PDB-7eum: Crystal structure of apo Nmar_1308 protein at cryogenic temperature

ID or keywords:

Entry

Database: PDB / ID: 7eum

Title

Crystal structure of apo Nmar_1308 protein at cryogenic temperature

Components

Enoyl-CoA hydratase/isomerase

Keywords

STRUCTURAL PROTEIN / Thaumarchaeota / ammonia-oxidizing Archaea (AOA) / CO2 fixation / 3HP/4HB cycle / crotonyl-CoA hydratase (CCAH) / 3-hydroxypropionyl-CoA dehydratase (3HPD)

Function / homology

Function and homology information

enoyl-CoA hydratase activity / fatty acid beta-oxidation / isomerase activity
Similarity search - Function

Biological species

Nitrosopumilus maritimus (archaea)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

FOURIER SYNTHESIS / Resolution: 2.15 Å

Authors

DeMirci, H. / Destan, E. / Yuksel, B. / Ayan, E.

Funding support

United States,

Turkey, 2items

Citation

Journal: To Be Published
Title: Crystal structure of apo Nmar_1308 protein at cryogenic temperature
Authors: DeMirci, H. / Destan, E. / Yuksel, B. / Ayan, E.

History

Deposition	May 18, 2021	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Sep 29, 2021	Provider: repository / Type: Initial release
Revision 1.1	May 29, 2024	Group: Data collection / Category: chem_comp_atom / chem_comp_bond

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7eum.cif.gz	536.4 KB	Display	PDBx/mmCIF format
PDB format	pdb7eum.ent.gz	449.4 KB	Display	PDB format
PDBx/mmJSON format	7eum.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7eum_validation.pdf.gz	478.5 KB	Display	wwPDB validaton report
Full document	7eum_full_validation.pdf.gz	503.2 KB	Display
Data in XML	7eum_validation.xml.gz	52.7 KB	Display
Data in CIF	7eum_validation.cif.gz	72.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/eu/7eum ftp://data.pdbj.org/pub/pdb/validation_reports/eu/7eum	HTTPS FTP

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Related structure data

Similar structure data	3qka-d 3pzk-2 2vre-1 4nat-1 3h81-1 1q50-1 4jyl-d 2qq3-2 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

C: Enoyl-CoA hydratase/isomerase

D: Enoyl-CoA hydratase/isomerase

F: Enoyl-CoA hydratase/isomerase

A: Enoyl-CoA hydratase/isomerase

E: Enoyl-CoA hydratase/isomerase

B: Enoyl-CoA hydratase/isomerase

164 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

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

Unit cell

Length a, b, c (Å)	75.868, 75.868, 207.965
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	145
Space group name H-M	P3₂

#1: Protein	Enoyl-CoA hydratase/isomerase Mass: 27322.469 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Nitrosopumilus maritimus (strain SCM1) (archaea) Gene: Nmar_1308 / Production host: Escherichia coli (E. coli) / References: UniProt: A9A2G5
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 335 / 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: 2.31 Å³/Da / Density % sol: 41.65 %
Crystal grow	Temperature: 293 K / Method: microbatch Details: 0.2M MgCl2, 0.1M sodium citrate tribasic dihydrate (pH 5), 10% w/v PEG

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

SSRL

/ Beamline: BL12-2 / Wavelength: 0.97 Å

Detector

Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 29, 2017

Radiation

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

Radiation wavelength

Wavelength: 0.97 Å / Relative weight: 1

Reflection

Resolution: 2.15→29.687 Å / Num. obs: 72865 / % possible obs: 99.7 % / Redundancy: 10.513 % / B_iso Wilson estimate: 52.095 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.127 / R_rim(I) all: 0.134 / Χ²: 1.141 / Net I/σ(I): 13.38 / Num. measured all: 766012

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. possible	Num. unique obs	CC_1/2	R_rim(I) all	% possible all
2.15-2.28	10.5	1.883	1.22	122771	11837	11693	0.522	1.979	98.8
2.28-2.43	10.395	1.124	2.16	115078	11077	11070	0.772	1.182	99.9
2.43-2.63	10.281	0.687	3.56	106310	10357	10340	0.927	0.723	99.8
2.63-2.88	10.809	0.404	6.25	101855	9431	9423	0.969	0.424	99.9
2.88-3.22	10.354	0.228	10.63	88955	8599	8591	0.985	0.239	99.9
3.22-3.71	10.821	0.114	21.14	81915	7585	7570	0.996	0.119	99.8
3.71-4.53	10.614	0.065	36.35	68323	6446	6437	0.998	0.068	99.9
4.53-6.36	10.48	0.056	40.89	51812	4952	4944	0.999	0.059	99.8
6.36-29.687	10.366	0.038	55.01	28993	2813	2797	0.999	0.04	99.4

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Processing

Software

Name	Version	Classification
XSCALE	XDS	data scaling
PHENIX	dev_3318	refinement
PDB_EXTRACT	3.27	data extraction
XDS		data reduction
PHENIX		phasing

Refinement

Method to determine structure:

FOURIER SYNTHESIS / Resolution: 2.15→29.687 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.71 / Phase error: 32.12 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2845	1657	2.28 %
R_work	0.2448	71017	-
obs	0.2458	72674	99.8 %

Solvent computation

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

Displacement parameters

B_iso max: 165.28 Å² / B_iso mean: 64.1625 Å² / B_iso min: 15.52 Å²

Refinement step

Cycle: final / Resolution: 2.15→29.687 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10432	0	0	336	10768
B_iso mean	-	-	-	51.41	-
Num. residues	-	-	-	-	1393

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	% reflection obs (%)
2.15-2.2133	0.3095	134	0.3015	5907	99
2.2133-2.2847	0.3665	139	0.3022	5948	100
2.2847-2.3663	0.3146	125	0.2934	5945	100
2.3663-2.461	0.3105	136	0.2864	5880	100
2.461-2.5729	0.3482	138	0.2768	5896	100
2.5729-2.7085	0.3235	146	0.2646	5994	100
2.7085-2.8781	0.2789	133	0.2589	5844	100
2.8781-3.1001	0.2842	142	0.2609	5917	100
3.1001-3.4116	0.3014	136	0.2477	5953	100
3.4116-3.9044	0.2985	140	0.2323	5909	100
3.9044-4.9155	0.2408	141	0.2092	5914	100
4.9155-29.68	0.2661	147	0.2365	5910	100

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	1.9098	-0.6259	0.4586	2.85	-0.8712	1.7985	-0.3347	-0.6606	-0.0107	-0.3723	0.0813	0.9973	-0.8786	-1.0126	-0.2251	0.8097	0.5788	-0.3147	0.9378	0.2348	0.8189	-0.73	105.428	17.687
2	2.247	0.298	0.4493	1.567	-0.2934	1.1809	-0.2232	0.2182	0.1538	-0.4939	0.3733	0.615	-0.6985	-0.6401	-0.0901	0.8185	0.2448	-0.1049	0.508	0.1642	0.4887	14.896	105.914	13.88
3	0.9096	-0.2338	0.4504	2.0553	-0.8279	1.854	0.1771	0.4382	0.3586	-0.3714	0.189	0.56	-0.221	-1.2325	-0.2781	0.6388	0.1346	-0.2757	1.0988	0.0658	0.6896	1.589	93.412	4.198
4	2.1817	-0.238	0.243	1.7727	-0.2234	2.9882	-0.125	0.3774	-0.1895	-0.178	0.3226	0.6333	0.59	-0.7001	-0.2751	0.4795	-0.0929	-0.1246	0.5494	0.1474	0.6345	9.424	80.947	22.852
5	4.1558	2.5837	-0.4243	6.0389	1.0191	1.7739	-0.233	0.2522	-1.1871	-0.9453	0.6468	-0.3526	0.5471	0.1344	0.0756	1.6734	0.0979	-0.4619	0.3443	-0.1303	0.9243	26.944	62.556	5.235
6	6.868	0.6573	0.6507	1.8107	0.2336	3.3694	0.4013	-0.5432	-1.0526	-0.4563	-0.0033	-0.0682	0.9983	-0.1928	-0.4175	1.4368	-0.0153	-0.3239	0.397	-0.1198	0.8313	25.85	65.155	11.872
7	3.0802	0.0098	0.2499	1.2347	-0.3851	2.7448	0.1583	0.3832	-0.521	-0.6893	0.1767	0.159	0.6124	-0.1101	-0.2506	0.8292	0.0255	-0.1404	0.2888	-0.0447	0.4302	27.555	78.436	11.552
8	8.2256	-2.7547	-0.3492	7.3802	-1.1098	7.0846	0.3837	0.8285	0.985	-0.216	-0.3994	-0.8347	-0.7565	0.835	-0.3024	0.9609	-0.2581	0.1868	0.5979	0.0535	0.4253	49.173	113.7	10.732
9	5.1076	-2.2012	-0.4491	8.5777	-0.4224	5.7002	-0.3922	0.5316	-0.032	-0.2043	0.433	-1.2231	0.103	1.5145	-0.0648	0.6614	-0.2252	0.0226	1.0708	-0.0914	0.2835	55.076	102.084	13.5
10	3.5732	-0.5358	-0.2168	5.6905	-0.8607	6.778	0.051	0.5019	-0.0369	-0.2769	0.113	-0.6492	-0.6535	0.7267	0.1314	0.8311	-0.1942	0.1365	0.595	0.0719	0.2288	45.746	110.624	11.686
11	2.718	-0.9819	0.4748	6.009	-1.7026	5.0907	0.0672	0.3923	-0.3715	-0.3668	-0.2741	-0.6123	-0.1211	1.1311	0.0487	0.4033	0.0178	0.1052	0.5285	-0.0607	0.4162	49.698	94.122	22.76
12	1.5531	-0.3567	-0.0327	2.0096	-0.4404	3.237	0.0178	0.2564	-0.0779	-0.7008	0.0716	-0.2352	-0.0563	0.7524	-0.0563	0.629	0.0808	0.0637	0.4716	-0.0759	0.2948	40.877	94.08	10.26
13	2.6082	0.091	0.1693	2.5149	-0.0809	1.4404	-0.107	1.0189	-0.0799	-0.5035	-0.2664	0.1973	0.3521	0.3878	-0.1341	0.8229	0.0004	0.0963	0.6082	-0.0558	0.2482	35.995	95.746	0.607
14	2.4491	-0.7376	0.329	0.5279	-0.2734	0.1865	-0.203	0.1425	0.1782	-0.3869	0.1565	0.0485	-0.9675	-0.3862	-0.0798	0.9487	0.0654	0.044	0.3482	0.0153	0.2472	29.545	111.654	18.653
15	2.9195	-0.6913	-1.5034	1.6852	1.0654	1.9005	0.1889	-0.3204	-0.0053	-0.0261	-0.5119	0.5322	0.0491	-0.6072	0.5906	0.8687	0.6482	0.5887	1.6528	0.3276	0.8433	1.674	101.932	53.005
16	0.7635	-0.8342	0.2361	2.2627	-0.1531	0.643	-0.0054	-0.2221	0.4483	-0.0578	0.1807	0.6855	-0.2373	-0.3978	0.2021	0.7946	0.7548	0.1045	1.041	0.3693	0.6912	5.148	106.863	43.789
17	1.2011	-0.8218	-0.8001	1.9699	-0.481	1.2788	0.1578	-0.0838	-0.0934	0.8357	0.5534	0.8152	-0.3951	-0.5682	1.5713	0.6017	0.7462	0.4092	1.1447	0.3025	0.6293	2.932	94.199	51.367
18	1.6812	0.7904	0.2932	2.3479	-0.2393	2.2082	-0.0835	-0.5886	-0.1102	0.4687	0.3307	0.6175	-0.4018	-0.789	-0.0814	0.5973	0.3385	0.2111	0.7226	0.1654	0.4678	17.153	96.663	46.794
19	3.6779	0.0094	-1.5694	4.3654	0.2328	5.1174	0.3707	-0.2702	-0.6342	-0.1618	0.1564	-0.2423	0.8003	0.2419	-0.3996	0.9834	0.0538	-0.2197	0.3411	0.1678	0.736	29.998	57.742	42.179
20	4.2042	1.9682	-2.5987	2.3301	-0.4125	2.8581	0.1535	0.3924	-1.0489	-0.188	0.3281	0.6318	0.4405	-0.0262	-0.7049	0.9556	0.0259	-0.0813	0.6391	0.3153	0.8599	23.532	61.9	44.058
21	2.4104	-0.1736	-1.1158	0.9908	1.2846	4.6744	0.4207	-0.1112	-0.3956	-0.3329	0.3658	-0.3191	0.7668	0.643	-0.3585	0.9348	0.1458	-0.1349	0.2144	0.0464	0.6124	38.603	67.763	30.944
22	2.1942	0.631	0.3215	1.6293	-0.1261	1.7976	0.3844	-0.5819	-0.4968	0.2706	-0.1081	-0.0088	0.6866	-0.0112	-0.2626	0.684	0.258	-0.044	0.3342	0.16	0.4409	34.739	74.355	44.92
23	2.0238	1.3029	0.0669	2.0989	-0.7176	2.811	0.426	-0.6528	-0.0995	0.7129	0.1043	0.1284	0.4104	0.0338	-0.262	0.9283	0.2163	-0.0503	0.7108	0.1558	0.5238	33.062	76.422	55.604
24	1.4423	0.2728	-0.083	1.5192	-0.2621	2.853	0.1003	-0.2677	-0.296	0.2348	-0.0911	0.3821	0.6134	-0.9548	-0.5206	0.5457	-0.0254	0.0664	0.7193	0.4807	0.7323	12.419	75.793	41.368
25	3.0245	3.0293	-0.5446	4.6326	2.7121	6.7614	0.2372	0.1094	0.21	0.1266	0.017	-1.0912	-1.627	1.0066	-0.4143	1.001	-0.184	-0.1351	0.9223	-0.0837	0.3276	54.999	104.066	48.924
26	4.9665	-2.8898	1.6003	7.4271	-1.3539	1.1836	0.0059	-0.4136	0.0586	0.335	0.1816	-0.581	-0.6012	0.3276	-0.3001	0.5665	-0.0813	-0.0152	0.6572	0.0114	0.2909	51.69	102.819	43.75
27	1.6485	0.2972	0.1684	2.0526	0.5467	3.5597	-0.0052	-0.3604	-0.1713	0.4247	0.1579	-0.1901	-0.2618	0.4546	-0.1323	0.531	0.1427	-0.0207	0.3988	-0.0025	0.2593	41.262	93.853	44.519

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 0:48 )	A	0 - 48
2	X-RAY DIFFRACTION	2	( CHAIN A AND RESID 49:182 )	A	49 - 182
3	X-RAY DIFFRACTION	3	( CHAIN A AND RESID 183:201 )	A	183 - 201
4	X-RAY DIFFRACTION	4	( CHAIN A AND RESID 202:242 )	A	202 - 242
5	X-RAY DIFFRACTION	5	( CHAIN B AND RESID 0:27 )	B	0 - 27
6	X-RAY DIFFRACTION	6	( CHAIN B AND RESID 28:73 )	B	28 - 73
7	X-RAY DIFFRACTION	7	( CHAIN B AND RESID 74:242 )	B	74 - 242
8	X-RAY DIFFRACTION	8	( CHAIN C AND RESID 0:17 )	C	0 - 17
9	X-RAY DIFFRACTION	9	( CHAIN C AND RESID 18:38 )	C	18 - 38
10	X-RAY DIFFRACTION	10	( CHAIN C AND RESID 41:61 )	C	41 - 61
11	X-RAY DIFFRACTION	11	( CHAIN C AND RESID 74:92 )	C	74 - 92
12	X-RAY DIFFRACTION	12	( CHAIN C AND RESID 93:162 )	C	93 - 162
13	X-RAY DIFFRACTION	13	( CHAIN C AND RESID 163:182 )	C	163 - 182
14	X-RAY DIFFRACTION	14	( CHAIN C AND RESID 183:242 )	C	183 - 242
15	X-RAY DIFFRACTION	15	( CHAIN D AND RESID 0:27 )	D	0 - 27
16	X-RAY DIFFRACTION	16	( CHAIN D AND RESID 28:48 )	D	28 - 48
17	X-RAY DIFFRACTION	17	( CHAIN D AND RESID 49:73 )	D	49 - 73
18	X-RAY DIFFRACTION	18	( CHAIN D AND RESID 74:242 )	D	74 - 242
19	X-RAY DIFFRACTION	19	( CHAIN E AND RESID 0:37 )	E	0 - 37
20	X-RAY DIFFRACTION	20	( CHAIN E AND RESID 38:62 )	E	38 - 62
21	X-RAY DIFFRACTION	21	( CHAIN E AND RESID 70:92 )	E	70 - 92
22	X-RAY DIFFRACTION	22	( CHAIN E AND RESID 93:162 )	E	93 - 162
23	X-RAY DIFFRACTION	23	( CHAIN E AND RESID 163:182 )	E	163 - 182
24	X-RAY DIFFRACTION	24	( CHAIN E AND RESID 183:242 )	E	183 - 242
25	X-RAY DIFFRACTION	25	( CHAIN F AND RESID 0:27 )	F	0 - 27
26	X-RAY DIFFRACTION	26	( CHAIN F AND RESID 28:73 )	F	28 - 73
27	X-RAY DIFFRACTION	27	( CHAIN F AND RESID 74:242 )	F	74 - 242

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