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

ID or keywords:

Entry

Database: PDB / ID: 3tfd

Title

Crystal structure of an H-NOX protein from Nostoc sp. PCC 7120, L66W 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: 1.96 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	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 / 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	3tfd.cif.gz	225.9 KB	Display	PDBx/mmCIF format
PDB format	pdb3tfd.ent.gz	188.8 KB	Display	PDB format
PDBx/mmJSON format	3tfd.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3tfd_validation.pdf.gz	1.1 MB	Display	wwPDB validaton report
Full document	3tfd_full_validation.pdf.gz	1.1 MB	Display
Data in XML	3tfd_validation.xml.gz	18 KB	Display
Data in CIF	3tfd_validation.cif.gz	24.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/tf/3tfd ftp://data.pdbj.org/pub/pdb/validation_reports/tf/3tfd	HTTPS FTP

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Related structure data

Related structure data	3tf0C 3tf1C 3tf8C 3tf9C 3tfaC 3tfeC 3tffC 3tfgC 2o09 2o0c 2o0g C: citing same article (ref.)
Similar structure data	2o0g-2 4iae-2 3tff-1 2o0c-1 2o09-2 4iah-2 3tf9-1 3tfg-1 3tfa-2 2o0c-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

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

1

A: Alr2278 protein

hetero molecules

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

Unit cell

Length a, b, c (Å)	123.170, 123.170, 123.170
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-265- HOH

#1: Protein	Alr2278 protein Mass: 21286.695 Da / Num. of mol.: 2 / Mutation: L66W 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.: 1 / Source method: obtained synthetically / Formula: C₃H₄O₄
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 190 / 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: 3.78 Å³/Da / Density % sol: 67.49 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 1.9-2.0 M malonic acid, pH 7.0, VAPOR DIFFUSION, SITTING 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: Oct 17, 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: 1.96→50 Å / Num. all: 42144 / Num. obs: 42144 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1
Reflection shell	Resolution: 1.96→1.99 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 / Resolution: 1.96→38.95 Å / SU ML: 0.2 / σ(F): 0 / Phase error: 18.92 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.186	2143	5.08 %
R_work	0.1626	-	-
obs	0.1638	42144	93.92 %
all	-	42144	-

Solvent computation

Shrinkage radii: 0.65 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 43.685 Å² / k_sol: 0.414 e/Å³

Refinement step

Cycle: LAST / Resolution: 1.96→38.95 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2883	0	93	190	3166

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	3083
X-RAY DIFFRACTION	f_angle_d	1.29	4204
X-RAY DIFFRACTION	f_dihedral_angle_d	15.425	1093
X-RAY DIFFRACTION	f_chiral_restr	0.064	427
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 (%)
1.96-2.0056	0.2579	122	0.2173	2414	X-RAY DIFFRACTION	86
2.0056-2.0558	0.2396	131	0.1972	2502	X-RAY DIFFRACTION	88
2.0558-2.1113	0.213	126	0.1905	2494	X-RAY DIFFRACTION	90
2.1113-2.1735	0.2068	140	0.1891	2538	X-RAY DIFFRACTION	90
2.1735-2.2436	0.1955	137	0.1761	2573	X-RAY DIFFRACTION	91
2.2436-2.3238	0.2079	138	0.176	2597	X-RAY DIFFRACTION	92
2.3238-2.4168	0.199	137	0.1759	2624	X-RAY DIFFRACTION	93
2.4168-2.5268	0.2061	145	0.1809	2636	X-RAY DIFFRACTION	94
2.5268-2.66	0.2	141	0.1771	2674	X-RAY DIFFRACTION	95
2.66-2.8266	0.1971	152	0.1834	2738	X-RAY DIFFRACTION	97
2.8266-3.0448	0.2273	152	0.1745	2767	X-RAY DIFFRACTION	98
3.0448-3.351	0.1938	155	0.1619	2790	X-RAY DIFFRACTION	98
3.351-3.8356	0.184	165	0.1435	2810	X-RAY DIFFRACTION	99
3.8356-4.831	0.1457	137	0.1242	2877	X-RAY DIFFRACTION	99
4.831-38.9574	0.1655	165	0.1727	2967	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	2.3362	0.2448	0.816	1.6353	-0.4277	0.7393	-0.0881	-0.4795	-0.2468	0.3516	0.0908	-0.1957	0.079	0.571	0.0051	0.3366	0.0609	-0.0398	0.5212	0.0149	0.2783	49.1668	46.7786	74.0223
2	0.0951	-0.0583	-0.0788	0.3303	-0.2502	0.3981	-0.2116	-0.4211	-0.0328	0.3977	0.1689	-0.2616	0.014	0.201	0.1924	0.5816	0.4289	0.0497	0.9051	0.5341	0.092	50.4089	40.1926	83.2251
3	0.5697	0.2906	0.4755	0.5501	0.2353	0.5148	-0.4062	-0.2149	-1.0154	0.0378	-0.0877	0.1326	0.4269	0.3176	-0.0846	0.3695	0.1413	0.1081	0.4662	0.1858	0.4443	49.4791	35.9687	70.6871
4	1.2779	-0.9372	-0.4731	1.7949	-0.5905	3.6252	-0.4903	-1.0447	-0.5331	0.4668	0.3304	0.7527	-0.4841	-0.1677	-0.1316	0.4783	0.1582	0.1431	0.6711	0.2021	0.4697	39.9671	42.5993	79.7925
5	1.8989	-0.093	-0.2816	1.0488	-0.1415	0.169	-0.2471	-0.707	-0.059	0.4975	0.0876	0.0689	-0.1542	0.5347	0.0542	0.3578	0.0205	0.041	0.4563	0.0024	0.2392	44.5586	53.4996	73.6884
6	1.1988	0.2786	-0.6935	1.5677	0.1448	1.7973	-0.1232	-0.6385	0.0994	-0.0465	-0.007	-0.361	-0.1326	0.1746	0.0283	0.2871	0.0159	0.0231	0.3814	0.0284	0.3043	49.2314	59.1762	59.8506
7	0.2351	0.0344	-0.0155	1.0816	-0.497	0.3357	0.0529	0.0138	0.0824	-0.3133	-0.2141	-0.1307	0.1116	-0.1634	0.088	0.3231	0.0371	0.0202	0.349	0.011	0.2408	40.5997	56.9622	57.0137
8	1.1856	-1.3068	-0.0901	2.4038	0.6937	1.2234	0.3677	0.4668	-0.2556	-0.6025	-0.5221	0.0597	-0.1064	-0.1648	0.0552	0.3522	0.039	-0.0244	0.3893	-0.0435	0.3016	34.6391	53.8076	59.603
9	0.9587	-0.0606	-0.4003	0.1822	0.4754	1.4059	-0.042	0.0596	-0.144	-0.1508	-0.2001	0.0303	-0.199	-0.2433	0.0792	0.3393	0.009	0.0027	0.4039	-0.0334	0.2946	30.5159	56.2757	65.2568
10	1.1786	0.6851	0.0609	2.0975	-0.3524	0.1297	0.041	-0.3127	0.0066	0.5243	0.0176	-0.0244	-0.1399	0.0058	-0.0355	0.3409	-0.0151	0.0322	0.361	-0.055	0.2797	39.7539	59.4395	70.9701
11	0.2246	-0.3387	-0.0849	0.391	0.2545	0.7274	-0.0766	0.0077	-0.0238	-0.0102	0.0192	-0.1162	-0.1894	-0.0799	0.005	0.3697	-0.0151	0.013	0.3727	-0.1034	0.3257	34.6496	65.5572	71.279
12	0.0145	-0.0506	-0.0651	2.5772	-1.0924	0.9439	-0.0434	0.3441	-0.4631	-0.2305	0.3504	1.2473	0.6513	-0.564	-0.0507	0.3408	-0.0858	0.0309	0.4011	-0.0999	0.5439	22.7259	50.3626	69.5348
13	1.2774	-0.1384	-0.405	2.5652	-0.8688	1.0781	0.2655	0.1024	-0.069	0.2896	-0.4309	-0.3009	-0.2757	-0.0666	0.0471	0.3846	0.0401	0.0188	0.342	-0.0159	0.2813	31.6611	65.9992	68.2724
14	0.6625	-0.44	-0.0428	0.6864	-0.5492	1.9501	0.158	0.1455	0.0511	-0.1573	-0.284	0.2297	-0.8045	-0.2019	0.0877	0.462	0.1032	-0.0608	0.3217	-0.0186	0.2982	15.1664	81.0656	74.8136
15	1.1465	0.342	-0.5096	0.8487	-0.8057	0.8923	0.1076	-0.0367	-0.3121	-0.2313	-0.5288	0.7697	-0.3959	-0.5736	-0.2739	0.4294	0.1719	-0.1211	0.3843	-0.1646	0.4365	6.8996	81.0312	81.6211
16	1.9961	-0.8482	0.5431	1.7142	1.4324	2.0743	0.0969	0.5559	-0.4768	-0.3407	-0.4057	0.322	-0.352	-0.0052	0.0627	0.3996	0.0874	-0.08	0.3996	-0.1041	0.3632	13.8099	71.4349	72.8522
17	1.0066	0.074	0.7442	0.6712	0.5243	0.6539	-0.1445	0.2227	0.0352	-0.2969	0.1064	0.0136	-0.4525	0.2479	0.016	0.3857	-0.0021	-0.0236	0.2884	-0.0287	0.2373	25.593	78.4009	83.2803
18	3.2805	-1.4389	-1.5033	1.3293	-0.5044	2.602	0.4544	0.6363	0.2263	-0.4955	-0.0503	-0.1572	0.4681	0.6074	-0.1625	0.3681	0.0653	-0.0366	0.4489	-0.0545	0.2905	35.5219	72.1351	93.4826
19	2.2084	0.6326	-1.212	2.9264	-0.8088	0.7907	-0.2634	-0.8136	0.2641	0.3952	-0.1288	-0.3772	-0.3559	-0.3423	0.0097	0.3656	0.0358	-0.0288	0.3903	-0.0938	0.2204	23.1016	74.3588	97.5309
20	2.3793	-1.5725	-0.4269	1.8738	-0.3125	1.4399	-0.3526	-0.6459	-0.1408	0.4691	0.3929	0.1938	0.0931	0.1711	-0.022	0.3764	0.0381	0.0031	0.3397	-0.0137	0.3023	24.8425	66.7828	93.3753
21	0.5076	-0.2944	0.1223	0.8511	-0.0711	1.3881	-0.0823	0.1016	-0.1298	0.1513	-0.109	0.0433	0.2988	0.2699	0.0386	0.3284	-0.0058	0.006	0.3252	-0.0076	0.251	27.6184	62.6443	87.7608
22	0.4202	0.3349	-0.1386	0.8163	-0.0875	0.8162	-0.1247	-0.0497	0.107	-0.3081	-0.0115	-0.0024	0.0216	0.3544	0.0381	0.3326	-0.0032	0.0431	0.3775	-0.0467	0.2612	33.6179	69.7117	81.9271
23	1.2837	-0.4217	0.1954	0.5785	0.1391	2.0445	-0.0929	0.2158	-0.278	0.0089	0.1774	0.0997	0.6234	0.1789	-0.0009	0.4218	-0.0206	0.0341	0.3788	-0.0424	0.3283	29.4369	58.6402	84.0104

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 63:80)
6	X-RAY DIFFRACTION	6	chain 'A' and (resseq 81:93)
7	X-RAY DIFFRACTION	7	chain 'A' and (resseq 94:111)
8	X-RAY DIFFRACTION	8	chain 'A' and (resseq 112:126)
9	X-RAY DIFFRACTION	9	chain 'A' and (resseq 127:141)
10	X-RAY DIFFRACTION	10	chain 'A' and (resseq 142:155)
11	X-RAY DIFFRACTION	11	chain 'A' and (resseq 156:166)
12	X-RAY DIFFRACTION	12	chain 'A' and (resseq 167:174)
13	X-RAY DIFFRACTION	13	chain 'A' and (resseq 175:183)
14	X-RAY DIFFRACTION	14	chain 'B' and (resseq 1:28)
15	X-RAY DIFFRACTION	15	chain 'B' and (resseq 29:44)
16	X-RAY DIFFRACTION	16	chain 'B' and (resseq 45:62)
17	X-RAY DIFFRACTION	17	chain 'B' and (resseq 63:90)
18	X-RAY DIFFRACTION	18	chain 'B' and (resseq 91:100)
19	X-RAY DIFFRACTION	19	chain 'B' and (resseq 101:111)
20	X-RAY DIFFRACTION	20	chain 'B' and (resseq 112:126)
21	X-RAY DIFFRACTION	21	chain 'B' and (resseq 127:141)
22	X-RAY DIFFRACTION	22	chain 'B' and (resseq 142:166)
23	X-RAY DIFFRACTION	23	chain 'B' and (resseq 167:182)

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Yorodumi