PDB-3tf8: Crystal structure of an H-NOX protein from Nostoc sp. PCC 7120

ID or keywords:

Entry

Database: PDB / ID: 3tf8

Title

Crystal structure of an H-NOX protein from Nostoc sp. PCC 7120

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: 2.1302 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	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_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_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_asym_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_asym_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 / _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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	3tf8.cif.gz	228.1 KB	Display	PDBx/mmCIF format
PDB format	pdb3tf8.ent.gz	189.6 KB	Display	PDB format
PDBx/mmJSON format	3tf8.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	3tf8_validation.pdf.gz	1.1 MB	Display	wwPDB validaton report
Full document	3tf8_full_validation.pdf.gz	1.1 MB	Display
Data in XML	3tf8_validation.xml.gz	18.6 KB	Display
Data in CIF	3tf8_validation.cif.gz	25.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/tf/3tf8 ftp://data.pdbj.org/pub/pdb/validation_reports/tf/3tf8	HTTPS FTP

-
Related structure data

Related structure data	3tf0C 3tf1C 3tf9C 3tfaC 3tfdC 3tfeC 3tffC 3tfgC 2o09S 2o0c 2o0g S: Starting model for refinement C: citing same article (ref.)
Similar structure data	2o0g-1 7lgk-2 2o0g-2 2o09-1 3tf9-2 3tfg-2 3tff-2 4iae-2 2o0c-1 2o09-2 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

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#133 - Jan 2011 Nitric Oxide Synthase similarity (5)

Deposited unit

A: Alr2278 protein

B: Alr2278 protein

hetero molecules

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

1

A: Alr2278 protein

hetero molecules

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

2

B: Alr2278 protein

hetero molecules

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

Unit cell

Length a, b, c (Å)	123.696, 123.696, 123.696
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	B-237- HOH

#1: Protein	Alr2278 protein Mass: 21213.643 Da / Num. of mol.: 2 / Fragment: Heme-based sensor domain (UNP Residues 1-183) 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-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 207 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

Crystal	Density Matthews: 3.83 Å³/Da / Density % sol: 67.88 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting 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, SITTING DROP, temperature 293K

-
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: Jul 22, 2010
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: 2.13→50 Å / Num. all: 33688 / Num. obs: 33688 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1
Reflection shell	Resolution: 2.13→2.17 Å / % possible all: 100

-
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 2O09

2o09

Resolution: 2.1302→39.116 Å / SU ML: 0.2 / σ(F): 0 / Phase error: 19.89 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2	1700	5.05 %	Random
R_work	0.1642	-	-	-
obs	0.166	33688	94.9 %	-
all	-	33688	-	-

Solvent computation

Shrinkage radii: 0.65 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 42.53 Å² / k_sol: 0.391 e/Å³

Refinement step

Cycle: LAST / Resolution: 2.1302→39.116 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2888	0	87	207	3182

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	3091
X-RAY DIFFRACTION	f_angle_d	1.233	4217
X-RAY DIFFRACTION	f_dihedral_angle_d	14.862	1105
X-RAY DIFFRACTION	f_chiral_restr	0.061	433
X-RAY DIFFRACTION	f_plane_restr	0.004	542

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 (%)
2.1302-2.1928	0.3301	117	0.2312	2449	X-RAY DIFFRACTION	88
2.1928-2.2636	0.2687	129	0.2143	2466	X-RAY DIFFRACTION	89
2.2636-2.3445	0.2478	129	0.2007	2592	X-RAY DIFFRACTION	92
2.3445-2.4384	0.2963	138	0.205	2540	X-RAY DIFFRACTION	92
2.4384-2.5493	0.243	144	0.1921	2580	X-RAY DIFFRACTION	93
2.5493-2.6837	0.2115	158	0.1888	2646	X-RAY DIFFRACTION	95
2.6837-2.8518	0.2018	146	0.1832	2680	X-RAY DIFFRACTION	97
2.8518-3.0719	0.1913	146	0.1747	2755	X-RAY DIFFRACTION	98
3.0719-3.3809	0.2062	146	0.1679	2753	X-RAY DIFFRACTION	98
3.3809-3.8697	0.1808	135	0.151	2807	X-RAY DIFFRACTION	99
3.8697-4.874	0.1675	159	0.1242	2803	X-RAY DIFFRACTION	99
4.874-39.1227	0.176	153	0.1552	2917	X-RAY DIFFRACTION	99

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	0.411	0.2154	0.9411	1.392	0.3054	2.2058	0.0521	0.135	-0.1019	0.1335	0.053	-0.4511	0.0103	0.3769	-0.0502	0.1838	-0.0105	-0.0036	0.2784	0.0485	0.3662	14.0281	11.9867	74.9131
2	0.2558	0.0279	0.2105	0.0894	0.0955	0.3227	0.036	0.0275	-0.0646	0.0366	-0.0562	-0.0013	-0.0104	0.0587	-0.055	0.0852	-0.1203	-0.37	0.6091	0.3229	0.6822	23.2989	11.0919	81.5196
3	1.6336	-0.2783	1.0583	0.2904	0.0117	0.8714	0.0891	-0.2783	-0.1855	0.4795	-0.2409	-0.1156	-0.4508	0.2634	-0.0032	0.384	-0.1028	-0.1041	0.3924	0.1345	0.3034	10.7401	11.9031	85.7792
4	1.8022	0.5413	1.2896	1.6635	-0.4811	1.4216	-0.0029	0.1529	-0.0043	0.4075	-0.2598	-0.6053	-0.3047	0.5038	0.1873	0.4276	-0.1451	-0.1442	0.4379	0.1034	0.4702	19.5342	21.3979	78.9388
5	0.2144	0.0747	0.3823	0.087	0.0638	0.6595	0.0934	0.2122	-0.355	-0.0371	0.0485	-0.2615	-0.0498	0.3862	-0.0782	0.2147	-0.0618	-0.0129	0.321	-0.0207	0.3605	8.6738	14.0592	66.8361
6	0.4341	-0.1019	-0.2157	0.2326	-0.082	0.297	0.1552	-0.2194	0.1702	0.0374	-0.0138	-0.0225	0.1235	-0.0724	-0.0743	0.2106	-0.0692	-0.0163	0.299	0.034	0.2483	-3.3604	19.2431	63.06
7	0.1524	0.0805	-0.1371	0.5553	-0.4588	0.655	-0.0229	-0.0152	0.0945	0.0994	0.2526	0.1925	-0.0479	-0.0531	-0.0958	0.3173	-0.0038	0.0402	0.2594	0.0501	0.3174	-1.1567	25.7712	67.6021
8	0.6028	-0.0669	-0.2225	0.308	-0.3707	0.8818	0.114	0.0336	0.2408	0.0088	-0.0647	-0.1077	-0.1231	0.0326	-0.0263	0.2715	-0.0402	0.051	0.2783	-0.008	0.3315	4.4334	30.0219	64.8043
9	0.1274	-0.0714	0.1327	0.6193	-0.1329	0.1718	0.1218	0.1935	-0.0233	-0.1756	-0.1331	-0.4589	-0.0143	0.2641	0.0217	0.2709	-0.0955	0.0806	0.3507	-0.0024	0.3427	10.2626	23.023	58.834
10	1.7804	-0.9652	-0.264	0.561	-0.0415	1.3484	-0.296	0.1839	0.5752	-0.0715	0.1813	-0.104	-0.0842	-0.052	0.0001	0.3535	-0.1081	0.0718	0.2831	-0.0039	0.3457	8.1482	33.1461	62.1093
11	0.3129	-0.2337	0.2239	0.385	-0.6131	1.2187	-0.0861	0.2816	0.7862	-0.0247	0.1554	0.3552	-0.4861	-0.0596	0.0081	0.4028	0.0095	-0.0492	0.216	0.1359	0.674	-19.217	47.0306	74.9312
12	0.2988	0.3757	-0.2004	0.9715	-0.2833	0.1538	-0.1673	0.6305	0.7617	-0.2233	-0.031	0.2423	-0.1949	0.2872	-0.1173	0.3315	-0.0734	-0.0881	0.3027	0.2751	0.5327	-14.1776	44.6261	69.9438
13	0.4832	0.007	-0.1241	0.1544	-0.0664	1.5045	-0.1304	-0.1581	0.6116	0.2292	0.1037	0.0632	-0.6279	-0.0863	-0.0394	0.3553	-0.0481	0.0043	0.2203	-0.0584	0.4771	-14.0977	42.9408	84.5244
14	0.709	0.5259	-0.0713	0.8241	0.355	0.3898	-0.0194	-0.0863	0.3728	0.0854	0.059	0.1703	0.0468	-0.1282	0.0349	0.2741	-0.0334	-0.0054	0.2763	-0.0077	0.3073	-18.5362	29.2376	90.2845
15	0.5079	-0.3634	0.0395	0.3793	-0.0511	0.4254	0.033	-0.0619	0.056	-0.1716	0.1129	-0.1935	0.1504	-0.1114	-0.1038	0.3205	-0.0576	-0.0351	0.2458	0.0049	0.3051	-9.9066	26.5311	87.993
16	0.374	0.0841	0.3204	0.39	0.2252	0.4981	0.211	0.0666	-0.1942	0.0553	0.0081	-0.1058	0.081	-0.0197	-0.1132	0.3036	-0.0008	-0.0472	0.2857	-0.0618	0.3167	-3.9743	29.1205	84.8169
17	0.7856	0.1021	-0.1166	1.071	0.1698	0.1009	0.0347	0.1352	0.1421	0.075	0.1081	-0.2251	0.0458	-0.0047	-0.0351	0.3	-0.074	0.0024	0.2651	-0.0465	0.3352	0.1414	34.8655	87.2491
18	0.3986	-0.2705	-0.139	0.248	-0.0194	0.6552	-0.0207	-0.0868	0.2069	0.0591	-0.0745	-0.1773	-0.2026	-0.0019	-0.0139	0.3061	-0.0986	0.0085	0.23	-0.0915	0.356	-9.1362	40.5788	90.4496
19	0.1104	0.0851	0.173	0.2459	0.0722	0.2437	-0.0138	0.0167	0.0483	-0.0094	-0.0253	-0.0532	-0.0396	0.0793	-0.0202	0.3556	-0.0886	0.0322	0.4079	-0.1323	0.4207	1.5702	39.9208	89.5049
20	0.3966	0.1677	0.2593	0.2921	0.0437	0.1845	0.0625	-0.1078	0.0387	0.1952	-0.0144	-0.0114	0.0713	-0.1461	0.0756	0.3718	-0.0735	-0.0477	0.3346	-0.1359	0.3056	-1.9991	38.3891	97.838

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 63:90)
6	X-RAY DIFFRACTION	6	chain 'A' and (resseq 91:111)
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 167:183)
11	X-RAY DIFFRACTION	11	chain 'B' and (resseq 1:28)
12	X-RAY DIFFRACTION	12	chain 'B' and (resseq 29:62)
13	X-RAY DIFFRACTION	13	chain 'B' and (resseq 63:80)
14	X-RAY DIFFRACTION	14	chain 'B' and (resseq 81:93)
15	X-RAY DIFFRACTION	15	chain 'B' and (resseq 94:111)
16	X-RAY DIFFRACTION	16	chain 'B' and (resseq 112:126)
17	X-RAY DIFFRACTION	17	chain 'B' and (resseq 127:141)
18	X-RAY DIFFRACTION	18	chain 'B' and (resseq 142:155)
19	X-RAY DIFFRACTION	19	chain 'B' and (resseq 156:174)
20	X-RAY DIFFRACTION	20	chain 'B' and (resseq 175:184)

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
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

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and 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

-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

-
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