PDB-7v5p: The dimeric structure of G80A/H81A myoglobin

ID or keywords:

Entry

Database: PDB / ID: 7v5p

Title

The dimeric structure of G80A/H81A 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: 1.16 Å

Authors

Xie, C. / Nagao, S. / Shibata, N. / Higuchi, Y. / Hirota, S.

Funding support

Japan, 3items

Organization	Grant number	Country
Japan Society for the Promotion of Science (JSPS)	JP21H02060	Japan
Japan Society for the Promotion of Science (JSPS)	JP19K05695	Japan
Japan Science and Technology	JP20338388	Japan

Citation

Journal: Rsc Adv / Year: 2021
Title: Experimental and theoretical study on converting myoglobin into a stable domain-swapped dimer by utilizing a tight hydrogen bond network at the hinge region.
Authors: Xie, C. / Shimoyama, H. / Yamanaka, M. / Nagao, S. / Komori, H. / Shibata, N. / Higuchi, Y. / Shigeta, Y. / Hirota, S.

History

Deposition	Aug 17, 2021	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Jun 29, 2022	Provider: repository / Type: Initial release
Revision 1.1	Nov 29, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_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	7v5p.cif.gz	141.6 KB	Display	PDBx/mmCIF format
PDB format	pdb7v5p.ent.gz	109.9 KB	Display	PDB format
PDBx/mmJSON format	7v5p.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7v5p_validation.pdf.gz	2 MB	Display	wwPDB validaton report
Full document	7v5p_full_validation.pdf.gz	2 MB	Display
Data in XML	7v5p_validation.xml.gz	16.8 KB	Display
Data in CIF	7v5p_validation.cif.gz	24.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/v5/7v5p ftp://data.pdbj.org/pub/pdb/validation_reports/v5/7v5p	HTTPS FTP

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Related structure data

Related structure data	7v5qC 7v5rC 3vm9S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	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) #111 - Mar 2009 Hydrogenase similarity (1) #89 - May 2007 Aconitase and Iron Regulatory Protein 1 similarity (1) #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

35.1 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)	57.527, 62.735, 83.355
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: 16930.471 Da / Num. of mol.: 2 / Mutation: G80A, H81A 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: Chemical	ChemComp-O / OXYGEN ATOM Mass: 15.999 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: O / Feature type: SUBJECT OF INVESTIGATION
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 316 / 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: 2.23 Å³/Da / Density % sol: 44.75 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.1 M Sodium acetate, 0.1 M Tris-HCl, 10% (w/v) PEG 6,000

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
Detector	Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 26, 2018
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.16→47.35 Å / Num. obs: 101566 / % possible obs: 97 % / Redundancy: 6.4 % / CC_1/2: 0.999 / R_merge(I) obs: 0.034 / Net I/σ(I): 23.1
Reflection shell	Resolution: 1.16→1.18 Å / Num. unique obs: 4675 / CC_1/2: 0.893

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
XDS		data reduction
SCALA		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3VM9

3vm9

Resolution: 1.16→41.71 Å / Cor.coef. F_o:F_c: 0.966 / Cor.coef. F_o:F_c free: 0.965 / SU B: 0.923 / SU ML: 0.028 / Cross valid method: THROUGHOUT / ESU R: 0.042 / ESU R Free: 0.042 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.20562	5098	5 %	RANDOM
R_work	0.19651	-	-	-
obs	0.19697	96318	96.73 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 19.062 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.66 Å²	0 Å²	0 Å²
2-	-	-0.23 Å²	0 Å²
3-	-	-	-0.43 Å²

Refinement step

Cycle: 1 / Resolution: 1.16→41.71 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2390	0	88	316	2794

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.013	2542
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	2436
X-RAY DIFFRACTION	r_angle_refined_deg	1.369	1.696	3446
X-RAY DIFFRACTION	r_angle_other_deg	1.482	1.621	5634
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.836	5	304
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.905	24.63	108
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.406	15	456
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	7.678	15	4
X-RAY DIFFRACTION	r_chiral_restr	0.072	0.2	310
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	2854
X-RAY DIFFRACTION	r_gen_planes_other	0.005	0.02	538
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
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
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: 4573 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.12 Å / Weight position: 0.05

Dom-ID	Auth asym-ID
1	A
2	B

LS refinement shell

Resolution: 1.16→1.19 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.266	379	-
R_work	0.245	6650	-
obs	-	-	91.89 %

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	1.3007	2.844	-1.1581	6.511	-3.6279	5.4065	0.0006	0.0291	0.0159	0.0206	0.1013	0.0729	-0.2387	-0.2534	-0.1019	0.091	0.0674	-0.0148	0.0569	0.003	0.0316	-0.8693	8.8122	-4.9498
2	3.0601	-0.2053	0.8817	0.7245	-0.1619	1.6955	0.0064	-0.1207	-0.0247	-0.0679	-0.0078	0.0379	0.1527	-0.1194	0.0015	0.0409	0.0027	0.0264	0.0314	0.0061	0.0449	7.2433	-0.671	11.0598
3	2.3369	2.8365	-1.8778	5.9844	-3.84	5.4643	0.0076	-0.2224	-0.0627	0.1747	-0.1754	-0.1782	-0.0785	0.3261	0.1677	0.0348	0.0122	0.0101	0.0623	0.0112	0.0312	10.5521	2.4811	23.0133
4	0.3956	-0.3357	0.2076	4.0146	-2.838	2.916	-0.0283	-0.0243	-0.02	-0.0137	-0.0017	-0.0238	0.1014	-0.049	0.03	0.0224	0.0006	0.0139	0.0503	0.0008	0.0554	1.6494	7.689	9.3488
5	0.6727	0.2483	-0.4082	2.2365	0.4141	3.2196	-0.0483	0.0034	0.0018	-0.2271	0.0002	-0.0902	0.1925	0.1998	0.0481	0.0627	-0.0088	0.0265	0.0534	-0.0004	0.0174	6.1464	36.4857	-12.7939
6	6.0056	-2.5608	-3.1262	3.7306	2.4498	5.6179	-0.1272	-0.4466	0.1146	0.1327	0.1891	0.106	-0.153	-0.0946	-0.0619	0.0453	0.0115	0.0042	0.0841	-0.0001	0.017	-3.6825	46.9119	2.7961
7	1.7208	-1.1425	-2.0422	2.9392	1.7682	4.6307	0.0172	-0.0589	0.0323	-0.0191	-0.0073	-0.082	-0.0559	0.095	-0.0099	0.0256	-0.0199	-0.0059	0.0626	-0.0004	0.0287	4.177	36.5998	2.7636
8	8.6845	-0.4162	-0.3241	14.1523	-2.7143	0.5463	-0.0283	-0.0112	-0.371	0.3699	-0.2066	-1.0988	-0.025	0.0561	0.2349	0.3063	0.098	0.0076	0.0924	0.0213	0.1095	12.6974	29.8798	-12.2882
9	1.9007	-1.3107	1.732	2.9062	-1.1695	1.9752	0.0362	-0.0609	0.0091	0.0052	-0.0491	-0.0579	0.1056	-0.0227	0.0129	0.0444	-0.0342	0.0135	0.0701	-0.0074	0.01	-3.6937	34.2415	8.9514
10	2.8153	1.4055	-0.944	2.5362	-0.2489	1.4898	-0.0052	-0.04	0.1807	-0.1708	0.0445	0.1268	-0.0535	-0.0119	-0.0394	0.0412	-0.0244	-0.0185	0.0253	0.0042	0.0292	-4.8056	46.7576	-6.4527
11	3.0935	-4.5475	1.213	7.457	-0.5663	5.2919	0.0475	0.0757	0.0405	-0.138	-0.0434	0.0377	-0.434	0.0678	-0.0041	0.2056	-0.0223	0.0193	0.0136	0.0126	0.0234	-0.7764	48.2224	-19.8778
12	3.9852	1.4739	-0.3036	10.9815	-2.9689	3.6541	0.1168	0.0158	-0.0013	-0.2012	-0.0039	0.4226	-0.174	-0.2326	-0.1128	0.088	0.0099	-0.0323	0.0472	0.0258	0.0451	-9.6137	50.5453	-14.4713
13	0.8058	-1.0974	1.2405	3.0034	-2.0339	2.5711	-0.0483	-0.0214	-0.0414	0.0002	0.0452	0.0281	0.0244	0.0919	0.0031	0.0264	0.0098	0.0012	0.0389	0.0216	0.0379	-3.5121	30.3363	-0.9332
14	4.3094	-3.024	1.1314	4.9474	-1.7008	4.6846	-0.2559	-0.1803	0.1792	0.5159	0.154	-0.2144	-0.3358	-0.1407	0.1019	0.0717	0.0139	-0.031	0.0269	-0.0243	0.0387	9.0977	17.5433	17.1562
15	1.0251	0.2379	0.6718	1.7791	0.3842	1.4013	0.0229	0.0682	-0.1005	-0.2646	-0.0262	-0.0973	-0.025	0.0035	0.0033	0.0469	0.0149	0.0178	0.0366	-0.0095	0.0518	8.76	3.6594	0.4591
16	1.8899	1.0846	1.1814	4.0378	0.5771	2.7734	0.0003	-0.0709	0.0856	-0.0319	-0.1109	-0.3467	-0.2032	0.0445	0.1106	0.028	-0.0015	0.0094	0.0193	0.011	0.0708	13.0062	19.1381	7.4266

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 - 49
4	X-RAY DIFFRACTION	4	A	50 - 87
5	X-RAY DIFFRACTION	5	A	88 - 106
6	X-RAY DIFFRACTION	6	A	107 - 122
7	X-RAY DIFFRACTION	7	A	123 - 145
8	X-RAY DIFFRACTION	8	A	146 - 153
9	X-RAY DIFFRACTION	9	B	1 - 15
10	X-RAY DIFFRACTION	10	B	16 - 39
11	X-RAY DIFFRACTION	11	B	40 - 50
12	X-RAY DIFFRACTION	12	B	51 - 63
13	X-RAY DIFFRACTION	13	B	64 - 86
14	X-RAY DIFFRACTION	14	B	87 - 99
15	X-RAY DIFFRACTION	15	B	100 - 133
16	X-RAY DIFFRACTION	16	B	134 - 153

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