PDB-6ltl: The dimeric structure of G80A myoglobin

ID or keywords:

Entry

Database: PDB / ID: 6ltl

Title

The dimeric structure of G80A myoglobin

Components

Myoglobin

Keywords

OXYGEN BINDING / OXYGEN STORAGE

Function / homology

Function and homology information

Oxidoreductases; Acting on other nitrogenous compounds as donors / nitrite reductase activity / oxygen transport / sarcoplasm / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / removal of superoxide radicals / oxygen carrier activity / peroxidase activity / oxygen binding / heme binding / metal ion binding
Similarity search - Function

Biological species

Equus caballus (horse)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.25 Å

Authors

Nagao, S. / Suda, A. / Kobayashi, H. / Shibata, N. / Higuchi, Y. / Hirota, S.

Funding support

Japan, 3items

Organization	Grant number	Country
Japan Society for the Promotion of Science (JSPS)	JP16K17935	Japan
Japan Society for the Promotion of Science (JSPS)	JP19K05695	Japan
Japan Society for the Promotion of Science (JSPS)	JP26288080	Japan

Citation

Journal: Chem Asian J / Year: 2020
Title: Thermodynamic Control of Domain Swapping by Modulating the Helical Propensity in the Hinge Region of Myoglobin.
Authors: Nagao, S. / Suda, A. / Kobayashi, H. / Shibata, N. / Higuchi, Y. / Hirota, S.

History

Deposition	Jan 22, 2020	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	May 6, 2020	Provider: repository / Type: Initial release
Revision 1.1	Jun 17, 2020	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2	Nov 29, 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_ncs_dom_lim 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.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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6ltl.cif.gz	143 KB	Display	PDBx/mmCIF format
PDB format	pdb6ltl.ent.gz	111.1 KB	Display	PDB format
PDBx/mmJSON format	6ltl.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/lt/6ltl ftp://data.pdbj.org/pub/pdb/validation_reports/lt/6ltl	HTTPS FTP

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Related structure data

Related structure data	6ls8C 6ltmC 3vm9S C: citing same article (ref.) S: Starting model for refinement
Similar structure data	7dgj-d 6ltm-d 7dgm-d 7dgn-d 7dgl-d 5jp2-2 2p9f-d 1n5l-d 5f5o-2 3vm9-d 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	#206 - Feb 2017 Globin Evolution similarity (2) #233 - May 2019 S-Nitrosylated Hemoglobin similarity (1) #262 - Oct 2021 Fifty Years of Open Access to PDB Structures similarity (1) #142 - Oct 2011 PDB Pioneers similarity (1)

Deposited unit

A: Myoglobin

B: Myoglobin

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	57.902, 63.060, 83.514
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: _ / Auth seq-ID: 1 - 153 / Label seq-ID: 1 - 153

Dom-ID	Auth asym-ID	Label asym-ID
1	A	A
2	B	B

#1: Protein	Myoglobin Mass: 16997.539 Da / Num. of mol.: 2 / Mutation: G80A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Equus caballus (horse) / Gene: MB / Production host: Escherichia coli (E. coli) / References: UniProt: P68082
#2: Chemical	ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃₄H₃₂FeN₄O₄ / Feature type: SUBJECT OF INVESTIGATION
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 347 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.24 Å³/Da / Density % sol: 45.15 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.1M Tris-HCl buffer, 0.1M sodium acetate, 10% (w/v) PEG 6000

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
Detector	Type: RAYONIX MX225HE / Detector: CCD / Date: Jul 25, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.25→50 Å / Num. obs: 85063 / % possible obs: 99.4 % / Redundancy: 6.3 % / R_merge(I) obs: 0.096 / Net I/σ(I): 23.9
Reflection shell	Resolution: 1.25→1.28 Å / R_merge(I) obs: 0.918 / Num. unique obs: 4107 / CC_1/2: 0.849

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0073	refinement
HKL-2000		data reduction
HKL-2000		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3VM9

3vm9

Resolution: 1.25→50 Å / Cor.coef. F_o:F_c: 0.945 / Cor.coef. F_o:F_c free: 0.917 / SU B: 1.91 / SU ML: 0.047 / Cross valid method: THROUGHOUT / ESU R: 0.057 / ESU R Free: 0.059 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.24544	4186	5 %	RANDOM
R_work	0.22103	-	-	-
obs	0.22226	80296	99.16 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å

Displacement parameters

B_iso mean: 14.073 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.18 Å²	0 Å²	0 Å²
2-	-	0.07 Å²	-0 Å²
3-	-	-	-0.24 Å²

Refinement step

Cycle: 1 / Resolution: 1.25→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2400	0	86	347	2833

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.02	0.02	2563
X-RAY DIFFRACTION	r_bond_other_d	0.007	0.02	2486
X-RAY DIFFRACTION	r_angle_refined_deg	2.07	2.04	3476
X-RAY DIFFRACTION	r_angle_other_deg	1.444	3	5739
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.956	5	306
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	39.439	25.14	107
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.317	15	459
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	6.856	15	4
X-RAY DIFFRACTION	r_chiral_restr	0.157	0.2	363
X-RAY DIFFRACTION	r_gen_planes_refined	0.014	0.02	2876
X-RAY DIFFRACTION	r_gen_planes_other	0.01	0.02	584
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.754	0.715	1227
X-RAY DIFFRACTION	r_mcbond_other	0.754	0.715	1226
X-RAY DIFFRACTION	r_mcangle_it	1.082	1.075	1532
X-RAY DIFFRACTION	r_mcangle_other	1.081	1.076	1533
X-RAY DIFFRACTION	r_scbond_it	1.501	0.893	1336
X-RAY DIFFRACTION	r_scbond_other	1.496	0.892	1334
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	2.179	1.274	1944
X-RAY DIFFRACTION	r_long_range_B_refined	4.017	7.381	3415
X-RAY DIFFRACTION	r_long_range_B_other	3.95	6.625	3211
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Ens-ID: 1 / Number: 8070 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.17 Å / Weight position: 0.05

Dom-ID	Auth asym-ID
1	A
2	B

LS refinement shell

Resolution: 1.25→1.282 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.434	292	-
R_work	0.417	5906	-
obs	-	-	99.44 %

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	1.4734	1.8329	0.9176	4.2647	2.339	3.1884	-0.0124	-0.0228	0.0276	-0.0005	0.0654	-0.1026	0.0474	0.104	-0.0529	0.0422	0.0175	0.0022	0.0205	-0.0079	0.0481	0.9394	-8.8007	-4.9629
2	2.7039	-0.1108	-0.6931	0.4849	0.0935	1.2938	0.0017	-0.0971	0.0155	-0.0375	0.0028	-0.0197	-0.0959	0.0885	-0.0045	0.0263	0.0051	-0.0144	0.0155	-0.0042	0.0387	-7.3398	0.7537	11.0146
3	3.3381	2.3666	0.2534	5.5351	0.4058	2.235	-0.0896	-0.1005	0.2153	0.0251	-0.0155	0.2579	-0.1071	-0.2117	0.1051	0.0299	0.0248	-0.024	0.0465	-0.0219	0.0335	-9.9783	1.6973	21.5405
4	0.2823	-0.5445	-0.5107	3.5021	2.9759	3.1672	-0.0138	-0.0563	0.0093	0.024	0.0997	-0.1208	-0.0371	0.1178	-0.0859	0.019	0.0053	-0.008	0.0239	-0.0048	0.0408	0.2487	-11.2155	7.5357
5	0.7868	0.4191	-0.0928	2.206	-0.8153	1.9596	-0.0466	0.0357	-0.0008	-0.1079	0.0453	0.0504	-0.0652	-0.162	0.0013	0.0349	-0.0019	-0.0179	0.0354	-0.0033	0.0349	-5.7828	-35.8203	-12.7084
6	6.0269	-2.1838	2.9607	2.7244	-1.9999	5.0572	-0.0529	-0.3015	-0.1848	0.1228	0.1254	-0.0064	0.1668	0.0987	-0.0725	0.0468	0.0106	-0.0038	0.0429	0.0056	0.0383	3.3587	-47.2166	2.2133
7	2.374	-0.8653	1.5646	4.6441	-3.54	7.3064	0.0166	-0.1415	-0.1201	0.0745	-0.0246	-0.0859	0.2048	0.0445	0.008	0.0549	-0.0123	0.0011	0.0451	-0.002	0.0556	-1.291	-39.7176	6.5859
8	1.1833	-0.3374	0.0113	0.8019	0.1411	1.5927	0.0077	0.1372	0.0512	-0.1055	-0.0027	0.1619	-0.2143	-0.1452	-0.005	0.0453	0.0074	-0.0192	0.0427	0.0161	0.0498	-10.6619	-30.2436	-8.9149
9	1.967	-1.6658	-1.8356	3.1316	1.5693	2.7315	0.0342	-0.1322	-0.0032	-0.0199	-0.0028	0.0716	-0.1591	0.0679	-0.0314	0.058	-0.0277	-0.0157	0.0473	0.0095	0.0173	3.7641	-34.2873	9.0191
10	2.0951	0.7891	0.5207	1.7231	0.0744	1.5406	0.0263	0.0313	-0.1385	-0.0839	0.021	-0.0879	0.044	0.0337	-0.0474	0.052	-0.0125	0.0133	0.0159	-0.0063	0.0489	4.1353	-46.755	-7.6504
11	2.9266	-4.9171	0.528	8.4964	-1.3381	2.0679	0.0488	0.0542	-0.0036	-0.0982	-0.0209	-0.0027	0.3063	0.0241	-0.0279	0.1565	0.0008	0.0068	0.053	-0.0232	0.0338	2.5495	-49.72	-19.9417
12	5.1749	2.8577	0.5768	12.9331	2.9394	2.8308	0.0462	0.0665	-0.0372	-0.0008	0.0862	-0.5102	0.0557	0.3146	-0.1324	0.0593	0.0121	0.0052	0.0863	-0.0063	0.0421	9.9152	-50.2203	-14.3482
13	0.9965	-1.2614	-1.3296	3.0687	2.5848	3.1372	-0.0262	-0.0382	0.0404	0.0324	0.0506	-0.0262	-0.0386	-0.0115	-0.0244	0.023	-0.0001	-0.0002	0.0161	0.0003	0.0403	3.6356	-30.2332	-0.711
14	2.6698	-1.5767	0.5625	3.2455	-0.659	2.2735	-0.0927	-0.165	-0.1758	0.2119	0.0638	0.0961	0.1277	0.043	0.0288	0.0566	-0.0042	0.0233	0.041	0.0097	0.0517	-11.4632	-15.7138	15.5254
15	2.4378	1.6817	-1.7531	2.224	-1.269	1.5198	0.0369	0.0697	0.0974	-0.0924	-0.0313	0.0215	-0.0832	-0.0368	-0.0056	0.0315	0.0075	-0.0019	0.0106	0.0049	0.0462	-7.9944	-1.0574	2.0738
16	1.3141	0.9307	-0.9909	2.2461	-1.1705	1.9452	-0.0303	-0.0066	-0.0088	-0.0649	0.0341	0.0902	0.0717	-0.0661	-0.0038	0.0411	0.0065	-0.0067	0.0225	-0.0029	0.0486	-10.7242	-14.2717	2.5483

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 18
2	X-RAY DIFFRACTION	2	A	19 - 39
3	X-RAY DIFFRACTION	3	A	40 - 56
4	X-RAY DIFFRACTION	4	A	57 - 86
5	X-RAY DIFFRACTION	5	A	87 - 106
6	X-RAY DIFFRACTION	6	A	107 - 121
7	X-RAY DIFFRACTION	7	A	122 - 138
8	X-RAY DIFFRACTION	8	A	139 - 153
9	X-RAY DIFFRACTION	9	B	1 - 15
10	X-RAY DIFFRACTION	10	B	16 - 42
11	X-RAY DIFFRACTION	11	B	43 - 51
12	X-RAY DIFFRACTION	12	B	52 - 63
13	X-RAY DIFFRACTION	13	B	64 - 86
14	X-RAY DIFFRACTION	14	B	87 - 103
15	X-RAY DIFFRACTION	15	B	104 - 121
16	X-RAY DIFFRACTION	16	B	122 - 153

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