PDB-3tf1: Crystal structure of an H-NOX protein from T. tengcongensis under...

ID or keywords:

Entry

Database: PDB / ID: 3tf1

Title

Crystal structure of an H-NOX protein from T. tengcongensis under 6 atm of xenon

Components

Methyl-accepting chemotaxis protein

Keywords

SIGNALING PROTEIN / Heme-based Methyl-accepting Chemotaxis Protein / Gas Binding

Function / homology

Function and homology information

heme binding / signal transduction / metal ion binding / membrane
Similarity search - Function

Biological species

Caldanaerobacter subterraneus subsp. tengcongensis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.0369 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_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.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	3tf1.cif.gz	243 KB	Display	PDBx/mmCIF format
PDB format	pdb3tf1.ent.gz	202.8 KB	Display	PDB format
PDBx/mmJSON format	3tf1.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3tf1_validation.pdf.gz	1.1 MB	Display	wwPDB validaton report
Full document	3tf1_full_validation.pdf.gz	1.1 MB	Display
Data in XML	3tf1_validation.xml.gz	18.4 KB	Display
Data in CIF	3tf1_validation.cif.gz	25.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/tf/3tf1 ftp://data.pdbj.org/pub/pdb/validation_reports/tf/3tf1	HTTPS FTP

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Related structure data

Related structure data	3tf0SC 3tf8C 3tf9C 3tfaC 3tfdC 3tfeC 3tffC 3tfgC 1u4h 1u55 1u56 S: Starting model for refinement C: citing same article (ref.)
Similar structure data	1u55-1 3tf0-2 1u4h-1 4fdk-1 3eee-2 5jrv-2 3lah-1 4fdk-2 3lah-2 3iqb-d 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 (4) #158 - Feb 2013 Proton-Gated Urea Channel similarity (4) #222 - Jun 2018 Proteins and Nanoparticles similarity (1) #263 - Nov 2021 Acetohydroxyacid Synthase similarity (1) #41 - May 2003 Hemoglobin similarity (1) #159 - Mar 2013 Erythrocruorin similarity (1) #186 - Jun 2015 Receptor for Advanced Glycation End Products similarity (1) #206 - Feb 2017 Globin Evolution similarity (1) #257 - May 2021 Fetal Hemoglobin similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#133 - Jan 2011
Nitric Oxide Synthase
similarity (4)
#158 - Feb 2013
Proton-Gated Urea Channel
similarity (4)
#222 - Jun 2018
Proteins and Nanoparticles
similarity (1)
#263 - Nov 2021
Acetohydroxyacid Synthase
similarity (1)
#41 - May 2003
Hemoglobin
similarity (1)
#159 - Mar 2013
Erythrocruorin
similarity (1)
#186 - Jun 2015
Receptor for Advanced Glycation End Products
similarity (1)
#206 - Feb 2017
Globin Evolution
similarity (1)
#257 - May 2021
Fetal Hemoglobin
similarity (1)

Deposited unit

A: Methyl-accepting chemotaxis protein

B: Methyl-accepting chemotaxis protein

hetero molecules

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

1

A: Methyl-accepting chemotaxis protein

hetero molecules

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

2

B: Methyl-accepting chemotaxis protein

hetero molecules

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

Unit cell

Length a, b, c (Å)	80.128, 130.214, 42.810
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P2₁2₁2

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Protein , 1 types, 2 molecules AB

#1: Protein	Methyl-accepting chemotaxis protein Mass: 22047.502 Da / Num. of mol.: 2 / Fragment: N-terminal Domain (UNP Residues 1-188) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Caldanaerobacter subterraneus subsp. tengcongensis (bacteria) Gene: Tar4, TTE0680 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8RBX6

#1: Protein

Methyl-accepting chemotaxis protein

Mass: 22047.502 Da / Num. of mol.: 2 / Fragment: N-terminal Domain (UNP Residues 1-188)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Caldanaerobacter subterraneus subsp. tengcongensis (bacteria)
Gene: Tar4, TTE0680 / Production host:

Escherichia coli (E. coli) / References: UniProt: Q8RBX6

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Non-polymers , 5 types, 154 molecules

#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-OXY / OXYGEN MOLECULE Mass: 31.999 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: O₂
#4: Chemical	ChemComp-XE / XENON Mass: 131.293 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Xe
#5: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₃O₂
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 145 / 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: 2.53 Å³/Da / Density % sol: 51.43 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 20-28% PEG 200, 200-250 mM Sodium Acetate pH 7.5, 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: 1.23 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 30, 2010
Radiation	Monochromator: KHOZU Double flat crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.23 Å / Relative weight: 1
Reflection	Resolution: 2.03→50 Å / Num. all: 52373 / Num. obs: 52373 / % possible obs: 94.66 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1
Reflection shell	Resolution: 2.03→2.07 Å / % possible all: 99.1

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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 3TF0

3tf0

Resolution: 2.0369→42.81 Å / SU ML: 0.25 / σ(F): 0 / Phase error: 20.87 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.221	2649	5.06 %	random
R_work	0.1797	-	-	-
obs	0.1818	52372	94.66 %	-

Solvent computation

Shrinkage radii: 0.77 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 39.74 Å² / k_sol: 0.4 e/Å³

Refinement step

Cycle: LAST / Resolution: 2.0369→42.81 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3096	0	98	145	3339

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.018	3291
X-RAY DIFFRACTION	f_angle_d	1.517	4453
X-RAY DIFFRACTION	f_dihedral_angle_d	15.329	1260
X-RAY DIFFRACTION	f_chiral_restr	0.095	456
X-RAY DIFFRACTION	f_plane_restr	0.008	559

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 (%)
2.0369-2.074	0.2682	105	0.2423	1907	X-RAY DIFFRACTION	70
2.074-2.1138	0.3097	115	0.2235	2420	X-RAY DIFFRACTION	87
2.1138-2.157	0.2301	150	0.2237	2461	X-RAY DIFFRACTION	89
2.157-2.2039	0.2681	119	0.1981	2518	X-RAY DIFFRACTION	91
2.2039-2.2552	0.2154	162	0.2067	2581	X-RAY DIFFRACTION	93
2.2552-2.3115	0.2217	138	0.178	2543	X-RAY DIFFRACTION	94
2.3115-2.374	0.2058	139	0.1861	2660	X-RAY DIFFRACTION	94
2.374-2.4439	0.2199	143	0.1728	2640	X-RAY DIFFRACTION	96
2.4439-2.5228	0.2829	119	0.1904	2669	X-RAY DIFFRACTION	96
2.5228-2.6129	0.2606	149	0.1748	2652	X-RAY DIFFRACTION	97
2.6129-2.7175	0.2278	122	0.1796	2714	X-RAY DIFFRACTION	97
2.7175-2.8412	0.2175	158	0.1842	2749	X-RAY DIFFRACTION	98
2.8412-2.9909	0.2209	169	0.1688	2669	X-RAY DIFFRACTION	99
2.9909-3.1783	0.1893	140	0.1807	2758	X-RAY DIFFRACTION	99
3.1783-3.4236	0.2818	144	0.1992	2739	X-RAY DIFFRACTION	99
3.4236-3.7679	0.2621	152	0.1912	2754	X-RAY DIFFRACTION	99
3.7679-4.3127	0.1741	132	0.1507	2791	X-RAY DIFFRACTION	100
4.3127-5.4318	0.1712	156	0.1516	2749	X-RAY DIFFRACTION	100
5.4318-42.8194	0.2116	137	0.1841	2749	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	0.499	-0.1162	0.0576	0.2576	-0.07	0.5765	-0.0474	-0.0828	0.0959	0.0872	-0.0124	-0.0542	0.0311	0.1921	0.0425	0.188	0.0138	-0.0349	0.2252	0.024	0.222	71.6535	-19.8263	44.3074
2	4.0743	-1.0652	-0.5574	1.2282	-0.5634	1.2203	0.1241	-0.304	-0.5185	0.1804	-0.063	0.1554	0.2716	0.1172	-0.0382	0.3693	0.0293	-0.013	0.2583	0.0408	0.2524	67.0827	-27.5494	49.953
3	1.0504	0.4078	0.0279	0.2174	0.1027	0.3346	-0.1668	-0.0629	0.4639	0.3466	0.0827	-0.0721	-0.2111	-0.0017	0.0718	0.3096	0.0009	-0.1156	0.2128	-0.084	0.3491	68.5167	-12.0734	49.2261
4	0.8549	-0.094	0.4427	0.4154	-0.2433	1.1805	-0.175	0.2098	0.272	-0.1303	-0.1621	0.0819	0.0344	0.1834	-0.064	0.1609	-0.003	-0.0162	0.148	-0.0197	0.1697	63.4775	-19.5554	32.7156
5	0.2588	-0.3267	-0.0127	0.4627	0.1087	0.9583	0.0136	0.0791	-0.1168	-0.0545	-0.1296	0.4632	0.1441	-0.2397	-0.0218	0.2261	-0.0774	-0.0552	0.2194	-0.0527	0.3083	50.6185	-22.3891	30.6996
6	0.5948	-0.3067	-0.287	0.5921	0.1585	0.6648	-0.3762	-0.004	0.0853	0.2494	-0.005	0.3068	0.0267	-0.1096	0.0193	0.2419	0.0025	0.0004	0.1897	-0.027	0.2662	47.7409	-21.5038	38.627
7	0.4747	-0.2118	0.3267	0.3149	0.2235	1.8153	-0.1634	-0.0621	0.3304	0.06	0.0901	0.33	0.0032	-0.1325	0.0504	0.2093	-0.0147	-0.0776	0.2201	-0.0364	0.3047	49.5757	-11.789	35.1623
8	1.404	-0.1446	0.0146	0.302	-0.308	2.077	-0.0953	0.1271	0.2984	-0.0057	-0.0755	-0.0402	0.1909	0.1137	0.0295	0.1567	0.0117	-0.0599	0.1448	0.0176	0.1798	59.8294	-13.3716	31.3657
9	0.6605	0.2601	0.3	0.5434	-0.5677	1.2361	-0.289	0.1341	0.4858	-0.0521	0.0035	0.1554	0.0317	0.0797	0.1006	0.2978	-0.0028	-0.137	0.2274	0.0267	0.3197	53.8392	-6.6733	29.6872
10	0.1344	-0.0341	0.0592	0.6848	0.5678	0.5357	-0.1658	0.0164	0.0562	-0.0365	-0.1388	0.577	-0.1748	-0.1127	0.1395	0.259	-0.0003	-0.0748	0.1834	0.0228	0.424	47.6961	-8.4043	34.9753
11	0.5034	-0.1182	0.2911	0.3299	0.18	0.7285	0.0651	-0.0614	-0.1065	-0.0354	0.2334	0.1661	0.182	0.0037	0.0522	0.4033	-0.2078	-0.3243	0.5213	0.1432	0.4417	41.655	-15.5664	15.9847
12	1.3388	-0.1116	0.63	0.1862	0.0904	0.5714	-0.0417	0.3304	0.066	-0.1271	0.0623	-0.0043	-0.0872	0.1706	-0.0005	0.2121	-0.0079	0.0336	0.2851	0.0322	0.2408	73.5978	19.0228	32.6449
13	1.2487	-0.1742	1.1894	0.833	-0.4191	1.2206	0.0234	0.3863	0.1405	-0.2858	-0.0558	0.0179	-0.0325	0.2651	0.061	0.4517	-0.0252	-0.0948	0.4879	0.2232	0.4324	68.8506	26.2377	26.2479
14	0.3312	0.0007	-0.2744	0.5855	0.0529	0.5917	-0.063	0.1554	-0.0373	-0.0912	0.1101	-0.2899	0.0182	0.2991	-0.0197	0.1568	0.0063	0.0368	0.2587	-0.0214	0.2125	69.5557	13.3391	35.3117
15	0.824	0.3708	0.0624	0.4028	0.1223	0.4743	-0.1564	-0.2026	0.3519	-0.1511	-0.0622	0.6432	-0.3071	-0.1162	-0.0448	0.2481	0.0325	0.0116	0.1153	-0.0738	0.3484	55.5175	23.5671	46.9407
16	0.2842	-0.0803	0.1501	0.6823	0.2207	1.1418	0.01	0.0922	0.0368	-0.0262	-0.2278	0.5513	-0.1034	-0.0948	0.0659	0.1905	-0.0134	0.0353	0.202	-0.0444	0.289	50.838	14.7204	40.3812
17	0.4083	-0.2655	-0.2191	0.937	-0.2044	0.578	0.0139	-0.1073	-0.1519	0.2457	-0.0774	0.3343	0.0005	0.0199	0.0468	0.2266	-0.0118	0.0277	0.1303	0.01	0.2147	56.542	8.6093	45.4597
18	0.15	-0.0097	-0.0248	0.0594	-0.009	0.0879	0.0076	-0.0486	0.055	0.072	-0.0256	0.1142	-0.0626	0.0555	-0.0625	0.442	-0.2519	0.448	0.7025	-0.1496	0.4209	45.5297	15.2555	61.4569

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resseq 1:29)
2	X-RAY DIFFRACTION	2	chain 'A' and (resseq 30:44)
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 91:104)
6	X-RAY DIFFRACTION	6	chain 'A' and (resseq 105:123)
7	X-RAY DIFFRACTION	7	chain 'A' and (resseq 124:137)
8	X-RAY DIFFRACTION	8	chain 'A' and (resseq 138:152)
9	X-RAY DIFFRACTION	9	chain 'A' and (resseq 153:165)
10	X-RAY DIFFRACTION	10	chain 'A' and (resseq 166:178)
11	X-RAY DIFFRACTION	11	chain 'A' and (resseq 179:188)
12	X-RAY DIFFRACTION	12	chain 'B' and (resseq 1:29)
13	X-RAY DIFFRACTION	13	chain 'B' and (resseq 30:44)
14	X-RAY DIFFRACTION	14	chain 'B' and (resseq 45:81)
15	X-RAY DIFFRACTION	15	chain 'B' and (resseq 82:106)
16	X-RAY DIFFRACTION	16	chain 'B' and (resseq 107:137)
17	X-RAY DIFFRACTION	17	chain 'B' and (resseq 138:178)
18	X-RAY DIFFRACTION	18	chain 'B' and (resseq 179:188)

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Protein , 1 types, 2 molecules AB

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Non-polymers , 5 types, 154 molecules

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