PDB-3tf9: Crystal structure of an H-NOX protein from Nostoc sp. PCC 7120 un...

ID or keywords:

Entry

Database: PDB / ID: 3tf9

Title

Crystal structure of an H-NOX protein from Nostoc sp. PCC 7120 under 1 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. PCC 7120 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.5901 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

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Download

PDBx/mmCIF format	3tf9.cif.gz	222.5 KB	Display	PDBx/mmCIF format
PDB format	pdb3tf9.ent.gz	185.1 KB	Display	PDB format
PDBx/mmJSON format	3tf9.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3tf9_validation.pdf.gz	1.1 MB	Display	wwPDB validaton report
Full document	3tf9_full_validation.pdf.gz	1.1 MB	Display
Data in XML	3tf9_validation.xml.gz	16.7 KB	Display
Data in CIF	3tf9_validation.cif.gz	21.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/tf/3tf9 ftp://data.pdbj.org/pub/pdb/validation_reports/tf/3tf9	HTTPS FTP

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Related structure data

Related structure data	3tf0C 3tf1C 3tf8SC 3tfaC 3tfdC 3tfeC 3tffC 3tfgC 2o09 2o0c 2o0g C: citing same article (ref.) S: Starting model for refinement
Similar structure data	3tfe-2 3tfd-1 3tfd-2 3tff-2 2o0g-2 3tfg-1 2o09-2 2o0c-1 3tf8-1 3tfa-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 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)	124.404, 124.404, 124.404
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 / Fragment: Heme-based sensor domain (UNP Residues 1-189) 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-XE / XENON Mass: 131.293 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Xe
#4: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 23 / 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: 3.9 Å³/Da / Density % sol: 68.43 %
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: 2.59→50 Å / Num. all: 36721 / Num. obs: 36721 / % possible obs: 99.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1
Reflection shell	Resolution: 2.59→2.623 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: 2.5901→43.983 Å / SU ML: 0.29 / σ(F): 0 / Phase error: 20.15 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2055	1902	5.18 %	Random
R_work	0.1701	-	-	-
obs	0.1719	36721	94.89 %	-
all	-	36721	-	-

Solvent computation

Shrinkage radii: 0.77 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 40.567 Å² / k_sol: 0.372 e/Å³

Refinement step

Cycle: LAST / Resolution: 2.5901→43.983 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2888	0	90	23	3001

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.021	3062
X-RAY DIFFRACTION	f_angle_d	1.881	4170
X-RAY DIFFRACTION	f_dihedral_angle_d	14.88	1088
X-RAY DIFFRACTION	f_chiral_restr	0.11	429
X-RAY DIFFRACTION	f_plane_restr	0.012	534

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 (%)
2.5901-2.6548	0.2871	113	0.2531	2212	X-RAY DIFFRACTION	84
2.6548-2.7266	0.2669	109	0.2436	2317	X-RAY DIFFRACTION	88
2.7266-2.8068	0.2944	159	0.2393	2354	X-RAY DIFFRACTION	91
2.8068-2.8974	0.2514	116	0.2203	2467	X-RAY DIFFRACTION	93
2.8974-3.0009	0.2247	146	0.2021	2422	X-RAY DIFFRACTION	95
3.0009-3.1211	0.2093	154	0.1827	2549	X-RAY DIFFRACTION	96
3.1211-3.2631	0.252	145	0.1943	2517	X-RAY DIFFRACTION	97
3.2631-3.435	0.2363	137	0.1908	2529	X-RAY DIFFRACTION	97
3.435-3.6501	0.1854	143	0.1611	2538	X-RAY DIFFRACTION	98
3.6501-3.9318	0.1514	154	0.1475	2547	X-RAY DIFFRACTION	98
3.9318-4.3272	0.1479	106	0.1315	2619	X-RAY DIFFRACTION	98
4.3272-4.9526	0.2274	150	0.1344	2586	X-RAY DIFFRACTION	99
4.9526-6.2369	0.2354	128	0.1807	2624	X-RAY DIFFRACTION	99
6.2369-43.9898	0.1744	142	0.1669	2538	X-RAY DIFFRACTION	97

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	0.2335	-0.1241	-0.2091	0.4824	0.0708	0.4318	0.1128	-0.1403	-0.3113	0.127	-0.3497	-0.1215	0.0142	0.0924	0.0613	0.4887	-0.0998	-0.188	0.494	0.1561	0.6813	17.6063	12.1081	77.8432
2	0.9455	-0.4655	0.4146	0.7506	-0.3228	0.7007	0.1611	-0.2306	-0.2512	0.2251	-0.0749	0.126	-0.2379	0.0157	-0.0406	0.4571	-0.1601	-0.0668	0.4588	0.1696	0.4529	10.7663	12.2868	86.1832
3	0.4608	0.1949	0.0074	0.2249	0.0401	0.0134	0.0852	-0.1533	0.074	0.3267	-0.2364	-0.1225	-0.0286	0.1165	-0.0033	0.6054	-0.1345	-0.2381	0.4521	0.1394	0.4837	19.403	21.9114	79.1691
4	1.2336	0.653	0.8704	1.004	0.3268	1.3902	0.3794	0.3152	-0.379	0.0109	-0.2014	-0.3156	-0.0174	0.4767	-0.085	0.398	-0.0117	-0.0126	0.4889	0.0094	0.4774	8.4745	14.4144	67.202
5	0.1027	-0.181	-0.1732	0.4225	0.107	0.7326	-0.0265	-0.0174	0.643	0.0461	0.1453	0.3268	-0.0434	0.1393	-0.1241	0.2287	-0.1414	-0.034	0.5205	0.1033	0.4963	-3.5067	19.4645	63.783
6	1.0205	0.2577	-0.8435	1.0693	-0.0846	1.2239	-0.1333	0.352	0.065	0.0802	0.0665	0.4667	-0.026	-0.2532	-0.0924	0.4277	0.056	-0.0061	0.5223	0.0527	0.5524	-1.4372	26.0524	67.9211
7	0.9174	-0.0597	-0.0479	0.5179	-0.2037	0.3059	0.2567	-0.2254	0.4289	0.0219	0.065	0.1499	-0.1586	-0.0946	-0.2011	0.408	0.0461	0.0612	0.4235	0.0451	0.5653	4.1004	30.3353	64.9672
8	0.1607	-0.1925	0.0841	0.3314	-0.4	1.029	-0.1608	0.3342	0.0999	0.0196	-0.4334	-0.2006	-0.0916	0.2098	0.2557	0.2546	-0.0337	-0.0084	0.453	0.076	0.468	9.9546	21.1254	61.9898
9	0.4859	-0.2064	-0.2394	0.091	0.1099	0.1244	-0.0781	0.0214	-0.0314	-0.0337	-0.0668	0.0444	0.019	0.0332	0.0505	0.493	-0.1553	0.1279	0.5872	-0.0057	0.6505	10.0489	25.7584	55.5987
10	1.4162	-1.0376	-0.0017	1.4194	-0.6261	0.9649	-0.2726	0.0163	0.5652	0.3505	0.0958	-0.2237	-0.4449	-0.1312	0.0347	0.5247	-0.0968	0.0628	0.4504	0.0524	0.5052	7.776	33.5579	62.1977
11	0.2878	0.2738	0.3491	0.3341	0.2797	0.657	0.2149	0.1197	0.8602	-0.0008	-0.1408	0.2489	0.0684	-0.4756	-0.0465	0.3342	0.0174	0.053	0.6008	0.1339	0.8062	-18.9778	43.811	77.9076
12	0.0167	-0.0137	-0.0151	0.007	0.0061	0.007	-0.0357	0.0029	0.0072	0.0042	-0.045	-0.0196	-0.0145	0.035	-0.1021	0.3584	-0.0498	-0.2959	0.2045	0.6775	0.9601	-20.8163	52.7699	70.7794
13	0.1358	0.138	-0.0844	0.1714	-0.087	0.0476	-0.1122	0.2823	0.18	-0.1058	-0.046	-0.0553	0.0948	0.2425	0.1141	0.3842	-0.1094	-0.1157	0.5326	0.3952	0.6486	-14.7122	44.8749	70.184
14	1.5796	1.0233	-0.0548	1.8183	0.0767	0.7987	-0.2645	-0.1527	0.8901	0.1051	0.3149	0.2065	-0.29	-0.0016	-0.0822	0.4188	0.0287	-0.0191	0.3322	-0.098	0.6503	-14.4848	43.3916	84.8941
15	0.9326	-0.0631	-0.499	2.5212	-0.7345	1.0442	-0.014	0.0792	0.4619	0.4958	-0.0086	-0.2422	-0.1693	-0.1278	0.0874	0.4223	-0.0981	-0.023	0.3504	0.053	0.4662	-14.3562	29.6812	92.5571
16	2.7176	-0.7984	2.9868	0.2778	-1.0663	4.1194	0.5302	0.0281	-0.3845	-0.0589	0.0585	-0.0866	0.6761	-0.0297	-0.5104	0.441	0.018	0.0053	0.3022	0.0164	0.5211	-11.9188	25.0166	83.7596
17	0.2265	0.1512	0.2133	0.1161	0.0933	0.3297	0.1727	0.003	-0.0615	0.1414	-0.0095	-0.0756	0.1508	-0.0298	-0.0949	0.4766	0.0157	-0.0484	0.4255	-0.0259	0.5261	-4.2503	29.5709	85.3117
18	0.2044	-0.0754	-0.0909	0.1519	0.1053	0.2156	0.0953	0.0156	0.0058	-0.0168	-0.0365	-0.0897	-0.0495	0.076	0.0192	0.4904	-0.0798	-0.068	0.3149	-0.1484	0.5239	-4.3203	39.0132	91.2419
19	0.7282	0.0038	0.4211	0.6238	0.226	0.5384	0.0947	0.2111	-0.05	0.0089	0.0017	-0.0965	0.1044	0.1988	-0.0647	0.4348	-0.0685	-0.0364	0.5111	-0.0976	0.4575	2.2717	39.4233	90.6571

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 63:90)
5	X-RAY DIFFRACTION	5	chain 'A' and (resseq 91:111)
6	X-RAY DIFFRACTION	6	chain 'A' and (resseq 112:126)
7	X-RAY DIFFRACTION	7	chain 'A' and (resseq 127:141)
8	X-RAY DIFFRACTION	8	chain 'A' and (resseq 142:155)
9	X-RAY DIFFRACTION	9	chain 'A' and (resseq 156:166)
10	X-RAY DIFFRACTION	10	chain 'A' and (resseq 167:183)
11	X-RAY DIFFRACTION	11	chain 'B' and (resseq 1:17)
12	X-RAY DIFFRACTION	12	chain 'B' and (resseq 18:28)
13	X-RAY DIFFRACTION	13	chain 'B' and (resseq 29:62)
14	X-RAY DIFFRACTION	14	chain 'B' and (resseq 63:80)
15	X-RAY DIFFRACTION	15	chain 'B' and (resseq 81:100)
16	X-RAY DIFFRACTION	16	chain 'B' and (resseq 101:111)
17	X-RAY DIFFRACTION	17	chain 'B' and (resseq 112:126)
18	X-RAY DIFFRACTION	18	chain 'B' and (resseq 127:166)
19	X-RAY DIFFRACTION	19	chain 'B' and (resseq 167:184)

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