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

ID or keywords:

Entry

Database: PDB / ID: 3tff

Title

Crystal structure of an H-NOX protein from Nostoc sp. PCC 7120, L67W 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. (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.9401 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	3tff.cif.gz	230.2 KB	Display	PDBx/mmCIF format
PDB format	pdb3tff.ent.gz	191.4 KB	Display	PDB format
PDBx/mmJSON format	3tff.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3tff_validation.pdf.gz	1.1 MB	Display	wwPDB validaton report
Full document	3tff_full_validation.pdf.gz	1.1 MB	Display
Data in XML	3tff_validation.xml.gz	19.2 KB	Display
Data in CIF	3tff_validation.cif.gz	26.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/tf/3tff ftp://data.pdbj.org/pub/pdb/validation_reports/tf/3tff	HTTPS FTP

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Related structure data

Related structure data	3tf0C 3tf1C 3tf8SC 3tf9C 3tfaC 3tfdC 3tfeC 3tfgC 2o09 2o0c 2o0g C: citing same article (ref.) S: Starting model for refinement
Similar structure data	3tfg-1 3tfd-1 3tfe-2 2o0c-1 3tfd-2 3l6j-2 6pj5-d 2o0g-2 3tf8-2 3tfg-2 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 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 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 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	123.211, 123.211, 123.211
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-266- HOH

#1: Protein	Alr2278 protein Mass: 21286.695 Da / Num. of mol.: 2 / Mutation: L67W Source method: isolated from a genetically manipulated source Source: (gene. exp.) Nostoc sp. (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.: 247 / 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: 3.81 Å³/Da / Density % sol: 67.7 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 1.9-2.0 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: Jan 27, 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: 1.94→50 Å / Num. all: 44430 / Num. obs: 44430 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1
Reflection shell	Resolution: 1.94→1.97 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: 1.9401→43.562 Å / SU ML: 0.21 / σ(F): 2 / Phase error: 18.33 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1873	2249	5.06 %	Random
R_work	0.1648	-	-	-
obs	0.1659	44430	96.02 %	-
all	-	44430	-	-

Solvent computation

Shrinkage radii: 0.65 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 43.565 Å² / k_sol: 0.408 e/Å³

Refinement step

Cycle: LAST / Resolution: 1.9401→43.562 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2870	0	100	247	3217

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	3114
X-RAY DIFFRACTION	f_angle_d	1.251	4255
X-RAY DIFFRACTION	f_dihedral_angle_d	15.017	1116
X-RAY DIFFRACTION	f_chiral_restr	0.066	433
X-RAY DIFFRACTION	f_plane_restr	0.004	547

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 (%)
1.9401-1.9823	0.2739	124	0.2325	2410	X-RAY DIFFRACTION	89
1.9823-2.0284	0.2518	130	0.2094	2474	X-RAY DIFFRACTION	92
2.0284-2.0792	0.2336	139	0.2027	2496	X-RAY DIFFRACTION	92
2.0792-2.1354	0.2373	136	0.1927	2539	X-RAY DIFFRACTION	93
2.1354-2.1982	0.1969	139	0.173	2558	X-RAY DIFFRACTION	94
2.1982-2.2692	0.2084	132	0.1696	2587	X-RAY DIFFRACTION	95
2.2692-2.3503	0.2175	153	0.1662	2603	X-RAY DIFFRACTION	96
2.3503-2.4444	0.2151	141	0.1742	2605	X-RAY DIFFRACTION	96
2.4444-2.5556	0.2275	151	0.1782	2648	X-RAY DIFFRACTION	97
2.5556-2.6903	0.2207	148	0.1771	2670	X-RAY DIFFRACTION	98
2.6903-2.8588	0.2241	132	0.1801	2710	X-RAY DIFFRACTION	98
2.8588-3.0795	0.2001	135	0.1727	2735	X-RAY DIFFRACTION	99
3.0795-3.3893	0.1976	152	0.1674	2726	X-RAY DIFFRACTION	100
3.3893-3.8795	0.17	146	0.1471	2764	X-RAY DIFFRACTION	99
3.8795-4.8867	0.1257	147	0.1239	2765	X-RAY DIFFRACTION	100
4.8867-43.5726	0.1755	144	0.1763	2891	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	0.7843	-0.2864	0.2061	0.1831	0.224	1.0933	-0.5316	-1.1801	-0.6487	0.3874	0.3843	0.0603	0.1672	0.5473	-0.0468	0.3933	0.2468	-0.0193	0.9109	0.1619	0.2355	50.3043	44.2757	77.7783
2	0.3397	0.5693	0.3463	1.3887	0.1491	1.0256	-0.4714	-0.77	-1.0903	0.2018	0.247	0.4924	0.2069	0.2173	0.0065	0.3329	0.1765	0.1159	0.5686	0.3216	0.5226	50.1413	35.875	70.7889
3	1.5181	-0.4998	0.612	0.3775	-1.0844	4.086	-0.6708	-1.4263	-0.7496	0.6648	0.4483	0.3846	-0.4147	0.056	-0.0922	0.4674	0.2597	0.1038	1.0049	0.3265	0.3781	40.6776	42.3082	80.2407
4	0.082	-0.1628	-0.0074	0.5444	-0.0327	0.115	-0.2396	-1.1887	0.0471	0.3822	0.2743	-0.0473	-0.335	0.4061	-0.0472	0.3148	0.0704	0.0193	0.5996	-0.0072	0.1985	44.8718	53.11	73.8268
5	0.9712	-0.2541	-0.6921	1.6104	0.6759	0.686	0.0418	-0.6277	0.2086	-0.122	0.0858	-0.2239	-0.2012	0.0159	-0.1887	0.316	0.0101	0.0214	0.3841	0.0023	0.3051	49.4465	59.2709	60.1741
6	0.1843	-0.2154	-0.0601	0.9968	-0.0461	0.0919	0.1594	0.1212	-0.0098	-0.3731	-0.3423	-0.2317	0.1102	-0.1504	0.204	0.3083	0.0472	0.0503	0.2949	-0.0011	0.216	40.7982	56.9957	57.4314
7	0.8747	-0.8233	-0.6471	2.5514	1.2845	1.3717	0.2994	0.2118	-0.084	-0.5548	-0.2294	-0.2381	-0.3024	-0.0786	-0.0166	0.3114	0.0642	0.0144	0.3817	-0.048	0.2694	34.95	53.7736	60.0593
8	0.995	0.0606	-0.4552	0.0822	0.2558	1.0251	0.1363	0.0986	-0.1066	-0.0929	-0.2979	0.095	-0.2407	-0.3402	0.1519	0.3197	0.0617	0.019	0.3629	-0.0285	0.2231	30.779	56.1329	65.7933
9	0.3105	-0.2138	-0.1025	0.1921	0.1373	0.0285	0.0548	-0.5078	0.171	0.2197	0.0086	-0.0325	-0.2584	0.2251	-0.015	0.3718	0.0003	0.0678	0.3889	-0.1065	0.2493	37.6256	61.9486	71.7674
10	0.139	0.2501	-0.2188	3.0525	-1.9431	2.4637	-0.1096	0.4657	-0.4206	-0.0984	0.4887	0.8641	0.7905	-0.5748	-0.1659	0.3224	0.0018	0.0499	0.4949	-0.1046	0.3928	23.0009	50.1203	70.0098
11	0.877	0.2633	-0.139	0.6992	-0.3977	0.4108	0.1853	-0.0302	0.0252	0.2209	-0.198	-0.0086	-0.2334	-0.1714	0.0243	0.3566	0.0672	0.0488	0.3493	-0.0645	0.2949	30.9573	64.5453	68.8264
12	0.338	0.0876	0.2589	1.9461	-1.8899	2.8691	0.2091	0.1089	0.2026	-0.1352	-0.0017	0.4199	-0.4216	0.0713	-0.0924	0.3938	0.0395	-0.0281	0.2682	-0.0308	0.2766	17.9143	80.1619	78.5717
13	0.1121	-0.0856	-0.1687	0.0724	0.1552	0.8745	0.1275	0.1803	0.2096	-0.3431	-0.2818	0.287	-0.6533	-0.2362	0.276	0.5748	0.2521	-0.1949	0.4812	-0.0626	0.3397	11.3807	81.2003	69.159
14	0.8977	-0.1609	0.0958	0.6664	-0.7812	1.0491	-0.1193	-0.0158	-0.1873	-0.25	-0.4191	0.5736	-0.3597	-0.5794	0.165	0.3969	0.1376	-0.1174	0.3365	-0.1369	0.3885	7.0279	80.4405	81.6048
15	1.2468	-0.6611	0.588	1.2513	1.2326	3.0201	-0.0346	0.3426	-0.6197	-0.2453	-0.3817	0.4561	0.1308	-0.0481	0.1922	0.3643	0.0798	-0.1113	0.3365	-0.116	0.323	14.1006	70.9694	72.9928
16	0.7148	0.2073	0.5738	0.6331	0.4035	0.5862	-0.1739	0.2742	0.0344	-0.2915	0.1054	0.008	-0.3697	0.4333	0.0474	0.3289	0.0133	-0.026	0.2767	-0.0378	0.2031	25.6333	77.9946	83.758
17	2.9053	-0.0005	-0.8644	1.0764	-1.7078	2.963	0.1087	0.6176	0.169	-0.424	0.1291	-0.0245	0.512	0.314	-0.1702	0.3305	0.0656	-0.0249	0.4073	-0.0769	0.2519	35.8878	72.452	94.0217
18	1.218	0.5221	-1.071	1.1886	-0.6413	1.0532	-0.4441	-0.4997	0.3253	0.4563	-0.1184	-0.2737	-0.0673	-0.2236	0.1116	0.3505	0.0468	-0.0678	0.368	-0.1048	0.2135	23.1125	74.1326	97.8928
19	2.4058	-1.9921	-0.6126	2.102	0.2281	0.6725	-0.2664	-0.4809	-0.1466	0.3576	0.3721	0.1752	0.1264	0.0499	-0.0961	0.3412	0.0692	0.0014	0.2858	-0.0106	0.3065	25.0775	66.567	93.783
20	0.154	-0.3268	-0.0943	1.1227	-0.1187	0.9992	0.0624	-0.0058	-0.1395	-0.1157	-0.0565	-0.0256	0.2761	0.3896	-0.0517	0.3184	0.0385	0.0058	0.3528	-0.0527	0.2387	31.5118	66.5949	84.7476
21	0.0745	-0.2097	0.1959	1.069	-0.3427	0.8411	-0.0354	0.2286	-0.3238	-0.286	0.1487	0.057	0.6139	0.2248	-0.0063	0.2651	0.0446	0.021	0.19	-0.0454	0.1295	28.9419	57.674	84.7324

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resseq 1:28)
2	X-RAY DIFFRACTION	2	chain 'A' and (resseq 29:44)
3	X-RAY DIFFRACTION	3	chain 'A' and (resseq 45:62)
4	X-RAY DIFFRACTION	4	chain 'A' and (resseq 63:80)
5	X-RAY DIFFRACTION	5	chain 'A' and (resseq 81:93)
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 175:182)
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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