PDB-4w8o: Structure of the luciferase-like enzyme from the nonluminescent Z...

ID or keywords:

Entry

Database: PDB / ID: 4w8o

Title

Structure of the luciferase-like enzyme from the nonluminescent Zophobas morio mealworm

Components

luciferase-like enzymeAMP-CoA-ligase

Keywords

OXIDOREDUCTASE / Luciferase-like enzyme

Function / homology

Function and homology information

catalytic activity
Similarity search - Function

Biological species

Zophobas atratus (giant mealworm beetle)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / Resolution: 2.05 Å

Authors

Santos, C.R. / Prado, R.A. / Viviani, V. / Murakami, M.T.

Funding support

Brazil, 1items

Citation

Journal: To Be Published
Title: Structure of the luciferase-like enzyme from the nonluminescent Zophobas morio mealworm
Authors: Santos, C.R. / Prado, R.A. / Viviani, V. / Murakami, M.T.

History

Deposition	Aug 25, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 21, 2015	Provider: repository / Type: Initial release
Revision 1.1	Apr 17, 2019	Group: Author supporting evidence / Data collection / Derived calculations Category: pdbx_audit_support / pdbx_struct_oper_list Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2	Jan 1, 2020	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3	Dec 27, 2023	Group: Data collection / Database references / Structure summary Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4w8o.cif.gz	344.1 KB	Display	PDBx/mmCIF format
PDB format	pdb4w8o.ent.gz	284.4 KB	Display	PDB format
PDBx/mmJSON format	4w8o.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4w8o_validation.pdf.gz	813.4 KB	Display	wwPDB validaton report
Full document	4w8o_full_validation.pdf.gz	820.3 KB	Display
Data in XML	4w8o_validation.xml.gz	34.2 KB	Display
Data in CIF	4w8o_validation.cif.gz	49 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/w8/4w8o ftp://data.pdbj.org/pub/pdb/validation_reports/w8/4w8o	HTTPS FTP

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Related structure data

Similar structure data	6h45-1 5u95-1 6h45-2 5gz2-d 3u16-1 3udz-2 2cz6-d 3udt-1 4xhl-d 4e5d-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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	#78 - Jun 2006 Luciferase similarity (4)

Deposited unit

A: luciferase-like enzymeAMP-CoA-ligase

B: luciferase-like enzymeAMP-CoA-ligase

hetero molecules

96.6 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: luciferase-like enzymeAMP-CoA-ligase

hetero molecules

defined by author&software
48.3 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: luciferase-like enzymeAMP-CoA-ligase

hetero molecules

defined by author&software
48.3 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	87.774, 91.005, 110.294
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	luciferase-like enzymeAMP-CoA-ligase Mass: 47922.906 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Zophobas atratus (giant mealworm beetle) Production host: Escherichia coli (E. coli) / References: UniProt: A0A0R4I967*PLUS
#2: Chemical	ChemComp-P33 / 3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL / HEPTAETHYLENE GLYCOL / PEG330 Mass: 326.383 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₄H₃₀O₈ / Comment: precipitant*YM
#3: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Cl
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 396 / 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: 46.72 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 100 mM HEPES, 200 mM ammonium chloride, 16% (w/v) PEG 6000

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.456 Å
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 9, 2013
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.456 Å / Relative weight: 1
Reflection	Resolution: 2.05→34.11 Å / Num. obs: 53794 / % possible obs: 95.7 % / Redundancy: 5 % / Net I/σ(I): 24.06

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0073	refinement
PDB_EXTRACT	3.15	data extraction
SCALEPACK		data scaling

Refinement

Resolution: 2.05→34.11 Å / Cor.coef. F_o:F_c: 0.962 / Cor.coef. F_o:F_c free: 0.939 / SU B: 10.645 / SU ML: 0.144 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.221 / ESU R Free: 0.183 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2319	2736	5.1 %	RANDOM
R_work	0.1876	50958	-	-
obs	0.1899	50958	95.47 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso max: 64.55 Å² / B_iso mean: 24.862 Å² / B_iso min: 12.93 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-2.01 Å²	0 Å²	-0 Å²
2-	-	2.18 Å²	0 Å²
3-	-	-	-0.17 Å²

Refinement step

Cycle: final / Resolution: 2.05→34.11 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6615	0	46	396	7057
B_iso mean	-	-	57.52	41.09	-
Num. residues	-	-	-	-	841

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.006	0.019	6789
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	6497
X-RAY DIFFRACTION	r_angle_refined_deg	1.033	1.98	9140
X-RAY DIFFRACTION	r_angle_other_deg	0.699	3	15052
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.531	5	838
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	30.996	24.049	284
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.822	15	1229
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.189	15	34
X-RAY DIFFRACTION	r_chiral_restr	0.061	0.2	1029
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.021	7483
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1487
X-RAY DIFFRACTION	r_mcbond_it	0.722	2.365	3361
X-RAY DIFFRACTION	r_mcbond_other	0.722	2.365	3360
X-RAY DIFFRACTION	r_mcangle_it	1.188	3.544	4196

LS refinement shell

Resolution: 2.048→2.102 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.299	157	-
R_work	0.279	3415	-
all	-	3572	-
obs	-	-	87.08 %

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	4.9549	1.7023	-1.4567	1.9413	-0.2557	2.8165	-0.1988	0.7995	-0.3196	-0.4265	0.0993	-0.0765	0.1918	-0.0593	0.0996	0.1963	0.0423	-0.0398	0.2102	-0.0375	0.0616	76.7963	25.6312	80.3911
2	1.6906	-0.5151	-0.2757	1.6209	0.1222	1.2578	0.0164	0.0247	-0.3109	0.0363	0.007	0.1861	0.1653	-0.0267	-0.0234	0.0992	-0.0197	-0.0256	0.0982	-0.0193	0.1377	66.4106	18.7705	104.1175
3	7.0746	-5.9916	0.0737	11.041	-7.0001	8.0698	-0.0643	-0.3931	0.3476	0.3784	-0.0523	-0.3769	-0.3823	0.4476	0.1166	0.1448	-0.0606	-0.0276	0.1884	-0.0283	0.1312	81.787	35.6154	114.834
4	3.3284	0.3777	0.1689	2.3105	-0.2036	2.3446	0.0806	-0.3473	-0.0339	0.3684	-0.0138	0.1248	-0.0037	-0.0405	-0.0668	0.1315	-0.0161	0.023	0.1577	0.0028	0.0655	69.3564	28.8881	118.0367
5	1.116	-0.4034	-0.1064	2.7271	0.8349	18.8867	-0.3917	-0.0322	-0.1125	-0.1437	-0.1799	0.5685	-0.4776	-1.2367	0.5716	0.2916	-0.0458	-0.0792	0.3637	0.0242	0.4505	51.8402	16.3474	108.8243
6	3.3283	0.5242	-0.8238	2.0185	-0.4139	1.5671	0.1257	0.069	0.0174	-0.0885	-0.0427	0.1443	-0.0113	-0.0842	-0.083	0.1548	0.0054	-0.0335	0.165	-0.0193	0.1277	66.9219	29.6108	97.6093
7	2.0222	-0.9282	0.3026	0.6793	-0.3791	1.8081	0.1156	0.2777	-0.0664	-0.1604	-0.0599	0.1502	-0.0133	0.2123	-0.0557	0.114	-0.0172	-0.0352	0.1857	-0.0034	0.0945	77.0973	27.8684	92.6382
8	1.5687	0.3499	0.6752	1.9238	0.3219	1.8942	0.0343	0.1453	-0.2789	-0.121	-0.0493	0.0026	0.1461	0.2069	0.015	0.1072	0.0382	-0.0289	0.1284	-0.0386	0.108	78.6661	16.0304	99.4256
9	3.4454	-0.1915	-0.4146	3.1434	-0.6729	1.4774	0.0316	-0.1124	-0.3631	0.2431	-0.0428	-0.0288	0.1044	0.0956	0.0113	0.1655	0.0701	-0.0645	0.1131	-0.012	0.1403	91.331	7.2756	104.6333
10	1.612	-0.4098	0.1491	1.7195	-1.0759	0.6826	0.1544	0.3346	-0.1243	-0.1855	-0.2452	-0.1362	0.124	0.1334	0.0908	0.1741	0.0771	-0.0485	0.2286	-0.0792	0.0708	92.4646	14.4676	91.9129
11	9.207	-4.3987	-2.9303	23.2981	0.7588	6.1472	-0.1735	0.0803	-0.3102	-0.4839	0.5078	-0.9184	0.1492	0.0709	-0.3344	0.3716	0.1369	-0.0144	0.5369	-0.0408	0.2344	98.0392	14.5433	81.9199
12	23.0803	-4.2314	16.6565	6.5633	-4.0928	13.3976	0.1156	0.0481	0.4214	-0.0572	-0.103	-0.5181	-0.1235	0.2136	-0.0126	0.1124	0.0056	0.0639	0.1744	-0.0486	0.174	94.8801	22.4136	85.2861
13	2.4902	-0.4344	-0.7365	0.8415	-0.0881	1.7266	0.1624	0.34	0.3725	-0.336	-0.0964	-0.1084	-0.3611	0.3764	-0.066	0.2587	-0.055	0.0424	0.3543	0.034	0.1161	88.4315	36.7705	84.7393
14	3.8396	-1.6598	-1.0966	2.3609	0.8647	1.642	0.0346	0.1157	-0.0024	-0.0979	-0.0907	-0.1533	-0.0033	0.298	0.056	0.1394	-0.0358	0.0213	0.2189	0.0239	0.0665	90.0433	36.1144	87.9503
15	10.0241	-9.8089	-6.394	14.1799	7.2491	9.6777	0.5497	0.2415	0.2734	-0.2248	-0.2511	-0.7822	-0.4272	0.272	-0.2986	0.269	-0.0622	-0.0593	0.3107	0.0409	0.3081	93.7582	42.0012	98.0612
16	2.9633	-0.4215	0.7948	1.9412	-1.197	3.1154	-0.2087	-0.9439	-0.1163	0.394	0.0929	-0.0058	0.0923	0.1074	0.1158	0.2935	0.0062	-0.0005	0.4492	0.0264	0.1104	45.204	30.8613	84.8084
17	2.9187	-1.321	-0.9563	10.5302	-0.8847	1.8855	0.0669	-0.3837	-0.0848	0.4954	-0.016	-0.3047	0.0281	0.3854	-0.0509	0.1389	-0.0151	-0.0454	0.2224	0.0171	0.1521	60.5221	21.9998	72.8487
18	1.7367	0.0539	0.0811	1.3944	-0.3879	1.2795	0.0122	0.0254	-0.1915	0.0101	-0.0543	-0.1226	0.0459	0.2399	0.0421	0.0724	-0.0048	-0.0013	0.1585	0	0.13	56.7893	24.3183	59.4764
19	7.1752	1.4318	-1.7441	5.5197	0.8098	4.9776	-0.0335	0.0335	0.1415	-0.1205	0.0033	0.2846	-0.1327	-0.1363	0.0302	0.1655	-0.0151	0.0061	0.1285	0.0279	0.1201	46.7401	38.6151	51.5546
20	2.2255	-1.4347	0.4338	6.6034	-1.4347	1.7762	0.0323	0.3394	-0.1053	-0.5099	0.0303	0.1861	0.1325	0.0308	-0.0626	0.1037	-0.0189	0.0077	0.161	-0.0114	0.084	51.0064	32.6568	45.3662
21	6.2259	-2.7894	-0.493	3.3085	-2.3654	3.2917	-0.0355	-0.0792	-0.0372	-0.0805	-0.0658	-0.0798	0.1168	0.1351	0.1012	0.0814	0.0005	0.0215	0.1403	-0.0307	0.1292	62.6035	24.3782	48.3596
22	8.6245	-5.9219	-0.5699	15.2706	2.4724	5.2025	-0.1416	-0.5171	0.2313	0.5823	0.1951	-0.8628	0.3252	0.9721	-0.0536	0.1143	-0.0215	-0.0555	0.2889	0.0467	0.1875	70.6872	28.1389	67.6119
23	4.0164	-0.5113	1.3575	3.7687	-1.109	4.1911	0.084	-0.0567	0.1249	0.0037	0.0385	0.0181	-0.2962	0.0103	-0.1225	0.1255	-0.0328	0.0364	0.1214	-0.0163	0.1206	48.5774	36.9473	67.7902
24	1.7214	-0.0676	0.0873	0.365	0.0749	1.5926	0.017	-0.2241	-0.2631	0.1153	-0.0384	-0.0648	0.1493	-0.0004	0.0214	0.0918	-0.0248	-0.0329	0.1378	0.0397	0.1347	46.1978	20.2637	70.0298
25	4.1735	-1.471	-0.444	2.2451	0.49	1.4054	-0.03	0.1564	-0.6696	-0.1185	-0.091	0.0161	0.1947	0.0159	0.121	0.1165	-0.0348	-0.0055	0.0745	0.002	0.2394	34.7308	9.1289	64.917
26	1.8882	0.9014	-0.4694	2.9184	1.0803	1.4715	0.0691	-0.1561	-0.3021	0.3293	-0.073	0.1131	0.2514	-0.0089	0.0039	0.1032	-0.0243	-0.0319	0.1798	0.0677	0.1474	33.1445	17.6812	75.452
27	4.2822	-1.7034	0.3023	3.5215	0.1614	2.5159	-0.0064	-0.3864	-0.2946	0.2462	0.0647	0.3041	0.2531	-0.2985	-0.0583	0.1909	-0.0515	0.0621	0.2672	0.0585	0.0652	30.1903	25.8475	82.1067
28	4.1989	-0.4519	-0.7733	11.2641	-2.6935	8.8141	0.0651	-0.1104	0.796	0.1431	0.237	0.7165	-0.8641	-0.585	-0.3021	0.1656	0.0497	0.029	0.2908	-0.0334	0.4204	22.0742	40.9356	81.4509
29	3.339	0.5262	-1.2766	1.0047	0.1874	1.516	0.3009	0.0055	0.5369	0.127	-0.0363	0.1428	-0.4675	-0.1324	-0.2647	0.2156	0.0169	0.0973	0.1278	-0.0169	0.1167	36.3416	40.7868	73.481
30	6.3969	0.5382	-0.7996	8.8527	0.1827	8.5734	0.1845	0.3091	-0.0915	-0.2646	0.1069	0.4394	-0.2834	-0.2089	-0.2914	0.1287	-0.0255	0.0585	0.2211	-0.0393	0.2122	24.101	29.7998	77.5745

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	3 - 19
2	X-RAY DIFFRACTION	2	A	20 - 102
3	X-RAY DIFFRACTION	3	A	103 - 112
4	X-RAY DIFFRACTION	4	A	113 - 160
5	X-RAY DIFFRACTION	5	A	161 - 166
6	X-RAY DIFFRACTION	6	A	167 - 188
7	X-RAY DIFFRACTION	7	A	189 - 214
8	X-RAY DIFFRACTION	8	A	215 - 247
9	X-RAY DIFFRACTION	9	A	248 - 286
10	X-RAY DIFFRACTION	10	A	287 - 339
11	X-RAY DIFFRACTION	11	A	340 - 345
12	X-RAY DIFFRACTION	12	A	346 - 352
13	X-RAY DIFFRACTION	13	A	353 - 389
14	X-RAY DIFFRACTION	14	A	390 - 421
15	X-RAY DIFFRACTION	15	A	422 - 427
16	X-RAY DIFFRACTION	16	B	3 - 19
17	X-RAY DIFFRACTION	17	B	20 - 33
18	X-RAY DIFFRACTION	18	B	34 - 106
19	X-RAY DIFFRACTION	19	B	107 - 120
20	X-RAY DIFFRACTION	20	B	121 - 144
21	X-RAY DIFFRACTION	21	B	145 - 164
22	X-RAY DIFFRACTION	22	B	165 - 173
23	X-RAY DIFFRACTION	23	B	174 - 203
24	X-RAY DIFFRACTION	24	B	204 - 247
25	X-RAY DIFFRACTION	25	B	248 - 306
26	X-RAY DIFFRACTION	26	B	307 - 338
27	X-RAY DIFFRACTION	27	B	339 - 362
28	X-RAY DIFFRACTION	28	B	363 - 376
29	X-RAY DIFFRACTION	29	B	377 - 411
30	X-RAY DIFFRACTION	30	B	412 - 423

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-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