PDB-3tfg: Crystal structure of an H-NOX protein from Nostoc sp. PCC 7120, L...

ID or keywords:

Entry

Database: PDB / ID: 3tfg

Title

Crystal structure of an H-NOX protein from Nostoc sp. PCC 7120, L66W/L67W double mutant

Components

Alr2278 protein

Keywords

SIGNALING PROTEIN / Heme-based sensor domain / Gas binding

Function / homology

Function and homology information

heme binding / metal ion binding
Similarity search - Function

Biological species

Nostoc sp. PCC 7120 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.9003 Å

Authors

Winter, M.B. / Herzik Jr., M.A. / Kuriyan, J. / Marletta, M.A.

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Tunnels modulate ligand flux in a heme nitric oxide/oxygen binding (H-NOX) domain.
Authors: Winter, M.B. / Herzik, M.A. / Kuriyan, J. / Marletta, M.A.

History

Deposition	Aug 15, 2011	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 9, 2011	Provider: repository / Type: Initial release
Revision 1.1	Apr 29, 2015	Group: Non-polymer description
Revision 1.2	Sep 13, 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 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3tfg.cif.gz	228.8 KB	Display	PDBx/mmCIF format
PDB format	pdb3tfg.ent.gz	189.7 KB	Display	PDB format
PDBx/mmJSON format	3tfg.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/tf/3tfg ftp://data.pdbj.org/pub/pdb/validation_reports/tf/3tfg	HTTPS FTP

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Related structure data

Related structure data	3tf0C 3tf1C 3tf8SC 3tf9C 3tfaC 3tfdC 3tfeC 3tffC 2o09 2o0c 2o0g C: citing same article (ref.) S: Starting model for refinement
Similar structure data	3tfd-2 2o0g-2 4iah-1 3tfe-2 3tff-1 3tfe-1 2o0c-1 3tfd-1 3tff-2 2o09-1 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	#133 - Jan 2011 Nitric Oxide Synthase similarity (5) #254 - Feb 2021 Cellulose Synthase similarity (1)

Deposited unit

A: Alr2278 protein

B: Alr2278 protein

hetero molecules

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

1

A: Alr2278 protein

hetero molecules

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

2

B: Alr2278 protein

hetero molecules

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

Unit cell

Length a, b, c (Å)	123.123, 123.123, 123.123
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	198
Space group name H-M	P2₁3

Components on special symmetry positions

ID	Model	Components
1	1	A-262- HOH
2	1	A-263- HOH

#1: Protein	Alr2278 protein Mass: 21359.748 Da / Num. of mol.: 2 / Mutation: L66W, L67W Source method: isolated from a genetically manipulated source Source: (gene. exp.) Nostoc sp. PCC 7120 (bacteria) / Strain: PCC 7120 / UTEX 2576 / Gene: alr2278 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8YUQ7
#2: Chemical	ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃₄H₃₂FeN₄O₄
#3: Chemical	ChemComp-MLA / MALONIC ACID / DICARBOXYLIC ACID C3 / PROPANEDIOLIC ACID / METHANEDICARBOXYLIC ACID Mass: 104.061 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₄O₄
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 262 / 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: 3.77 Å³/Da / Density % sol: 67.34 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 1.9-2.1 M malonic acid (pH 7.0), VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 0.977 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 29, 2011
Radiation	Monochromator: KHOZU Double flat crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.977 Å / Relative weight: 1
Reflection	Resolution: 1.9→50 Å / Num. all: 47646 / Num. obs: 47646 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1
Reflection shell	Resolution: 1.9→1.93 Å / % possible all: 100

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Processing

Software

Name	Version	Classification
Blu-Ice		data collection
PHASER		phasing
PHENIX	(phenix.refine: 1.7_650)	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3TF8

3tf8

Resolution: 1.9003→43.531 Å / SU ML: 0.19 / σ(F): 2 / Phase error: 16.99 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1829	2412	5.06 %	Random
R_work	0.1603	-	-	-
obs	0.1615	47646	96.96 %	-
all	-	47646	-	-

Solvent computation

Shrinkage radii: 0.89 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 45.504 Å² / k_sol: 0.433 e/Å³

Refinement step

Cycle: LAST / Resolution: 1.9003→43.531 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2898	0	100	262	3260

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.018	3125
X-RAY DIFFRACTION	f_angle_d	1.667	4267
X-RAY DIFFRACTION	f_dihedral_angle_d	16.353	1111
X-RAY DIFFRACTION	f_chiral_restr	0.117	430
X-RAY DIFFRACTION	f_plane_restr	0.008	546

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 (%)
1.9003-1.9391	0.2324	148	0.2173	2439	X-RAY DIFFRACTION	90
1.9391-1.9812	0.2146	134	0.201	2478	X-RAY DIFFRACTION	92
1.9812-2.0273	0.2223	130	0.1841	2557	X-RAY DIFFRACTION	94
2.0273-2.078	0.2265	137	0.1883	2528	X-RAY DIFFRACTION	95
2.078-2.1342	0.2284	163	0.1699	2614	X-RAY DIFFRACTION	95
2.1342-2.197	0.1602	130	0.1597	2644	X-RAY DIFFRACTION	97
2.197-2.2679	0.1601	125	0.1497	2638	X-RAY DIFFRACTION	97
2.2679-2.349	0.1765	143	0.1501	2659	X-RAY DIFFRACTION	98
2.349-2.443	0.2052	145	0.1621	2666	X-RAY DIFFRACTION	98
2.443-2.5542	0.21	130	0.161	2695	X-RAY DIFFRACTION	98
2.5542-2.6888	0.2046	162	0.1643	2702	X-RAY DIFFRACTION	99
2.6888-2.8573	0.2102	111	0.1682	2744	X-RAY DIFFRACTION	99
2.8573-3.0778	0.198	151	0.1687	2731	X-RAY DIFFRACTION	99
3.0778-3.3874	0.1863	153	0.1611	2727	X-RAY DIFFRACTION	100
3.3874-3.8773	0.1743	135	0.1514	2783	X-RAY DIFFRACTION	100
3.8773-4.884	0.1379	155	0.1267	2751	X-RAY DIFFRACTION	100
4.884-43.542	0.1761	160	0.1764	2878	X-RAY DIFFRACTION	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	0.0219	-0.1034	-0.0378	0.6489	-0.0344	0.6384	-0.0166	0.2374	0.0533	-0.1545	0.1337	0.2961	-0.075	-0.6105	-0.1019	0.2232	-0.0104	-0.038	0.4916	0.0705	0.2725	18.5534	45.7785	43.0909
2	0.1821	0.0291	-0.0191	0.0672	-0.0304	0.0152	0.012	0.1007	0.0098	-0.0266	0.0752	0.0694	0.0088	-0.1094	0.0187	0.2548	0.3163	0.0305	0.9115	0.2318	0.5229	9.0583	52.5834	41.638
3	0.9463	-0.51	0.0849	0.4408	-0.0347	0.0554	0.1477	0.2388	0.193	0.233	0.0825	0.084	-0.5949	-0.6815	-0.113	0.4054	0.1738	0.0744	0.4726	0.1177	0.3247	21.8044	56.4733	42.8387
4	1.3334	-0.2627	-0.2831	0.2727	-0.1297	0.2109	-0.0598	0.1091	-0.0624	0.2338	0.2063	0.3456	-0.3411	-0.5443	-0.0749	0.3731	0.2848	0.1082	0.7387	0.1324	0.391	12.4824	50.0235	52.1659
5	0.1675	-0.3906	-0.1869	1.4119	0.2821	0.526	-0.0313	0.1424	-0.1449	-0.0872	0.0105	0.3017	0.0876	-0.5539	0.0528	0.1838	-0.0188	0.0085	0.3952	0.0003	0.2402	23.528	37.1874	46.2524
6	0.1503	0.034	0.0833	0.7109	-0.1111	0.1708	0.1191	-0.0475	0.116	-0.0865	-0.149	-0.2411	-0.0333	0.0252	0.0614	0.1792	0.004	0.0388	0.2484	0.0356	0.2623	35.307	35.4653	51.8475
7	0.5162	0.3461	-0.0333	1.3587	-0.5724	0.4897	0.0259	-0.0124	-0.1524	-0.0451	-0.1882	-0.3521	-0.1181	0.2945	0.1414	0.2345	-0.0318	0.0043	0.2899	0.0735	0.2792	32.6802	38.6028	57.7379
8	1.0254	0.5621	-0.1959	0.3136	-0.163	0.5324	0.1096	-0.2736	-0.1588	0.1235	-0.1533	-0.1901	-0.0876	0.0213	0.0116	0.2219	-0.03	0.026	0.2988	0.0136	0.2617	27.0585	36.1357	61.8636
9	0.1853	-0.004	-0.0991	0.1338	-0.0924	0.2031	0.0151	0.0262	-0.1457	0.0003	0.0153	0.2247	0.0496	-0.2692	-0.0074	0.2158	-0.0865	0.0403	0.3179	0.0049	0.289	21.15	30.2502	54.9784
10	0.0171	0.0435	-0.0029	0.326	-0.2186	0.4484	0.0477	-0.0471	0.1218	0.2843	0.1359	0.032	-0.2261	0.1443	-0.0254	0.3258	-0.057	0.0299	0.3356	-0.0156	0.2804	22.8857	42.0781	69.6989
11	0.8029	-0.109	-0.3043	0.4966	0.0282	0.6009	0.0373	-0.0275	-0.3948	-0.0508	-0.2457	0.0194	0.008	0.1082	0.0948	0.2492	-0.0427	0.0604	0.2713	0.0285	0.3573	23.8956	26.1432	60.4843
12	1.389	0.452	1.0341	1.2011	0.4339	0.8282	-0.0752	-0.2329	-0.1438	0.1423	0.0728	-0.1756	0.006	0.2102	-0.0319	0.2151	0.0496	0.0034	0.3086	-0.0032	0.1843	49.757	48.5198	75.5153
13	0.1968	0.0097	0.0183	0.213	-0.0642	0.1311	-0.0015	-0.0772	-0.1427	0.0866	0.0424	0.0122	0.1195	0.1033	0.0458	0.3438	0.3816	-0.0078	0.573	0.4156	0.0774	50.9528	41.9523	84.9225
14	0.0895	0.144	0.0329	0.7986	-0.8017	1.4373	-0.2069	-0.2656	-0.4429	0.002	0.0062	0.1429	0.278	0.357	0.0488	0.3044	0.1427	0.0924	0.3434	0.0787	0.345	50.2449	37.734	72.4244
15	0.922	-0.5239	-0.2582	1.2058	-0.628	1.0093	-0.2665	-0.2872	-0.2638	0.3827	0.1564	0.2012	-0.0831	0.0494	-0.0163	0.3308	0.0694	0.0718	0.3298	0.0815	0.2728	40.5964	44.5351	81.2192
16	0.3001	0.1756	-0.2547	0.6308	-0.5876	0.5935	0.0108	-0.2105	-0.0192	0.1974	-0.1059	-0.0279	-0.1986	0.3314	0.0141	0.2358	0.0024	0.0358	0.2974	0.0101	0.1958	47.333	56.2066	70.7461
17	0.1273	-0.2464	-0.0272	0.6097	0.3159	0.7009	0.0164	-0.0519	0.0426	0.1495	0.2302	-0.0499	-0.124	-0.0939	-0.0787	0.2972	0.0317	0.0548	0.2811	0.0212	0.225	41.0181	66.1914	60.6922
18	0.9278	-0.0512	0.2451	0.7785	0.3487	0.2496	-0.1693	0.4113	0.1268	-0.3686	-0.1984	-0.2028	0.2085	0.2029	0.1213	0.2869	0.0299	0.0845	0.2869	0.0546	0.2036	43.476	53.8809	56.3683
19	1.1955	-1.0347	-0.0635	1.3424	0.2683	0.4865	0.1593	0.2451	-0.1765	-0.2517	-0.1127	0.1033	-0.0659	-0.1605	-0.011	0.2399	0.0625	0.0219	0.2515	0.0067	0.2188	35.9475	55.7102	60.591
20	0.4463	-0.0316	0.0979	0.1526	0.0462	0.5651	-0.0136	-0.1007	-0.0073	0.0115	0.0275	-0.0117	-0.2388	-0.1385	-0.0146	0.2885	0.0093	0.0555	0.2593	-0.0123	0.2055	35.9129	62.1682	69.7126
21	0.5535	-0.6099	0.3869	1.3628	0.6709	1.9942	-0.0654	-0.0673	0.0799	-0.0414	0.0575	0.2089	-0.1277	-0.4474	-0.0249	0.2566	0.0056	0.056	0.3017	-0.0241	0.2584	27.7591	60.3209	69.9046

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resseq 1:17)
2	X-RAY DIFFRACTION	2	chain 'A' and (resseq 18:28)
3	X-RAY DIFFRACTION	3	chain 'A' and (resseq 29:44)
4	X-RAY DIFFRACTION	4	chain 'A' and (resseq 45:62)
5	X-RAY DIFFRACTION	5	chain 'A' and (resseq 63:93)
6	X-RAY DIFFRACTION	6	chain 'A' and (resseq 94:111)
7	X-RAY DIFFRACTION	7	chain 'A' and (resseq 112:126)
8	X-RAY DIFFRACTION	8	chain 'A' and (resseq 127:141)
9	X-RAY DIFFRACTION	9	chain 'A' and (resseq 142:166)
10	X-RAY DIFFRACTION	10	chain 'A' and (resseq 167:174)
11	X-RAY DIFFRACTION	11	chain 'A' and (resseq 175:183)
12	X-RAY DIFFRACTION	12	chain 'B' and (resseq 1:17)
13	X-RAY DIFFRACTION	13	chain 'B' and (resseq 18:28)
14	X-RAY DIFFRACTION	14	chain 'B' and (resseq 29:44)
15	X-RAY DIFFRACTION	15	chain 'B' and (resseq 45:62)
16	X-RAY DIFFRACTION	16	chain 'B' and (resseq 63:90)
17	X-RAY DIFFRACTION	17	chain 'B' and (resseq 91:100)
18	X-RAY DIFFRACTION	18	chain 'B' and (resseq 101:111)
19	X-RAY DIFFRACTION	19	chain 'B' and (resseq 112:126)
20	X-RAY DIFFRACTION	20	chain 'B' and (resseq 127:166)
21	X-RAY DIFFRACTION	21	chain 'B' and (resseq 167:182)

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