PDB-6spi: A4V MUTANT OF HUMAN SOD1 WITH EBSELEN DERIVATIVE 4

ID or keywords:

Entry

Database: PDB / ID: 6spi

Title

A4V MUTANT OF HUMAN SOD1 WITH EBSELEN DERIVATIVE 4

Components

Superoxide dismutase [Cu-Zn]

Keywords

OXIDOREDUCTASE / A4V SOD1 mutant / ebselen / ebselen derivatives

Function / homology

Function and homology information

action potential initiation / neurofilament cytoskeleton organization / protein phosphatase 2B binding / regulation of organ growth / relaxation of vascular associated smooth muscle / anterograde axonal transport / positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / response to superoxide / regulation of T cell differentiation in thymus / peripheral nervous system myelin maintenance ...action potential initiation / neurofilament cytoskeleton organization / protein phosphatase 2B binding / regulation of organ growth / relaxation of vascular associated smooth muscle / anterograde axonal transport / positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / response to superoxide / regulation of T cell differentiation in thymus / peripheral nervous system myelin maintenance / retina homeostasis / auditory receptor cell stereocilium organization / hydrogen peroxide biosynthetic process / retrograde axonal transport / superoxide anion generation / myeloid cell homeostasis / regulation of GTPase activity / superoxide metabolic process / muscle cell cellular homeostasis / superoxide dismutase / heart contraction / Detoxification of Reactive Oxygen Species / superoxide dismutase activity / negative regulation of reproductive process / negative regulation of developmental process / transmission of nerve impulse / regulation of multicellular organism growth / ectopic germ cell programmed cell death / response to axon injury / neuronal action potential / ovarian follicle development / positive regulation of phagocytosis / axon cytoplasm / glutathione metabolic process / embryo implantation / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / removal of superoxide radicals / dendrite cytoplasm / reactive oxygen species metabolic process / placenta development / thymus development / positive regulation of superoxide anion generation / positive regulation of cytokine production / regulation of mitochondrial membrane potential / determination of adult lifespan / locomotory behavior / sensory perception of sound / response to hydrogen peroxide / mitochondrial intermembrane space / regulation of blood pressure / small GTPase binding / negative regulation of inflammatory response / peroxisome / Platelet degranulation / protein-folding chaperone binding / response to heat / cytoplasmic vesicle / response to ethanol / spermatogenesis / negative regulation of neuron apoptotic process / gene expression / intracellular iron ion homeostasis / positive regulation of MAPK cascade / positive regulation of apoptotic process / mitochondrial matrix / response to xenobiotic stimulus / copper ion binding / neuronal cell body / apoptotic process / protein homodimerization activity / protein-containing complex / mitochondrion / extracellular space / extracellular exosome / extracellular region / zinc ion binding / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.8 Å

Authors

Chantadul, V. / Amporndanai, K. / Wright, G. / Antonyuk, S. / Hasnain, S.

Citation

Journal: Commun Biol / Year: 2020
Title: Ebselen as template for stabilization of A4V mutant dimer for motor neuron disease therapy.
Authors: Chantadul, V. / Wright, G.S.A. / Amporndanai, K. / Shahid, M. / Antonyuk, S.V. / Washbourn, G. / Rogers, M. / Roberts, N. / Pye, M. / O'Neill, P.M. / Hasnain, S.S.

History

Deposition	Sep 1, 2019	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Mar 18, 2020	Provider: repository / Type: Initial release
Revision 1.1	Jan 24, 2024	Group: Advisory / Data collection ...Advisory / 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_unobs_or_zero_occ_atoms / struct_conn / struct_conn_type / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn_type.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
Revision 1.2	Oct 23, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	6spi.cif.gz	349.8 KB	Display	PDBx/mmCIF format
PDB format	pdb6spi.ent.gz	286.3 KB	Display	PDB format
PDBx/mmJSON format	6spi.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	6spi_validation.pdf.gz	3.4 MB	Display	wwPDB validaton report
Full document	6spi_full_validation.pdf.gz	3.5 MB	Display
Data in XML	6spi_validation.xml.gz	68.4 KB	Display
Data in CIF	6spi_validation.cif.gz	87.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/sp/6spi ftp://data.pdbj.org/pub/pdb/validation_reports/sp/6spi	HTTPS FTP

-
Related structure data

Related structure data	6spaC 6sphC 6spjC 6spkC 1uxmS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6foi-2 2c9u-d 6z4m-d 1n18-5 1uxm-1 1sos-4 5yul-4 6a9o-1 3ecu-1 1n18-1 4a7u-d 6z4l-d 5k02-1 1hl5-2 6z4k-d 5k02-10 4mcm-5 1uxl-1 5k02-9 5ytu-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) Search similar-shape structures by Omokage search (details) 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

Related structure data

S: Starting model for refinement

C: citing same article (ref.)

Similar structure data

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#94 - Oct 2007 Superoxide Dismutase similarity (11) #212 - Aug 2017 Glutathione Transferases similarity (1) #233 - May 2019 S-Nitrosylated Hemoglobin similarity (1) #255 - Mar 2021 Cisplatin and DNA similarity (1) #57 - Sep 2004 Catalase similarity (1) #128 - Aug 2010 Interferons similarity (1) #163 - Jul 2013 HIV Capsid similarity (1)

Deposited unit

A: Superoxide dismutase [Cu-Zn]

B: Superoxide dismutase [Cu-Zn]

C: Superoxide dismutase [Cu-Zn]

D: Superoxide dismutase [Cu-Zn]

E: Superoxide dismutase [Cu-Zn]

F: Superoxide dismutase [Cu-Zn]

G: Superoxide dismutase [Cu-Zn]

H: Superoxide dismutase [Cu-Zn]

I: Superoxide dismutase [Cu-Zn]

J: Superoxide dismutase [Cu-Zn]

K: Superoxide dismutase [Cu-Zn]

L: Superoxide dismutase [Cu-Zn]

hetero molecules

198 kDa, 12 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Superoxide dismutase [Cu-Zn]

J: Superoxide dismutase [Cu-Zn]

hetero molecules

defined by author
Evidence: gel filtration
33.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Superoxide dismutase [Cu-Zn]

K: Superoxide dismutase [Cu-Zn]

hetero molecules

defined by author
Evidence: gel filtration
33.2 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: Superoxide dismutase [Cu-Zn]

I: Superoxide dismutase [Cu-Zn]

hetero molecules

defined by author
Evidence: gel filtration
32.8 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

D: Superoxide dismutase [Cu-Zn]

L: Superoxide dismutase [Cu-Zn]

hetero molecules

defined by author
Evidence: gel filtration
33 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

5

E: Superoxide dismutase [Cu-Zn]

G: Superoxide dismutase [Cu-Zn]

hetero molecules

defined by author
Evidence: gel filtration
32.9 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

6

F: Superoxide dismutase [Cu-Zn]

H: Superoxide dismutase [Cu-Zn]

hetero molecules

defined by author
Evidence: gel filtration
33 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	113.526, 194.671, 146.526
Angle α, β, γ (deg.)	90.000, 93.440, 90.000
Int Tables number	5
Space group name H-M	C121

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Component-ID: _ / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / Refine code: _

Dom-ID	Ens-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	GLN	GLN	A	A	1 - 153	2 - 154
2	1	GLN	GLN	B	B	1 - 153	2 - 154
1	2	GLN	GLN	A	A	1 - 153	2 - 154
2	2	GLN	GLN	C	C	1 - 153	2 - 154
1	3	GLN	GLN	A	A	1 - 153	2 - 154
2	3	GLN	GLN	D	D	1 - 153	2 - 154
1	4	GLN	GLN	A	A	1 - 153	2 - 154
2	4	GLN	GLN	E	E	1 - 153	2 - 154
1	5	GLN	GLN	A	A	1 - 153	2 - 154
2	5	GLN	GLN	F	F	1 - 153	2 - 154
1	6	GLN	GLN	A	A	1 - 153	2 - 154
2	6	GLN	GLN	G	G	1 - 153	2 - 154
1	7	GLN	GLN	A	A	1 - 153	2 - 154
2	7	GLN	GLN	H	H	1 - 153	2 - 154
1	8	ILE	ILE	A	A	1 - 151	2 - 152
2	8	ILE	ILE	I	I	1 - 151	2 - 152
1	9	GLN	GLN	A	A	1 - 153	2 - 154
2	9	GLN	GLN	J	J	1 - 153	2 - 154
1	10	GLN	GLN	A	A	1 - 153	2 - 154
2	10	GLN	GLN	K	K	1 - 153	2 - 154
1	11	GLN	GLN	A	A	1 - 153	2 - 154
2	11	GLN	GLN	L	L	1 - 153	2 - 154
1	12	GLN	GLN	B	B	1 - 153	2 - 154
2	12	GLN	GLN	C	C	1 - 153	2 - 154
1	13	GLN	GLN	B	B	1 - 153	2 - 154
2	13	GLN	GLN	D	D	1 - 153	2 - 154
1	14	GLN	GLN	B	B	1 - 153	2 - 154
2	14	GLN	GLN	E	E	1 - 153	2 - 154
1	15	GLN	GLN	B	B	1 - 153	2 - 154
2	15	GLN	GLN	F	F	1 - 153	2 - 154
1	16	GLN	GLN	B	B	1 - 153	2 - 154
2	16	GLN	GLN	G	G	1 - 153	2 - 154
1	17	GLN	GLN	B	B	1 - 153	2 - 154
2	17	GLN	GLN	H	H	1 - 153	2 - 154
1	18	ILE	ILE	B	B	1 - 151	2 - 152
2	18	ILE	ILE	I	I	1 - 151	2 - 152
1	19	GLN	GLN	B	B	1 - 153	2 - 154
2	19	GLN	GLN	J	J	1 - 153	2 - 154
1	20	GLN	GLN	B	B	1 - 153	2 - 154
2	20	GLN	GLN	K	K	1 - 153	2 - 154
1	21	GLN	GLN	B	B	1 - 153	2 - 154
2	21	GLN	GLN	L	L	1 - 153	2 - 154
1	22	GLN	GLN	C	C	1 - 153	2 - 154
2	22	GLN	GLN	D	D	1 - 153	2 - 154
1	23	GLN	GLN	C	C	1 - 153	2 - 154
2	23	GLN	GLN	E	E	1 - 153	2 - 154
1	24	GLN	GLN	C	C	1 - 153	2 - 154
2	24	GLN	GLN	F	F	1 - 153	2 - 154
1	25	GLN	GLN	C	C	1 - 153	2 - 154
2	25	GLN	GLN	G	G	1 - 153	2 - 154
1	26	GLN	GLN	C	C	1 - 153	2 - 154
2	26	GLN	GLN	H	H	1 - 153	2 - 154
1	27	ILE	ILE	C	C	1 - 151	2 - 152
2	27	ILE	ILE	I	I	1 - 151	2 - 152
1	28	GLN	GLN	C	C	1 - 153	2 - 154
2	28	GLN	GLN	J	J	1 - 153	2 - 154
1	29	GLN	GLN	C	C	1 - 153	2 - 154
2	29	GLN	GLN	K	K	1 - 153	2 - 154
1	30	GLN	GLN	C	C	1 - 153	2 - 154
2	30	GLN	GLN	L	L	1 - 153	2 - 154
1	31	GLN	GLN	D	D	1 - 153	2 - 154
2	31	GLN	GLN	E	E	1 - 153	2 - 154
1	32	GLN	GLN	D	D	1 - 153	2 - 154
2	32	GLN	GLN	F	F	1 - 153	2 - 154
1	33	GLN	GLN	D	D	1 - 153	2 - 154
2	33	GLN	GLN	G	G	1 - 153	2 - 154
1	34	GLN	GLN	D	D	1 - 153	2 - 154
2	34	GLN	GLN	H	H	1 - 153	2 - 154
1	35	ILE	ILE	D	D	1 - 151	2 - 152
2	35	ILE	ILE	I	I	1 - 151	2 - 152
1	36	GLN	GLN	D	D	1 - 153	2 - 154
2	36	GLN	GLN	J	J	1 - 153	2 - 154
1	37	GLN	GLN	D	D	1 - 153	2 - 154
2	37	GLN	GLN	K	K	1 - 153	2 - 154
1	38	GLN	GLN	D	D	1 - 153	2 - 154
2	38	GLN	GLN	L	L	1 - 153	2 - 154
1	39	GLN	GLN	E	E	1 - 153	2 - 154
2	39	GLN	GLN	F	F	1 - 153	2 - 154
1	40	GLN	GLN	E	E	1 - 153	2 - 154
2	40	GLN	GLN	G	G	1 - 153	2 - 154
1	41	GLN	GLN	E	E	1 - 153	2 - 154
2	41	GLN	GLN	H	H	1 - 153	2 - 154
1	42	ILE	ILE	E	E	1 - 151	2 - 152
2	42	ILE	ILE	I	I	1 - 151	2 - 152
1	43	GLN	GLN	E	E	1 - 153	2 - 154
2	43	GLN	GLN	J	J	1 - 153	2 - 154
1	44	GLN	GLN	E	E	1 - 153	2 - 154
2	44	GLN	GLN	K	K	1 - 153	2 - 154
1	45	GLN	GLN	E	E	1 - 153	2 - 154
2	45	GLN	GLN	L	L	1 - 153	2 - 154
1	46	GLN	GLN	F	F	1 - 153	2 - 154
2	46	GLN	GLN	G	G	1 - 153	2 - 154
1	47	GLN	GLN	F	F	1 - 153	2 - 154
2	47	GLN	GLN	H	H	1 - 153	2 - 154
1	48	ILE	ILE	F	F	1 - 151	2 - 152
2	48	ILE	ILE	I	I	1 - 151	2 - 152
1	49	GLN	GLN	F	F	1 - 153	2 - 154
2	49	GLN	GLN	J	J	1 - 153	2 - 154
1	50	GLN	GLN	F	F	1 - 153	2 - 154
2	50	GLN	GLN	K	K	1 - 153	2 - 154
1	51	GLN	GLN	F	F	1 - 153	2 - 154
2	51	GLN	GLN	L	L	1 - 153	2 - 154
1	52	GLN	GLN	G	G	1 - 153	2 - 154
2	52	GLN	GLN	H	H	1 - 153	2 - 154
1	53	ILE	ILE	G	G	1 - 151	2 - 152
2	53	ILE	ILE	I	I	1 - 151	2 - 152
1	54	GLN	GLN	G	G	1 - 153	2 - 154
2	54	GLN	GLN	J	J	1 - 153	2 - 154
1	55	GLN	GLN	G	G	1 - 153	2 - 154
2	55	GLN	GLN	K	K	1 - 153	2 - 154
1	56	GLN	GLN	G	G	1 - 153	2 - 154
2	56	GLN	GLN	L	L	1 - 153	2 - 154
1	57	ILE	ILE	H	H	1 - 151	2 - 152
2	57	ILE	ILE	I	I	1 - 151	2 - 152
1	58	GLN	GLN	H	H	1 - 153	2 - 154
2	58	GLN	GLN	J	J	1 - 153	2 - 154
1	59	GLN	GLN	H	H	1 - 153	2 - 154
2	59	GLN	GLN	K	K	1 - 153	2 - 154
1	60	GLN	GLN	H	H	1 - 153	2 - 154
2	60	GLN	GLN	L	L	1 - 153	2 - 154
1	61	ILE	ILE	I	I	1 - 151	2 - 152
2	61	ILE	ILE	J	J	1 - 151	2 - 152
1	62	ILE	ILE	I	I	1 - 151	2 - 152
2	62	ILE	ILE	K	K	1 - 151	2 - 152
1	63	ILE	ILE	I	I	1 - 151	2 - 152
2	63	ILE	ILE	L	L	1 - 151	2 - 152
1	64	GLN	GLN	J	J	1 - 153	2 - 154
2	64	GLN	GLN	K	K	1 - 153	2 - 154
1	65	GLN	GLN	J	J	1 - 153	2 - 154
2	65	GLN	GLN	L	L	1 - 153	2 - 154
1	66	GLN	GLN	K	K	1 - 153	2 - 154
2	66	GLN	GLN	L	L	1 - 153	2 - 154

NCS ensembles :

#1: Protein	Superoxide dismutase [Cu-Zn] / Superoxide dismutase 1 / hSod1 Mass: 15986.812 Da / Num. of mol.: 12 / Mutation: A4V Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SOD1 / Plasmid: pET303C / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P00441, superoxide dismutase
#2: Chemical	ChemComp-LQW / ~{N}-[(4-chlorophenyl)methyl]-2-selanyl-benzamide Mass: 324.664 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C₁₄H₁₂ClNOSe / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Zn
#4: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: SO₄
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 230 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 4.25 Å³/Da / Density % sol: 71.06 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.6 / Details: 100mM Tris-HCl pH 7.8, 2.6 M ammonium sulphate

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
Detector	Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jun 29, 2019 / Details: mirrors
Radiation	Monochromator: Double crystal InSb(111) and InSb(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9795 Å / Relative weight: 1
Reflection	Resolution: 2.8→58.54 Å / Num. obs: 77624 / % possible obs: 99.7 % / Redundancy: 3.1 % / B_iso Wilson estimate: 25.1 Å² / CC_1/2: 0.965 / R_merge(I) obs: 0.202 / R_pim(I) all: 0.136 / R_rim(I) all: 0.245 / Net I/σ(I): 3.7
Reflection shell	Resolution: 2.8→2.86 Å / Redundancy: 3 % / R_merge(I) obs: 0.724 / Num. unique obs: 4567 / CC_1/2: 0.538 / R_pim(I) all: 0.51 / R_rim(I) all: 0.89 / % possible all: 99.7

-
Processing

Software

Name	Version	Classification
REFMAC	5.8.0238	refinement
Aimless	0.7.4	data scaling
PDB_EXTRACT	3.25	data extraction
DIALS		data reduction
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1UXM

1uxm

Resolution: 2.8→58.54 Å / Cor.coef. F_o:F_c: 0.92 / Cor.coef. F_o:F_c free: 0.903 / SU B: 14.759 / SU ML: 0.266 / Cross valid method: THROUGHOUT / ESU R: 0.535 / ESU R Free: 0.299

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2411	3867	5 %	RANDOM
R_work	0.2132	-	-	-
obs	0.2146	73673	99.5 %	-

Solvent computation

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

Displacement parameters

B_iso max: 136.49 Å² / B_iso mean: 32.709 Å² / B_iso min: 2.57 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-2.99 Å²	0 Å²	0 Å²
2-	-	-1.6 Å²	0 Å²
3-	-	-	4.55 Å²

Refinement step

Cycle: final / Resolution: 2.8→58.54 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	13344	0	318	230	13892
B_iso mean	-	-	83.23	18.21	-
Num. residues	-	-	-	-	1836

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.012	13967
X-RAY DIFFRACTION	r_angle_refined_deg	1.353	1.65	18864
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.047	5	1835
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.333	24.459	628
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.004	15	2229
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.481	15	48
X-RAY DIFFRACTION	r_chiral_restr	0.094	0.2	1747
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	10732

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-ID	Dom-ID	Auth asym-ID	Number	Rms dev position (Å)
1	1	A	4620	0.05
1	2	B	4620	0.05
2	1	A	4592	0.06
2	2	C	4592	0.06
3	1	A	4614	0.05
3	2	D	4614	0.05
4	1	A	4611	0.04
4	2	E	4611	0.04
5	1	A	4639	0.05
5	2	F	4639	0.05
6	1	A	4639	0.05
6	2	G	4639	0.05
7	1	A	4612	0.06
7	2	H	4612	0.06
8	1	A	4567	0.06
8	2	I	4567	0.06
9	1	A	4629	0.05
9	2	J	4629	0.05
10	1	A	4634	0.05
10	2	K	4634	0.05
11	1	A	4610	0.05
11	2	L	4610	0.05
12	1	B	4630	0.06
12	2	C	4630	0.06
13	1	B	4658	0.06
13	2	D	4658	0.06
14	1	B	4629	0.06
14	2	E	4629	0.06
15	1	B	4657	0.05
15	2	F	4657	0.05
16	1	B	4669	0.06
16	2	G	4669	0.06
17	1	B	4653	0.05
17	2	H	4653	0.05
18	1	B	4611	0.06
18	2	I	4611	0.06
19	1	B	4678	0.05
19	2	J	4678	0.05
20	1	B	4672	0.05
20	2	K	4672	0.05
21	1	B	4641	0.05
21	2	L	4641	0.05
22	1	C	4634	0.05
22	2	D	4634	0.05
23	1	C	4618	0.05
23	2	E	4618	0.05
24	1	C	4649	0.05
24	2	F	4649	0.05
25	1	C	4639	0.05
25	2	G	4639	0.05
26	1	C	4640	0.05
26	2	H	4640	0.05
27	1	C	4585	0.05
27	2	I	4585	0.05
28	1	C	4637	0.06
28	2	J	4637	0.06
29	1	C	4648	0.05
29	2	K	4648	0.05
30	1	C	4644	0.05
30	2	L	4644	0.05
31	1	D	4601	0.05
31	2	E	4601	0.05
32	1	D	4635	0.04
32	2	F	4635	0.04
33	1	D	4636	0.03
33	2	G	4636	0.03
34	1	D	4621	0.05
34	2	H	4621	0.05
35	1	D	4596	0.03
35	2	I	4596	0.03
36	1	D	4640	0.04
36	2	J	4640	0.04
37	1	D	4647	0.03
37	2	K	4647	0.03
38	1	D	4606	0.05
38	2	L	4606	0.05
39	1	E	4630	0.05
39	2	F	4630	0.05
40	1	E	4616	0.06
40	2	G	4616	0.06
41	1	E	4620	0.05
41	2	H	4620	0.05
42	1	E	4573	0.05
42	2	I	4573	0.05
43	1	E	4626	0.05
43	2	J	4626	0.05
44	1	E	4611	0.05
44	2	K	4611	0.05
45	1	E	4593	0.06
45	2	L	4593	0.06
46	1	F	4671	0.04
46	2	G	4671	0.04
47	1	F	4639	0.06
47	2	H	4639	0.06
48	1	F	4607	0.04
48	2	I	4607	0.04
49	1	F	4655	0.04
49	2	J	4655	0.04
50	1	F	4655	0.05
50	2	K	4655	0.05
51	1	F	4634	0.05
51	2	L	4634	0.05
52	1	G	4651	0.05
52	2	H	4651	0.05
53	1	G	4601	0.04
53	2	I	4601	0.04
54	1	G	4665	0.04
54	2	J	4665	0.04
55	1	G	4663	0.04
55	2	K	4663	0.04
56	1	G	4625	0.05
56	2	L	4625	0.05
57	1	H	4591	0.04
57	2	I	4591	0.04
58	1	H	4647	0.05
58	2	J	4647	0.05
59	1	H	4646	0.04
59	2	K	4646	0.04
60	1	H	4629	0.05
60	2	L	4629	0.05
61	1	I	4644	0.04
61	2	J	4644	0.04
62	1	I	4649	0.04
62	2	K	4649	0.04
63	1	I	4630	0.04
63	2	L	4630	0.04
64	1	J	4669	0.04
64	2	K	4669	0.04
65	1	J	4616	0.05
65	2	L	4616	0.05
66	1	K	4626	0.04
66	2	L	4626	0.04

LS refinement shell

Resolution: 2.8→2.873 Å / R_factor R_free error: 0 / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.4	294	-
R_work	0.347	5386	-
all	-	5680	-
obs	-	-	99.35 %

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi