #39 - Mar 2003 lac Repressor similarity (1) #241 - Jan 2020 Twenty Years of Molecules similarity (1)

Deposited unit

A: Cyanate hydratase

B: Cyanate hydratase

C: Cyanate hydratase

D: Cyanate hydratase

E: Cyanate hydratase

F: Cyanate hydratase

G: Cyanate hydratase

H: Cyanate hydratase

I: Cyanate hydratase

J: Cyanate hydratase

K: Cyanate hydratase

L: Cyanate hydratase

M: Cyanate hydratase

N: Cyanate hydratase

O: Cyanate hydratase

P: Cyanate hydratase

Q: Cyanate hydratase

R: Cyanate hydratase

S: Cyanate hydratase

T: Cyanate hydratase

hetero molecules

333 kDa, 20 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Cyanate hydratase

B: Cyanate hydratase

C: Cyanate hydratase

D: Cyanate hydratase

E: Cyanate hydratase

F: Cyanate hydratase

G: Cyanate hydratase

H: Cyanate hydratase

I: Cyanate hydratase

J: Cyanate hydratase

hetero molecules

defined by author&software
Evidence: Same assembly present in crystal structures of other cyanases.
166 kDa, 10 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

K: Cyanate hydratase

L: Cyanate hydratase

M: Cyanate hydratase

N: Cyanate hydratase

O: Cyanate hydratase

P: Cyanate hydratase

Q: Cyanate hydratase

R: Cyanate hydratase

S: Cyanate hydratase

T: Cyanate hydratase

hetero molecules

defined by author&software
166 kDa, 10 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	90.121, 90.121, 736.358
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	170
Space group name H-M	P6₅

#1: Protein	Cyanate hydratase / Cyanase / Cyanate hydrolase / Cyanate lyase Mass: 16605.107 Da / Num. of mol.: 20 / Source method: isolated from a natural source / Details: Approximate sequence, unidentified contaminant. / Source: (natural) unidentified (others) / References: UniProt: A0A3E2EMR4, cyanase
#2: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: Cl
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 23 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.6 Å³/Da / Density % sol: 52.68 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop Details: PEGION H11: 1% w/v Tryptone, 0.001 M Sodium azide, 0.05 M HEPES sodium pH 7.0, 12% w/v Polyethylene glycol 3350

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

SOLEIL

/ Beamline: PROXIMA 1 / Wavelength: 0.97857 Å

Detector

Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 5, 2018

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97857 Å / Relative weight: 1

Reflection

Resolution: 2.8→78.05 Å / Num. obs: 79858 / % possible obs: 96.5 % / Redundancy: 4.16 % / CC_1/2: 0.992 / R_rim(I) all: 0.29 / Net I/av σ(I): 8.16 / Net I/σ(I): 56.32

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	Mean I/σ(I) obs	Num. unique obs	CC_1/2	R_rim(I) all	% possible all
8.35-96.5	4.085	37.83	2894	0.999	0.038	92.5
5.92-8.35	4.2109	19.15	5358	0.996	0.086	95.2
4.84-5.92	4.1278	13.78	6985	0.989	0.125	95.9
4.19-4.84	4.1645	13.84	8242	0.991	0.128	96
3.75-4.19	4.2154	9.68	9365	0.982	0.187	96.6
3.43-3.75	4.2365	5.68	10523	0.945	0.329	97.5
3.17-3.43	4.0923	3.35	11387	0.841	0.54	97.4
2.97-3.17	4.2692	2.03	12257	0.649	0.914	97.4
2.8-2.97	3.9984	1.25	12846	0.417	1.35	0.962

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Processing

Software

Name	Version	Classification
PHENIX	1.20.1_4487	refinement
XDS	20210323	data reduction
XDS	20210323	data scaling
SIMBAD		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.8→78.05 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.99 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2358	3981	4.99 %
R_work	0.2016	-	-
obs	0.2033	79751	96.58 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.8→78.05 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	23296	0	20	23	23339

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	23776
X-RAY DIFFRACTION	f_angle_d	0.633	32400
X-RAY DIFFRACTION	f_dihedral_angle_d	13.046	8612
X-RAY DIFFRACTION	f_chiral_restr	0.043	3880
X-RAY DIFFRACTION	f_plane_restr	0.005	4184

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 (%)
2.8-2.83	0.3727	144	0.3619	2666	X-RAY DIFFRACTION	96
2.83-2.87	0.389	143	0.3459	2720	X-RAY DIFFRACTION	98
2.87-2.91	0.3604	147	0.3306	2813	X-RAY DIFFRACTION	98
2.91-2.95	0.3475	136	0.3172	2662	X-RAY DIFFRACTION	98
2.95-2.99	0.3481	141	0.3063	2740	X-RAY DIFFRACTION	97
2.99-3.03	0.3515	145	0.2979	2702	X-RAY DIFFRACTION	97
3.03-3.08	0.3404	158	0.2832	2711	X-RAY DIFFRACTION	97
3.08-3.13	0.3413	142	0.2843	2733	X-RAY DIFFRACTION	97
3.13-3.19	0.2951	154	0.2697	2749	X-RAY DIFFRACTION	97
3.19-3.24	0.2978	126	0.2641	2741	X-RAY DIFFRACTION	97
3.24-3.31	0.2871	123	0.2681	2713	X-RAY DIFFRACTION	97
3.31-3.37	0.2918	150	0.2466	2703	X-RAY DIFFRACTION	97
3.37-3.45	0.2442	190	0.2167	2724	X-RAY DIFFRACTION	97
3.45-3.53	0.2375	125	0.2128	2701	X-RAY DIFFRACTION	97
3.53-3.62	0.2675	133	0.2114	2799	X-RAY DIFFRACTION	97
3.62-3.71	0.2633	138	0.2034	2691	X-RAY DIFFRACTION	97
3.71-3.82	0.2713	144	0.1964	2698	X-RAY DIFFRACTION	97
3.82-3.95	0.2139	136	0.1903	2715	X-RAY DIFFRACTION	97
3.95-4.09	0.2142	143	0.1764	2738	X-RAY DIFFRACTION	97
4.09-4.25	0.1847	154	0.1792	2660	X-RAY DIFFRACTION	96
4.25-4.44	0.1789	141	0.1672	2685	X-RAY DIFFRACTION	96
4.44-4.68	0.191	131	0.1495	2693	X-RAY DIFFRACTION	96
4.68-4.97	0.1892	151	0.1551	2713	X-RAY DIFFRACTION	96
4.97-5.36	0.2135	134	0.1716	2674	X-RAY DIFFRACTION	96
5.36-5.89	0.2366	147	0.1925	2665	X-RAY DIFFRACTION	96
5.9-6.75	0.2179	157	0.1859	2664	X-RAY DIFFRACTION	95
6.75-8.5	0.1866	124	0.1525	2683	X-RAY DIFFRACTION	95
8.5-78.05	0.1461	124	0.1333	2614	X-RAY DIFFRACTION	92

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	1.2614	-1.0529	-0.1313	1.027	-0.0844	1.2822	-0.0133	-0.1281	0.1037	0.2105	0.079	-0.0604	-0.0906	0.0247	-0.0662	0.4898	-0.0333	0.0135	0.3822	-0.0403	0.4884	8.3376	36.336	10.1679
2	2.4846	0.6204	-0.6339	1.5239	0.3251	1.5946	0.1774	0.0143	0.4238	0.1783	-0.0244	0.3855	-0.3829	-0.2635	-0.0744	0.4826	0.1285	0.0826	0.4056	0.0704	0.5521	-15.7681	36.2586	-5.9723
3	1.0913	0.031	-0.3371	1.0954	-0.2575	1.792	0.0494	-0.05	0.1096	0.2049	0.0111	0.1339	-0.0569	-0.2615	-0.0362	0.404	-0.0077	-0.0095	0.5321	0.0183	0.4869	-29.0002	10.5952	-2.6434
4	1.6601	0.0367	0.7234	1.3736	0.1892	1.1504	0.0462	-0.2398	-0.1376	0.2022	0.0245	0.0736	0.1828	-0.4217	-0.1073	0.4608	-0.0148	-0.0071	0.4983	0.0479	0.4614	-13.1095	-4.9477	15.9276
5	0.738	0.0454	-0.2324	1.581	0.2893	1.8274	-0.0075	-0.1501	-0.0231	0.1681	-0.016	0.0414	-0.0196	0.0449	-0.0028	0.4479	0.0543	-0.0325	0.3689	0.0034	0.4517	10.3404	10.7523	23.798
6	1.1221	0.1065	-0.7958	0.5599	-0.0156	1.4084	-0.0589	0.2976	0.058	-0.0689	0.1257	0.0143	0.1323	-0.0956	-0.1273	0.3986	0.0314	-0.0287	0.5646	0.0475	0.5115	-10.3428	23.6235	-24.0556
7	1.2367	-0.5637	-0.3022	0.6367	0.3689	2.0138	0.0462	0.1807	-0.1246	-0.0386	0.0912	0.0089	0.2726	0.0428	-0.1218	0.4066	-0.0097	-0.0623	0.4633	-0.0099	0.5125	-16.0627	-3.6276	-14.9835
8	1.2426	0.3812	-0.2011	0.9645	0.35	1.3204	0.0366	0.128	-0.2415	0.0677	0.0924	-0.0656	0.1824	0	-0.0688	0.4853	0.0681	-0.0569	0.3586	0.0169	0.5087	4.4217	-12.0535	3.3146
9	1.1001	-0.0927	-0.5234	1.7922	0.2868	2.1142	0.0136	0.0307	-0.0938	-0.067	-0.0311	-0.1152	0.0318	0.378	0.0197	0.3357	0.0177	-0.0694	0.5415	-0.0184	0.4497	23.7295	9.7246	5.4492
10	1.6575	-0.0611	0.333	0.225	-0.4174	1.8247	0.0739	0.1715	0.0433	-0.0291	-0.0055	0.0273	-0.1106	0.0498	-0.0625	0.4349	0.0238	0.0418	0.3344	0.0134	0.4516	14.4925	31.7684	-11.1563
11	1.067	-0.3962	-0.216	1.0229	-0.086	0.7009	0.012	0.0796	-0.0129	-0.4109	0.003	0.0393	-0.1443	0.0163	-0.0633	0.5498	0.0327	0.0073	0.4232	0.0392	0.449	-17.6101	60.2314	42.61
12	1.5843	0.1754	-0.2857	1.0859	0.0083	2.1476	-0.1188	0.1421	-0.0619	-0.2352	0.057	0.2729	0.0556	-0.0789	0.0576	0.4763	0.0304	-0.1084	0.3433	0.0521	0.5122	-45.1885	50.292	41.8264
13	1.4175	-0.1004	0.6268	1.3901	0.12	2.4775	0.1229	0.0762	-0.3235	-0.1281	-0.0516	0.227	0.4217	-0.2461	-0.0455	0.5614	-0.0528	-0.0719	0.4426	0.0619	0.6268	-47.0464	26.0067	57.4916
14	1.5023	-0.2146	-0.0606	0.8934	0.1496	1.2216	0.0533	0.1777	-0.2444	-0.1197	0.0553	-0.0003	0.0767	0.0357	-0.1089	0.6104	0.0803	-0.0705	0.3673	0.0102	0.4971	-20.6515	20.4103	68.1537
15	0.6054	-0.357	0.252	2.2671	0.5069	1.5532	0.028	0.1353	0.0077	-0.3072	0.0773	-0.085	0.0873	0.1521	-0.13	0.4722	0.0106	0.0278	0.4603	-0.0224	0.442	-2.5082	41.3141	58.6508
16	1.3683	0.0033	0.1079	1.3646	-0.0195	0.4512	-0.1003	-0.247	-0.0661	0.2781	0.16	0.3115	0.1381	-0.0805	-0.0646	0.6001	0.0392	0.0498	0.4754	0.0837	0.5213	-32.4112	30.738	84.6115
17	0.8958	0.1142	0.105	1.9859	-0.478	2.0339	-0.0594	-0.1259	0.039	0.1721	0.0199	0.4107	-0.0637	-0.2539	-0.031	0.4358	0.0083	0.0196	0.5251	0.0685	0.6772	-54.4986	43.0538	70.6852
18	1.0049	-0.3795	0.5749	1.197	0.2301	1.1645	-0.0747	-0.1635	0.1017	0.0163	0.0446	0.272	-0.0736	0.0207	0.0702	0.4782	0.0192	-0.011	0.4616	0.0383	0.5646	-44.1975	66.711	57.5527
19	1.6283	-0.5086	-0.8621	1.5263	0.7407	2.281	-0.0687	-0.141	0.0967	0.0122	0.0409	0.0128	-0.1165	0.1433	-0.0139	0.4597	-0.0182	-0.0162	0.3971	-0.029	0.4689	-15.8532	69.007	63.4764
20	0.3815	0.0286	-0.6158	1.6051	-0.304	1.9822	0.0319	-0.1525	-0.0899	0.2881	0.0304	-0.0465	0.0013	0.1911	-0.0592	0.4989	0.102	-0.0621	0.439	-0.0345	0.4547	-8.3706	46.3935	80.0854

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain 'A' and resid 2 through 156)
2	X-RAY DIFFRACTION	2	(chain 'B' and resid 2 through 156)
3	X-RAY DIFFRACTION	3	(chain 'C' and resid 2 through 156)
4	X-RAY DIFFRACTION	4	(chain 'D' and resid 2 through 156)
5	X-RAY DIFFRACTION	5	(chain 'E' and resid 2 through 156)
6	X-RAY DIFFRACTION	6	(chain 'F' and resid 2 through 156)
7	X-RAY DIFFRACTION	7	(chain 'G' and resid 2 through 156)
8	X-RAY DIFFRACTION	8	(chain 'H' and resid 2 through 156)
9	X-RAY DIFFRACTION	9	(chain 'I' and resid 2 through 156)
10	X-RAY DIFFRACTION	10	(chain 'J' and resid 2 through 156)
11	X-RAY DIFFRACTION	11	(chain 'K' and resid 2 through 156)
12	X-RAY DIFFRACTION	12	(chain 'L' and resid 2 through 156)
13	X-RAY DIFFRACTION	13	(chain 'M' and resid 2 through 156)
14	X-RAY DIFFRACTION	14	(chain 'N' and resid 2 through 156)
15	X-RAY DIFFRACTION	15	(chain 'O' and resid 2 through 156)
16	X-RAY DIFFRACTION	16	(chain 'P' and resid 2 through 156)
17	X-RAY DIFFRACTION	17	(chain 'Q' and resid 2 through 156)
18	X-RAY DIFFRACTION	18	(chain 'R' and resid 2 through 156)
19	X-RAY DIFFRACTION	19	(chain 'S' and resid 2 through 156)
20	X-RAY DIFFRACTION	20	(chain 'T' and resid 2 through 156)

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