PDB-3tfa: Crystal structure of an H-NOX protein from Nostoc sp. PCC 7120 un...

ID or keywords:

Entry

Database: PDB / ID: 3tfa

Title

Crystal structure of an H-NOX protein from Nostoc sp. PCC 7120 under 6 atm of xenon

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: 2.2711 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	Feb 28, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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	3tfa.cif.gz	223.1 KB	Display	PDBx/mmCIF format
PDB format	pdb3tfa.ent.gz	186.3 KB	Display	PDB format
PDBx/mmJSON format	3tfa.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/3tfa ftp://data.pdbj.org/pub/pdb/validation_reports/tf/3tfa	HTTPS FTP

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Related structure data

Related structure data	3tf0C 3tf1C 3tf8C 3tf9C 3tfdC 3tfeC 3tffC 3tfgC 2o09 2o0c 2o0g C: citing same article (ref.)
Similar structure data	2o09-2 2o0c-2 3tf9-1 3tfd-2 3tf9-2 4iae-2 2o09-1 3tfg-1 3tfe-2 3tfd-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) #222 - Jun 2018 Proteins and Nanoparticles similarity (1)

Deposited unit

A: Alr2278 protein

B: Alr2278 protein

hetero molecules

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

1

A: Alr2278 protein

hetero molecules

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

2

B: Alr2278 protein

hetero molecules

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

Unit cell

Length a, b, c (Å)	123.937, 123.937, 123.937
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	198
Space group name H-M	P2₁3

#1: Protein	Alr2278 protein Mass: 21213.643 Da / Num. of mol.: 2 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 / Heme B Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃₄H₃₂FeN₄O₄
#3: Chemical	ChemComp-XE / XENON / Xenon Mass: 131.293 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Xe
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 107 / 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: 3.87 Å³/Da / Density % sol: 68.2 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 1.8 M DL-malic acid (pH 7.0) with and without 100 mM BIS-TRIS propane (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: 1.4 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 30, 2010
Radiation	Monochromator: KHOZU Double flat crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.4 Å / Relative weight: 1
Reflection	Resolution: 2.27→50 Å / Num. all: 55405 / Num. obs: 55405 / % possible obs: 99.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1
Reflection shell	Resolution: 2.27→2.31 Å / % possible all: 92.9

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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 / Resolution: 2.2711→43.818 Å / SU ML: 0.3 / σ(F): 0 / Phase error: 18.86 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1902	2824	5.1 %	Random
R_work	0.1626	-	-	-
obs	0.164	55405	97.6 %	-
all	-	55405	-	-

Solvent computation

Shrinkage radii: 0.65 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 43.647 Å² / k_sol: 0.42 e/Å³

Refinement step

Cycle: LAST / Resolution: 2.2711→43.818 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2882	0	92	107	3081

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	3069
X-RAY DIFFRACTION	f_angle_d	1.267	4183
X-RAY DIFFRACTION	f_dihedral_angle_d	14.482	1095
X-RAY DIFFRACTION	f_chiral_restr	0.063	429
X-RAY DIFFRACTION	f_plane_restr	0.004	538

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 (%)
2.2711-2.3103	0.3066	120	0.2308	2496	X-RAY DIFFRACTION	92
2.3103-2.3523	0.2508	166	0.2074	2523	X-RAY DIFFRACTION	96
2.3523-2.3975	0.2401	132	0.1949	2553	X-RAY DIFFRACTION	94
2.3975-2.4465	0.2275	107	0.1944	2561	X-RAY DIFFRACTION	95
2.4465-2.4996	0.2048	115	0.2017	2611	X-RAY DIFFRACTION	96
2.4996-2.5578	0.2563	143	0.1951	2600	X-RAY DIFFRACTION	96
2.5578-2.6217	0.2156	131	0.2069	2623	X-RAY DIFFRACTION	97
2.6217-2.6926	0.2811	163	0.2035	2624	X-RAY DIFFRACTION	98
2.6926-2.7718	0.2606	124	0.1979	2625	X-RAY DIFFRACTION	98
2.7718-2.8613	0.1934	146	0.1877	2665	X-RAY DIFFRACTION	99
2.8613-2.9635	0.1958	129	0.1912	2662	X-RAY DIFFRACTION	99
2.9635-3.0822	0.1946	137	0.173	2694	X-RAY DIFFRACTION	99
3.0822-3.2224	0.1778	143	0.1736	2660	X-RAY DIFFRACTION	99
3.2224-3.3922	0.2077	159	0.1632	2638	X-RAY DIFFRACTION	99
3.3922-3.6047	0.1616	173	0.1575	2647	X-RAY DIFFRACTION	99
3.6047-3.8828	0.1854	129	0.1458	2738	X-RAY DIFFRACTION	100
3.8828-4.2733	0.1558	142	0.1276	2699	X-RAY DIFFRACTION	100
4.2733-4.8909	0.1599	166	0.1232	2640	X-RAY DIFFRACTION	100
4.8909-6.1593	0.1753	156	0.1539	2678	X-RAY DIFFRACTION	99
6.1593-43.8265	0.1873	143	0.1604	2644	X-RAY DIFFRACTION	98

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	3.5258	-0.685	0.2107	0.3664	-0.1576	0.4075	0.0627	0.0206	-0.8246	0.2506	-0.2668	-0.0194	0.0121	0.2212	0.0016	0.2932	-0.0396	-0.105	0.3447	0.0881	0.4747	17.628	11.9479	77.6457
2	0.9605	-0.4213	0.5468	0.2181	-0.3726	0.9342	0.4306	-0.5353	-0.1994	0.7552	-0.3595	-0.1234	-0.2396	-0.1128	-0.0459	0.4459	-0.1449	-0.1286	0.3845	0.1214	0.4159	10.736	11.9815	85.9038
3	1.8139	0.0666	0.8663	1.101	-0.5259	0.6827	0.4028	-0.2268	-0.065	0.5053	-0.3537	-0.449	-0.4266	0.3752	0.0903	0.4183	-0.1301	-0.1281	0.4278	0.0867	0.4166	19.4246	21.6438	78.9674
4	1.2254	1.4264	0.9078	2.2933	0.8667	0.9797	0.3302	0.4631	-0.5262	0.2059	-0.0939	-0.5945	-0.0056	0.3873	-0.0779	0.2918	-0.028	-0.0015	0.3692	-0.0043	0.4365	12.9373	16.3857	67.7923
5	0.9388	-0.3045	0.5853	0.7482	-0.0204	0.3617	0.0332	0.3889	-0.0001	0.0486	-0.1672	-0.6037	-0.0861	0.3964	0.0731	0.2867	-0.0426	-0.047	0.3784	0.0341	0.3882	-1.2228	15.6225	60.5646
6	1.172	-0.5916	0.9301	0.6595	-0.2569	0.8787	0.0261	-0.4019	0.0914	-0.2683	0.1564	-0.2147	0.3351	-0.3218	-0.0726	0.3367	-0.0611	0.0048	0.4168	0.0273	0.4186	-5.4	18.1806	69.6851
7	0.5819	0.0841	-0.8071	0.6489	-0.2913	1.213	-0.0841	0.2559	0.2774	0.0604	0.1443	0.3133	0.026	-0.4556	-0.0892	0.3053	0.0026	0.0203	0.3933	0.0747	0.4037	-1.3224	25.916	67.6425
8	0.8043	0.0425	-0.5233	0.93	0.556	1.2145	0.227	0.0669	0.4061	0.189	0.0579	0.0757	0.1288	-0.2441	-0.1005	0.2674	0.0112	0.0282	0.305	0.0404	0.3524	4.2068	30.1949	64.7771
9	0.8388	-0.2976	0.5457	0.3894	-0.4635	0.6687	-0.1211	0.5382	0.123	-0.0659	-0.2571	-0.1579	0.013	0.2175	0.139	0.2597	-0.0309	0.0136	0.3903	0.0088	0.3585	10.0005	20.8795	61.8061
10	1.309	-0.0508	-0.1856	0.3621	0.16	0.4955	-0.0239	0.3747	0.2909	-0.1485	0.1446	-0.1689	-0.0419	0.0776	-0.1049	0.3755	-0.0796	0.0936	0.4108	0.0236	0.4518	10.1262	25.6204	55.4299
11	1.4842	-0.752	-0.4137	0.6704	-0.4948	1.8659	-0.3216	0.1786	0.7596	-0.0461	0.3206	-0.058	-0.6542	0.0505	-0.0631	0.3164	-0.0578	0.0272	0.3272	0.0307	0.4805	7.7593	34.4695	63.1322
12	0.5961	-0.3035	0.0055	1.3101	0.3422	0.268	-0.2708	0.3922	0.6987	0.1175	0.0961	0.6925	-0.1367	-0.0298	-0.2373	0.2851	0.0308	-0.0939	0.2602	0.1863	0.7649	-19.5406	47.1304	74.8904
13	0.5775	0.4116	-0.3718	0.7841	-0.2426	0.3089	-0.2972	1.1851	1.048	-0.2192	0.1131	0.2713	-0.1401	0.328	-0.2156	0.3919	-0.0943	-0.1197	0.5144	0.3351	0.767	-14.5503	44.6998	69.9774
14	0.553	0.0152	0.195	0.4309	-0.1319	0.9964	-0.1013	-0.0739	0.5375	0.1491	0.1397	-0.0212	-0.2384	-0.0909	0.0145	0.3006	-0.0249	0.0053	0.2565	-0.0114	0.4764	-16.2352	38.8353	85.7745
15	0.4479	0.1978	0.0869	1.7628	0.4131	1.149	0.2118	-0.1531	-0.0907	-0.256	0.1121	-0.5216	0.0494	-0.2428	-0.1568	0.3435	-0.03	-0.0557	0.2646	-0.0194	0.3482	-10.4609	27.1525	89.4378
16	0.9018	0.3485	0.4326	1.4873	0.6963	1.2127	0.2855	0.2056	-0.5119	0.299	0.0312	-0.2207	0.2352	-0.0401	-0.1143	0.3594	0.018	-0.049	0.3377	-0.0765	0.4368	-4.1771	29.3928	84.9955
17	1.1697	0.3532	0.2221	0.8266	0.4189	0.731	0.0782	-0.0445	0.1644	0.222	-0.0524	0.0253	-0.0285	0.0363	-0.0401	0.3646	-0.0793	0.0075	0.2501	-0.0603	0.3661	-4.2113	38.7745	90.962
18	1.302	-0.3731	0.7753	1.6702	0.5112	1.0641	0.1546	0.2346	-0.0762	0.1972	-0.0708	-0.3729	0.1571	0.3731	-0.0841	0.2965	-0.0632	-0.0443	0.3466	-0.0632	0.3403	2.9972	39.0749	89.67

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 81:100)
6	X-RAY DIFFRACTION	6	chain 'A' and (resseq 101:111)
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 142:155)
10	X-RAY DIFFRACTION	10	chain 'A' and (resseq 156:166)
11	X-RAY DIFFRACTION	11	chain 'A' and (resseq 167:182)
12	X-RAY DIFFRACTION	12	chain 'B' and (resseq 1:28)
13	X-RAY DIFFRACTION	13	chain 'B' and (resseq 29:62)
14	X-RAY DIFFRACTION	14	chain 'B' and (resseq 63:90)
15	X-RAY DIFFRACTION	15	chain 'B' and (resseq 91:111)
16	X-RAY DIFFRACTION	16	chain 'B' and (resseq 112:126)
17	X-RAY DIFFRACTION	17	chain 'B' and (resseq 127:166)
18	X-RAY DIFFRACTION	18	chain 'B' and (resseq 167:183)

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