PDB-4fdk: F78L Tt H-NOX

ID or keywords:

Entry

Database: PDB / ID: 4fdk

Title

F78L Tt H-NOX

Components

Methyl-accepting chemotaxis protein

Keywords

SIGNALING PROTEIN / O2-sensor

Function / homology

Function and homology information

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

Biological species

Thermoanaerobacter tengcongensis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.1 Å

Authors

Weinert, E.E. / Phillips-Piro, C.M. / Marletta, M.A.

Citation

Journal: J.Inorg.Biochem. / Year: 2013
Title: Porphyrin pi-stacking in a heme protein scaffold tunes gas ligand affinity.
Authors: Weinert, E.E. / Phillips-Piro, C.M. / Marletta, M.A.

History

Deposition	May 28, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 28, 2013	Provider: repository / Type: Initial release
Revision 1.1	Nov 15, 2017	Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.2	Jul 17, 2019	Group: Data collection / Refinement description / Category: software / Item: _software.name / _software.version
Revision 1.3	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_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_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_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	4fdk.cif.gz	249.7 KB	Display	PDBx/mmCIF format
PDB format	pdb4fdk.ent.gz	207.1 KB	Display	PDB format
PDBx/mmJSON format	4fdk.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4fdk_validation.pdf.gz	1.1 MB	Display	wwPDB validaton report
Full document	4fdk_full_validation.pdf.gz	1.1 MB	Display
Data in XML	4fdk_validation.xml.gz	20.7 KB	Display
Data in CIF	4fdk_validation.cif.gz	28.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/fd/4fdk ftp://data.pdbj.org/pub/pdb/validation_reports/fd/4fdk	HTTPS FTP

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Related structure data

Related structure data	1u55S 1u4h 1u56 S: Starting model for refinement
Similar structure data	1u4h-1 3tf1-1 3tf0-2 1u4h-2 1u55-1 1u56-1 3lai-2 3eee-1 3eee-2 5jrv-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 (4) #158 - Feb 2013 Proton-Gated Urea Channel similarity (4) #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)
#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

45.3 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
22.7 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
22.7 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	80.552, 127.426, 42.935
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P2₁2₁2

#1: Protein	Methyl-accepting chemotaxis protein / H-NOX protein Mass: 22013.484 Da / Num. of mol.: 2 / Fragment: UNP residues 1-188 / Mutation: F78L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermoanaerobacter tengcongensis (bacteria) Strain: DSM 15242 / JCM 11007 / NBRC 100824 / MB4 / Gene: Tar4, TTE0680 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8RBX6
#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: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 280 / 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: 2.5 Å³/Da / Density % sol: 50.85 %
Crystal grow	Method: vapor diffusion, sitting drop / pH: 4.4 Details: 0.2 M sodium citrate, pH 4.4, 25% w/v PEG3350, 25 mg/mL protein in 20 mM TEA, pH 7.5, VAPOR DIFFUSION, SITTING DROP

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 11, 2010
Radiation	Monochromator: Double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.1→50 Å / Num. all: 26664 / Num. obs: 26525 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shell	Resolution: 2.1→2.14 Å / Redundancy: 4 % / Mean I/σ(I) obs: 3 / R_sym value: 0.414 / % possible all: 100

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Processing

Software

Name	Version	Classification
PHENIX	(phenix.refine: 1.7.3_928)	refinement
PHASER		phasing
ELVES		refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1U55 CHAIN A

1u55

Resolution: 2.1→49.971 Å / SU ML: 0.28 / σ(F): 1.34 / Phase error: 22.83 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2309	1334	5.03 %	RANDOM
R_work	0.1696	-	-	-
obs	0.1728	26525	99.67 %	-
all	-	26664	-	-

Solvent computation

Shrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 55.239 Å² / k_sol: 0.328 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-6.9025 Å²	0 Å²	-0 Å²
2-	-	7.6214 Å²	0 Å²
3-	-	-	-0.7189 Å²

Refinement step

Cycle: LAST / Resolution: 2.1→49.971 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3096	0	90	280	3466

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.014	3289
X-RAY DIFFRACTION	f_angle_d	1.392	4447
X-RAY DIFFRACTION	f_dihedral_angle_d	16.6	1261
X-RAY DIFFRACTION	f_chiral_restr	0.08	457
X-RAY DIFFRACTION	f_plane_restr	0.007	558

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 (%)
2.1-2.1751	0.3295	118	0.23	2512	X-RAY DIFFRACTION	100
2.1751-2.2622	0.2455	126	0.1868	2471	X-RAY DIFFRACTION	100
2.2622-2.3651	0.2012	147	0.1747	2463	X-RAY DIFFRACTION	100
2.3651-2.4898	0.3222	128	0.1826	2483	X-RAY DIFFRACTION	100
2.4898-2.6458	0.2665	129	0.1886	2498	X-RAY DIFFRACTION	100
2.6458-2.8501	0.2587	131	0.1827	2534	X-RAY DIFFRACTION	100
2.8501-3.1368	0.2498	143	0.1694	2489	X-RAY DIFFRACTION	100
3.1368-3.5906	0.2265	138	0.1677	2529	X-RAY DIFFRACTION	100
3.5906-4.5234	0.2113	130	0.1414	2546	X-RAY DIFFRACTION	99
4.5234-49.9853	0.2061	144	0.1727	2666	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	0.0972	-0.0434	-0.1125	0.012	0.0454	0.1167	-0.1464	-0.252	-0.1295	-0.1495	0.096	-0.1049	-0.2558	-0.1096	-0.0004	0.2746	0.0026	0.0712	0.2691	-0.0422	0.2785	12.2172	20.6014	19.8427
2	0.0083	-0.0066	-0.0098	0.0311	0.0311	0.0315	-0.1485	-0.4913	-0.0388	0.0456	0.2213	0.1181	-0.114	-0.1887	-0.0003	0.3321	0.0133	0.0529	0.3756	-0.0045	0.244	3.0631	17.9122	27.663
3	0.462	0.1767	-0.1822	0.1079	0.0083	0.2017	0.319	-0.5418	1.1893	0.216	0.194	0.0249	-0.2997	-0.2246	0.0068	0.4649	-0.0429	0.1258	0.413	-0.07	0.5276	12.6061	26.9764	28.5228
4	0.9607	-0.0315	0.1816	0.1075	0.0472	0.2307	-0.2474	-0.3895	-0.8706	0.5036	0.0175	-0.0255	0.4157	0.2461	-0.0105	0.3696	-0.0166	0.1019	0.385	0.0797	0.3477	11.0981	11.5657	28.0017
5	0.2004	-0.0325	-0.125	0.0182	0.0274	0.0808	-0.0383	0.1562	-0.2152	-0.1121	0.1301	0.1272	0.1003	-0.023	0	0.2313	0.0019	0.0873	0.2523	0.0169	0.2892	13.8836	15.5984	14.3814
6	0.0613	0.0191	0.0071	0.0498	-0.0388	0.0356	0.0721	-0.1446	0.0383	-0.3674	-0.2599	0.1072	-0.1518	0.0459	0.0003	0.5375	-0.0966	0.0321	0.3697	0.0257	0.2863	21.4158	26.5808	4.8509
7	0.261	-0.2929	-0.0506	0.3244	0.0522	0.0082	-0.0221	0.2711	0.1818	-0.2487	0.0497	-0.7492	-0.0756	0.3559	-0.0427	0.3408	-0.0271	0.1167	0.2367	-0.0255	0.3511	28.8723	22.8437	10.6884
8	0.4698	0.0744	-0.2486	0.5009	0.0822	0.162	-0.2765	-0.2478	-0.2113	0.4535	0.0685	-0.5139	0.1118	0.1498	-0.0513	0.3251	0.0213	-0.0432	0.267	-0.0408	0.224	31.2644	24.4948	21.9761
9	0.1106	-0.157	0.0435	0.4005	-0.0031	0.0433	-0.219	0.0526	-0.5523	0.0549	0.1509	-0.4133	0.2102	0.0496	-0.0727	0.3018	-0.0234	0.1736	0.2917	-0.0275	0.3569	31.5584	11.766	11.9429
10	0.0839	-0.1139	0.1571	0.6761	-0.1296	0.5457	-0.138	0.0852	-0.3022	-0.0059	-0.2571	0.0495	-0.0794	-0.2655	-0.1584	0.2737	-0.0188	0.123	0.301	-0.0514	0.2481	20.0588	13.0802	10.1246
11	0.7675	0.083	-0.4375	0.1362	-0.0032	0.2705	-0.3312	0.2487	-0.4953	0.0714	0.0523	-0.3981	-0.1228	-0.2766	-0.123	0.3215	0.0187	0.0983	0.2642	-0.0773	0.4861	27.1505	6.0936	9.9839
12	0.198	0.1042	-0.1108	0.1849	-0.0443	0.0596	0.074	-0.1674	-0.0168	0.1655	-0.0018	-0.6365	0.0835	0.3797	0.0044	0.3369	-0.0243	0.0407	0.2912	-0.035	0.4621	31.8384	8.523	13.0705
13	0.0053	-0.0398	0.0429	0.3736	-0.4036	0.4321	0.1032	-0.0656	0.3268	-0.0745	0.322	-0.1672	-0.4504	-0.1017	1.0809	0.4944	-0.5146	0.6791	0.7549	-0.2342	0.4806	37.5249	15.3298	-5.2422
14	0.1885	-0.0997	-0.1678	0.106	0.0141	0.1895	-0.2314	-0.5709	0.0457	0.2254	0.1238	0.1066	0.2963	0.4989	-0.0006	0.3588	0.0711	-0.0499	0.3418	-0.0274	0.254	33.13	45.1658	30.9814
15	0.0797	0.075	-0.0027	0.0688	0.0157	0.0453	-0.1447	-0.2908	-0.3058	0.5446	0.0435	-0.1329	0.7843	0.5846	0.0002	0.8246	0.0591	0.1215	0.7555	0.0312	0.4289	28.6491	38.8913	38.1457
16	0.6943	-0.0706	0.166	0.9074	-0.4807	0.2806	-0.2754	-0.5005	0.6585	0.9226	0.2797	-0.3619	-0.4308	-0.1888	0.0545	0.477	0.061	-0.1126	0.4654	-0.1506	0.4293	31.0889	53.7355	35.5649
17	0.4567	-0.205	-0.3026	0.3019	-0.062	0.3323	-0.1724	0.2071	-0.0407	-0.0306	-0.1277	0.0648	0.0749	-0.1444	-0.0087	0.2352	0.0047	-0.0083	0.2267	-0.1022	0.3171	25.2669	44.8139	19.8799
18	0.4762	0.0246	-0.0004	0.5836	0.2622	0.1175	0.0163	-0.0106	-0.5721	-0.0775	-0.2477	0.7289	0.235	-0.4782	-0.0965	0.2622	-0.036	-0.0148	0.2805	-0.0566	0.5059	12.2953	41.47	19.927
19	0.9699	-0.2581	-0.6559	0.874	0.8976	1.1138	-0.3993	-0.1359	-0.3418	0.1604	-0.0456	0.623	0.6476	-0.439	-0.4844	0.3726	-0.0047	0.0678	0.3662	-0.0473	0.4326	9.0341	45.2942	25.1326
20	0.3926	-0.2771	-0.0257	0.3767	-0.0662	0.0705	-0.2494	0.2463	0.1271	-0.064	-0.0782	0.3274	0.0114	0.0486	-0.0051	0.2628	0.0141	-0.053	0.2961	-0.0427	0.2653	17.1292	52.1048	19.7128
21	0.4337	0.0732	0.0715	0.573	-0.0642	0.0224	-0.0727	-0.0715	0.0431	-0.1382	-0.1902	0.5155	0.0578	0.2187	-0.0251	0.3628	0.1102	-0.0337	0.4391	0.0074	0.3153	13.0172	57.5614	18.8105
22	0.1895	0.0088	-0.0975	0.8138	-0.1362	0.0739	0.0725	0.0393	-0.091	-0.0795	0.1055	0.1042	0.1562	0.5562	0.1034	0.6291	0.362	-0.2592	1.0065	-0.1609	0.4448	4.747	48.2483	2.6597

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 18:29)
3	X-RAY DIFFRACTION	3	chain 'A' and (resseq 30:44)
4	X-RAY DIFFRACTION	4	chain 'A' and (resseq 45:62)
5	X-RAY DIFFRACTION	5	chain 'A' and (resseq 63:81)
6	X-RAY DIFFRACTION	6	chain 'A' and (resseq 82:90)
7	X-RAY DIFFRACTION	7	chain 'A' and (resseq 91:106)
8	X-RAY DIFFRACTION	8	chain 'A' and (resseq 107:118)
9	X-RAY DIFFRACTION	9	chain 'A' and (resseq 119:137)
10	X-RAY DIFFRACTION	10	chain 'A' and (resseq 138:152)
11	X-RAY DIFFRACTION	11	chain 'A' and (resseq 153:166)
12	X-RAY DIFFRACTION	12	chain 'A' and (resseq 167:178)
13	X-RAY DIFFRACTION	13	chain 'A' and (resseq 179:188)
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 91:107)
19	X-RAY DIFFRACTION	19	chain 'B' and (resseq 108:123)
20	X-RAY DIFFRACTION	20	chain 'B' and (resseq 124:152)
21	X-RAY DIFFRACTION	21	chain 'B' and (resseq 153:178)
22	X-RAY DIFFRACTION	22	chain 'B' and (resseq 179:188)

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