PDB-4wp9: Crystal structure of Adenylyl cyclase MA1120 from Mycobacterium A...

ID or keywords:

Entry

Database: PDB / ID: 4wp9

Title

Crystal structure of Adenylyl cyclase MA1120 from Mycobacterium Avium bound to 2'5'-DD-3'-ATP, Calcium and Magnesium ion

Components

Ma1120

Keywords

LYASE / 2'5'-dd-3'-ATP / P-site inhibitor / Adenylyl Cyclase

Function / homology

Function and homology information

cyclic nucleotide biosynthetic process / adenylate cyclase / adenylate cyclase activity / intracellular signal transduction / metal ion binding
Similarity search - Function

Biological species

Mycobacterium avium (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.382 Å

Authors

Bharambe, N.G. / Barathy, D.V. / Suguna, K.

Citation

Journal: J.Struct.Biol. / Year: 2015
Title: Autoinhibitory mechanism and activity-related structural changes in a mycobacterial adenylyl cyclase
Authors: Barathy, D.V. / Bharambe, N.G. / Syed, W. / Zaveri, A. / Visweswariah, S.S. / Cola sigmaf o, M. / Misquith, S. / Suguna, K.

History

Deposition	Oct 17, 2014	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Sep 2, 2015	Provider: repository / Type: Initial release
Revision 1.1	Nov 8, 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 / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _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

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Download

PDBx/mmCIF format	4wp9.cif.gz	203.3 KB	Display	PDBx/mmCIF format
PDB format	pdb4wp9.ent.gz	164.1 KB	Display	PDB format
PDBx/mmJSON format	4wp9.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4wp9_validation.pdf.gz	961.1 KB	Display	wwPDB validaton report
Full document	4wp9_full_validation.pdf.gz	963.1 KB	Display
Data in XML	4wp9_validation.xml.gz	19 KB	Display
Data in CIF	4wp9_validation.cif.gz	28.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/wp/4wp9 ftp://data.pdbj.org/pub/pdb/validation_reports/wp/4wp9	HTTPS FTP

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Related structure data

Related structure data	4wp3C 4wp8SC 4wpaC C: citing same article (ref.) S: Starting model for refinement
Similar structure data	5d15-d 1jkt-1 6ol2-d 1npy-3 5av3-d 6j4s-d 1m6u-1 3nx1-d 5rbx-d 1wvw-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
Related items in Molecule of the Month	#251 - Nov 2020 Adenylyl Cyclase similarity (7) #133 - Jan 2011 Nitric Oxide Synthase similarity (5) #58 - Oct 2004 G Proteins similarity (6) #28 - Apr 2002 Anthrax Toxin similarity (1) #44 - Aug 2003 Calmodulin similarity (1)

Deposited unit

A: Ma1120

B: Ma1120

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	52.470, 56.090, 55.770
Angle α, β, γ (deg.)	90.00, 110.72, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Ma1120 / Cya1120 / Adenylyl cyclase Mass: 19587.342 Da / Num. of mol.: 2 / Fragment: UNP residues 53-222 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium avium (bacteria) / Strain: TN 104 / Gene: cya1120 / Plasmid: pPROExHT / Details (production host): A / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q5UFR5, adenylate cyclase
#2: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Chemical	ChemComp-ZDA / 2',5'-dideoxyadenosine 3'-(tetrahydrogen triphosphate) / 2',5'-DIDEOXYADENOSINE 3'-TRIPHOSPHATE Mass: 475.182 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₀H₁₆N₅O₁₁P₃
#4: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: Ca
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 407 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 1.96 Å³/Da / Density % sol: 37.23 %
Crystal grow	Temperature: 291 K / Method: microbatch / pH: 9.1 Details: 0.2M Sodium phosphate dibasic dihydrate, 20 % w/v Polyethylene glycol 3,350

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97857 Å
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 27, 2013
Radiation	Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97857 Å / Relative weight: 1
Reflection	Resolution: 1.38→28.05 Å / Num. obs: 61217 / % possible obs: 98.7 % / Redundancy: 3.6 % / R_merge(I) obs: 0.087 / Net I/σ(I): 7
Reflection shell	Resolution: 1.38→1.46 Å / Redundancy: 3.5 % / R_merge(I) obs: 0.78 / Mean I/σ(I) obs: 1.6 / % possible all: 97.2

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Processing

Software

Name: PHENIX / Version: (phenix.refine: 1.9_1692) / Classification: refinement

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4WP8

4wp8

Resolution: 1.382→26.949 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.09 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2638	2958	4.91 %	random selection
R_work	0.2309	-	-	-
obs	0.2326	60234	97.08 %	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.382→26.949 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2385	0	64	407	2856

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.011	2528
X-RAY DIFFRACTION	f_angle_d	1.177	3425
X-RAY DIFFRACTION	f_dihedral_angle_d	13.159	905
X-RAY DIFFRACTION	f_chiral_restr	0.057	391
X-RAY DIFFRACTION	f_plane_restr	0.005	441

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 (%)
1.382-1.4047	0.3446	129	0.3103	2569	X-RAY DIFFRACTION	91
1.4047-1.4289	0.2993	139	0.3035	2780	X-RAY DIFFRACTION	100
1.4289-1.4549	0.5228	141	0.4781	2631	X-RAY DIFFRACTION	94
1.4549-1.4828	0.6446	151	0.6001	2568	X-RAY DIFFRACTION	93
1.4828-1.5131	0.3358	162	0.3104	2767	X-RAY DIFFRACTION	99
1.5131-1.546	0.4782	148	0.4231	2788	X-RAY DIFFRACTION	99
1.546-1.582	0.2607	138	0.2188	2766	X-RAY DIFFRACTION	100
1.582-1.6215	0.2319	177	0.2067	2771	X-RAY DIFFRACTION	100
1.6215-1.6654	0.2342	131	0.2	2811	X-RAY DIFFRACTION	100
1.6654-1.7144	0.2029	144	0.2044	2786	X-RAY DIFFRACTION	100
1.7144-1.7697	0.203	134	0.1927	2809	X-RAY DIFFRACTION	100
1.7697-1.8329	0.1999	151	0.2026	2789	X-RAY DIFFRACTION	100
1.8329-1.9063	0.2587	126	0.2444	2743	X-RAY DIFFRACTION	97
1.9063-1.993	0.2969	101	0.2895	2336	X-RAY DIFFRACTION	82
1.993-2.0981	0.2651	111	0.2351	2830	X-RAY DIFFRACTION	100
2.0981-2.2294	0.2439	159	0.22	2748	X-RAY DIFFRACTION	98
2.2294-2.4015	0.3232	131	0.322	2598	X-RAY DIFFRACTION	92
2.4015-2.643	0.2332	120	0.2025	2856	X-RAY DIFFRACTION	100
2.643-3.025	0.2458	130	0.1947	2818	X-RAY DIFFRACTION	100
3.025-3.8094	0.2371	175	0.1737	2818	X-RAY DIFFRACTION	100
3.8094-26.9537	0.2038	160	0.1722	2694	X-RAY DIFFRACTION	93

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	1.0359	0.5479	0.1347	3.1807	-0.6307	2.3031	0.0626	-0.0757	0.1415	-0.1276	-0.2363	-0.4536	-0.2708	0.3673	0.1748	0.159	-0.0228	-0.0157	0.1803	-0.0059	0.1693	107.8149	4.6041	59.4732
2	2.847	3.5605	-0.1457	4.8578	0.9406	2.818	0.2508	-0.2152	-0.7031	0.3394	-0.0998	-0.3909	0.5894	0.0352	-0.1111	0.2089	-0.0297	-0.023	0.1457	0.0416	0.1655	91.2721	-17.2952	61.804
3	6.9371	5.288	3.2668	5.3509	4.2467	3.9183	-0.0405	-0.1966	0.0525	0.221	-0.0031	0.1167	-0.0379	-0.054	0.048	0.1966	0.0298	0.0033	0.1905	0.0001	0.0712	90.6566	-2.6259	67.4236
4	6.7574	3.8935	2.1777	5.5344	2.084	5.5531	-0.1236	-0.1113	0.3339	-0.0164	-0.009	0.0253	-0.3248	-0.218	0.1207	0.1272	0.0328	-0.0109	0.1015	-0.0157	0.143	99.5928	3.1211	61.9613
5	6.8174	2.6052	-1.3119	4.9133	-1.4658	5.154	0.328	-0.7369	0.0163	0.977	-0.089	0.0087	-0.1367	-0.0887	-0.1377	0.2893	0.0146	-0.091	0.2715	-0.0094	0.1415	102.5518	-1.4491	74.6405
6	4.4889	2.9325	-2.1514	8.2126	-3.8044	5.3403	0.0273	-0.2699	0.0675	-0.0451	-0.0051	-0.1769	0.0083	0.0082	-0.0135	0.1244	0.0033	-0.0237	0.1104	-0.0637	0.0898	105.7316	-0.6247	62.1383
7	2.0409	1.3118	0.4408	3.1979	-2.5203	3.7684	-0.0808	-0.1087	0.044	-0.0215	0.185	-0.1026	-0.0974	0.0758	-0.0995	0.1427	-0.0275	-0.0073	0.1471	-0.0541	0.1679	108.3621	0.2394	55.7684
8	2.976	0.9471	-0.0517	2.23	-0.2247	3.0626	0.1434	-0.276	-0.1296	0.477	-0.0856	-0.6795	-0.0407	0.457	-0.0418	0.1525	0.0097	-0.0867	0.217	-0.0122	0.2355	113.9298	-3.7671	67.7205
9	2.9695	-0.0106	-0.6459	1.6642	0.1392	6.3773	-0.0056	-0.5855	-0.063	0.3283	0.0763	-0.3294	0.0596	0.5739	-0.0185	0.1802	0.0003	-0.0836	0.3202	-0.0299	0.295	117.06	-5.5722	66.9464
10	5.2016	1.8404	-0.1989	2.8809	-0.1913	1.7646	0.1762	0.0639	0.0102	0.1614	-0.0723	0.243	-0.0959	-0.117	-0.0871	0.131	-0.0005	0	0.1055	-0.005	0.1168	88.9156	-8.1109	46.5567
11	7.7257	2.6245	1.2309	3.4172	-0.0855	3.3226	-0.2386	0.6878	-0.0887	-0.3452	0.3272	-0.3997	-0.2421	0.5573	-0.0918	0.1534	-0.0316	0.0315	0.2466	-0.011	0.2294	113.1021	-2.042	44.3978
12	8.417	1.8648	3.119	1.7413	0.5898	3.3393	-0.1304	0.1811	0.7406	-0.1643	-0.0532	0.0419	-0.4033	0.1269	0.2653	0.2326	-0.0238	0.0097	0.1251	0.0336	0.168	99.9122	4.8845	39.9921
13	5.0598	-1.1328	6.859	4.4891	-1.3879	9.8606	-0.1285	-0.1138	0.526	-0.1033	-0.0839	0.4401	-0.1602	-0.3002	0.199	0.1395	0.0349	0.0068	0.1691	0.0174	0.1348	89.4383	1.0944	46.0018
14	7.5305	3.5192	-0.3469	6.1095	1.8111	1.6102	-0.1566	-0.2219	0.3595	-0.0961	0.0404	0.1	-0.1904	-0.0687	0.1451	0.1442	0.0142	0.0052	0.0968	0.0196	0.0847	91.9011	-3.1265	44.3497
15	6.9249	1.6098	-1.7314	4.526	-0.9085	4.8233	0.1339	0.7889	0.022	-0.6807	0.0086	0.0361	-0.1666	-0.0417	-0.1316	0.2655	0.0234	-0.0054	0.2239	0	0.0973	92.0927	-5.5326	32.8807
16	4.4704	-0.0855	-1.9705	2.3561	-0.0168	4.5401	0.2385	-0.0921	0.1101	-0.0728	-0.1497	0.177	-0.2588	-0.0932	-0.0811	0.1447	0.0114	-0.0322	0.0735	-0.0181	0.113	90.0286	-8.5202	45.4564
17	2.0325	-0.9171	-2.2481	4.2795	2.8402	4.772	0.0948	-0.0989	-0.0267	-0.0541	-0.0435	0.0383	0.0363	0.0225	-0.0599	0.0919	-0.0008	-0.0293	0.1077	0.0141	0.1133	90.4404	-11.2504	50.9422
18	6.839	0.7545	-1.5065	1.5315	-1.5044	1.8592	0.109	0.3266	-0.2906	-0.2844	0.0143	0.1419	0.1353	-0.0055	-0.0909	0.181	0.0177	-0.0629	0.1232	-0.0376	0.1357	90.9694	-16.6672	38.1596
19	3.6103	-0.7764	0.508	2.0634	0.8722	3.2219	0.063	0.4536	-0.1283	-0.3574	-0.1125	0.0431	0.1246	0.2403	-0.0329	0.1885	-0.0512	-0.0194	0.1056	-0.0146	0.1796	90.8533	-20.9104	39.8618
20	4.9646	1.5385	-0.7261	6.753	-3.5757	2.1159	-0.0227	0.4214	-0.2776	-0.4946	-0.153	-0.052	0.5601	0.6007	0.1108	0.1673	0.0067	-0.0333	0.1731	-0.0318	0.1548	92.2902	-20.7742	38.224

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 49 through 62 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 63 through 73 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 74 through 95 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 96 through 113 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 114 through 131 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 132 through 154 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 155 through 172 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 173 through 187 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 188 through 219 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 50 through 62 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 63 through 73 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 74 through 95 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 96 through 102 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 103 through 113 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 114 through 129 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 130 through 154 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 155 through 172 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 173 through 187 )
19	X-RAY DIFFRACTION	19	chain 'B' and (resid 188 through 210 )
20	X-RAY DIFFRACTION	20	chain 'B' and (resid 211 through 217 )

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Yorodumi