PDB-3eya: Structural basis for membrane binding and catalytic activation of...

ID or keywords:

Entry

Database: PDB / ID: 3eya

Title

Structural basis for membrane binding and catalytic activation of the peripheral membrane enzyme pyruvate oxidase from Escherichia coli

Components

Pyruvate dehydrogenase [cytochrome]

Keywords

OXIDOREDUCTASE / Pyruvate oxidase / membrane-associated flavoprotein dehydrogenase / interactions with lipids Cell membrane / FAD / Flavoprotein / Lipid-binding / Magnesium / Membrane / Thiamine pyrophosphate

Function / homology

Function and homology information

pyruvate dehydrogenase (quinone) / pyruvate dehydrogenase (quinone) activity / pyruvate catabolic process / thiamine pyrophosphate binding / pyruvate metabolic process / ubiquinone binding / flavin adenine dinucleotide binding / lipid binding / magnesium ion binding / protein-containing complex ...
Similarity search - Function

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 2.5 Å

Authors

Neumann, P. / Weidner, A. / Pech, A. / Stubbs, M.T. / Tittmann, K.

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 2008
Title: Structural basis for membrane binding and catalytic activation of the peripheral membrane enzyme pyruvate oxidase from Escherichia coli.
Authors: Neumann, P. / Weidner, A. / Pech, A. / Stubbs, M.T. / Tittmann, K.

History

Deposition	Oct 20, 2008	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Nov 4, 2008	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 2.0	Aug 18, 2021	Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary Category: atom_site / chem_comp ...atom_site / chem_comp / database_2 / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_conn / struct_site / struct_site_gen Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _entity.pdbx_description / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_validate_close_contact.auth_atom_id_2 / _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.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id / _struct_site_gen.auth_comp_id / _struct_site_gen.label_comp_id
Revision 2.1	Nov 1, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	3eya.cif.gz	2.4 MB	Display	PDBx/mmCIF format
PDB format	pdb3eya.ent.gz	2 MB	Display	PDB format
PDBx/mmJSON format	3eya.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ey/3eya ftp://data.pdbj.org/pub/pdb/validation_reports/ey/3eya	HTTPS FTP

-
Related structure data

Related structure data	3ey9SC 1pow S: Starting model for refinement C: citing same article (ref.)
Similar structure data	3iae-1 4qq8-d 4qpz-2 4qpz-1 3iaf-d 2uz1-d 2ag1-d 3lq1-3 2ag0-d 3d7k-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) 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

3ey9SC

1pow

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	#263 - Nov 2021 Acetohydroxyacid Synthase similarity (11) #213 - Sep 2017 Sirtuins similarity (1) #153 - Sep 2012 Pyruvate Dehydrogenase Complex similarity (2) #154 - Oct 2012 Citric Acid Cycle similarity (1)

Deposited unit

A: Pyruvate dehydrogenase [cytochrome]

B: Pyruvate dehydrogenase [cytochrome]

C: Pyruvate dehydrogenase [cytochrome]

D: Pyruvate dehydrogenase [cytochrome]

E: Pyruvate dehydrogenase [cytochrome]

F: Pyruvate dehydrogenase [cytochrome]

G: Pyruvate dehydrogenase [cytochrome]

H: Pyruvate dehydrogenase [cytochrome]

I: Pyruvate dehydrogenase [cytochrome]

J: Pyruvate dehydrogenase [cytochrome]

K: Pyruvate dehydrogenase [cytochrome]

L: Pyruvate dehydrogenase [cytochrome]

hetero molecules

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

1

A: Pyruvate dehydrogenase [cytochrome]

B: Pyruvate dehydrogenase [cytochrome]

C: Pyruvate dehydrogenase [cytochrome]

D: Pyruvate dehydrogenase [cytochrome]

hetero molecules

defined by author&software
244 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

E: Pyruvate dehydrogenase [cytochrome]

F: Pyruvate dehydrogenase [cytochrome]

G: Pyruvate dehydrogenase [cytochrome]

H: Pyruvate dehydrogenase [cytochrome]

hetero molecules

defined by author&software
244 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

I: Pyruvate dehydrogenase [cytochrome]

J: Pyruvate dehydrogenase [cytochrome]

K: Pyruvate dehydrogenase [cytochrome]

L: Pyruvate dehydrogenase [cytochrome]

hetero molecules

defined by author&software
244 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	203.243, 207.051, 214.542
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Refine code	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	1	2	A	A	5 - 282	5 - 282
2	1	1	2	B	B	5 - 282	5 - 282
3	1	1	2	C	C	5 - 282	5 - 282
4	1	1	2	D	D	5 - 282	5 - 282
5	1	1	2	E	E	5 - 282	5 - 282
6	1	1	2	F	F	5 - 282	5 - 282
7	1	1	2	G	G	5 - 282	5 - 282
8	1	1	2	H	H	5 - 282	5 - 282
9	1	1	2	I	I	5 - 282	5 - 282
10	1	1	2	J	J	5 - 282	5 - 282
11	1	1	2	K	K	5 - 282	5 - 282
12	1	1	2	L	L	5 - 282	5 - 282
1	2	1	2	A	A	288 - 464	288 - 464
2	2	1	2	B	B	288 - 464	288 - 464
3	2	1	2	C	C	288 - 464	288 - 464
4	2	1	2	D	D	288 - 464	288 - 464
5	2	1	2	E	E	288 - 464	288 - 464
6	2	1	2	F	F	288 - 464	288 - 464
7	2	1	2	G	G	288 - 464	288 - 464
8	2	1	2	H	H	288 - 464	288 - 464
9	2	1	2	I	I	288 - 464	288 - 464
10	2	1	2	J	J	288 - 464	288 - 464
11	2	1	2	K	K	288 - 464	288 - 464
12	2	1	2	L	L	288 - 464	288 - 464
1	3	1	2	A	A	486 - 527	486 - 527
2	3	1	2	B	B	486 - 527	486 - 527
3	3	1	2	C	C	486 - 527	486 - 527
4	3	1	2	D	D	486 - 527	486 - 527
5	3	1	2	E	E	486 - 527	486 - 527
6	3	1	2	F	F	486 - 527	486 - 527
7	3	1	2	G	G	486 - 527	486 - 527
8	3	1	2	H	H	486 - 527	486 - 527
9	3	1	2	I	I	486 - 527	486 - 527
10	3	1	2	J	J	486 - 527	486 - 527
11	3	1	2	K	K	486 - 527	486 - 527
12	3	1	2	L	L	486 - 527	486 - 527
1	1	2	6	A	A	611 - 613	611 - 613
2	1	2	6	B	B	611 - 613	611 - 613
3	1	2	6	C	C	611 - 613	611 - 613
4	1	2	6	D	D	611 - 613	611 - 613
5	1	2	6	E	E	611 - 613	611 - 613
6	1	2	6	F	F	611 - 613	611 - 613
7	1	2	6	G	G	611 - 613	611 - 613
8	1	2	6	H	H	611 - 613	611 - 613
9	1	2	6	I	I	611 - 613	611 - 613
10	1	2	6	J	J	611 - 613	611 - 613
11	1	2	6	K	K	611 - 613	611 - 613
12	1	2	6	L	L	611 - 613	611 - 613
1	1	3	6	A	A	1 - 4	1 - 4
2	1	3	6	B	B	1 - 4	1 - 4
3	1	3	6	C	C	1 - 4	1 - 4
4	1	3	6	D	D	1 - 4	1 - 4
5	1	3	6	E	E	1 - 4	1 - 4
6	1	3	6	F	F	1 - 4	1 - 4
7	1	3	6	G	G	1 - 4	1 - 4
8	1	3	6	H	H	1 - 4	1 - 4
9	1	3	6	I	I	1 - 4	1 - 4
10	1	3	6	J	J	1 - 4	1 - 4
11	1	3	6	K	K	1 - 4	1 - 4
12	1	3	6	L	L	1 - 4	1 - 4
1	2	3	6	A	A	465 - 485	465 - 485
2	2	3	6	B	B	465 - 485	465 - 485
3	2	3	6	C	C	465 - 485	465 - 485
4	2	3	6	D	D	465 - 485	465 - 485
5	2	3	6	E	E	465 - 485	465 - 485
6	2	3	6	F	F	465 - 485	465 - 485
7	2	3	6	G	G	465 - 485	465 - 485
8	2	3	6	H	H	465 - 485	465 - 485
9	2	3	6	I	I	465 - 485	465 - 485
10	2	3	6	J	J	465 - 485	465 - 485
11	2	3	6	K	K	465 - 485	465 - 485
12	2	3	6	L	L	465 - 485	465 - 485
1	3	3	6	A	A	535 - 540	535 - 540
2	3	3	6	B	B	535 - 540	535 - 540
3	3	3	6	C	C	535 - 540	535 - 540
4	3	3	6	D	D	535 - 540	535 - 540
5	3	3	6	E	E	535 - 540	535 - 540
6	3	3	6	F	F	535 - 540	535 - 540
7	3	3	6	G	G	535 - 540	535 - 540
8	3	3	6	H	H	535 - 540	535 - 540
9	3	3	6	I	I	535 - 540	535 - 540
10	3	3	6	J	J	535 - 540	535 - 540
11	3	3	6	K	K	535 - 540	535 - 540
12	3	3	6	L	L	535 - 540	535 - 540
1	1	4	4	A	A	528 - 533	528 - 533
2	1	4	4	B	B	528 - 533	528 - 533
3	1	4	4	C	C	528 - 533	528 - 533
4	1	4	4	D	D	528 - 533	528 - 533
5	1	4	4	E	E	528 - 533	528 - 533
6	1	4	4	F	F	528 - 533	528 - 533
7	1	4	4	G	G	528 - 533	528 - 533
8	1	4	4	H	H	528 - 533	528 - 533
9	1	4	4	I	I	528 - 533	528 - 533
10	1	4	4	J	J	528 - 533	528 - 533
11	1	4	4	K	K	528 - 533	528 - 533
12	1	4	4	L	L	528 - 533	528 - 533

NCS ensembles :

ID
1
2
3
4

-
Protein , 1 types, 12 molecules ABCDEFGHIJKL

#1: Protein	Pyruvate dehydrogenase [cytochrome] / Pyruvate oxidase / POX / Pyruvate dehydrogenase / Alpha-peptide Mass: 59455.125 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: poxB, b0871, JW0855 / Plasmid: pYYC102 / Production host: Escherichia coli (E. coli) / Strain (production host): ZK126 / References: UniProt: P07003, EC: 1.2.2.2

#1: Protein

Pyruvate dehydrogenase [cytochrome] / Pyruvate oxidase / POX / Pyruvate dehydrogenase / Alpha-peptide

Mass: 59455.125 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Escherichia coli (E. coli) / Gene: poxB, b0871, JW0855 / Plasmid: pYYC102 / Production host:

Escherichia coli (E. coli) / Strain (production host): ZK126 / References: UniProt: P07003, EC: 1.2.2.2

-
Non-polymers , 5 types, 1401 molecules

#2: Chemical	ChemComp-TPP / THIAMINE DIPHOSPHATE Mass: 425.314 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C₁₂H₁₉N₄O₇P₂S
#3: Chemical	ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE Mass: 785.550 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C₂₇H₃₃N₉O₁₅P₂ / Comment: FAD*YM
#4: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Mg
#5: Chemical	... ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 36 / Source method: obtained synthetically / Formula: PO₄
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1329 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 3.16 Å³/Da / Density % sol: 61.12 % / Mosaicity: 0.431 °
Crystal grow	Temperature: 286 K / Method: vapor diffusion, hanging drop / pH: 6.2 Details: 0.1M MES/NaOH, 20-35% 2-methyl-2,4-pentanediol (MPD), pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 286K

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 22, 2007 / Details: mirrors
Radiation	Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9184 Å / Relative weight: 1
Reflection	Resolution: 2.5→84.82 Å / Num. obs: 309368 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.2 % / B_iso Wilson estimate: 52.76 Å² / R_merge(I) obs: 0.132 / R_sym value: 0.132 / Net I/σ(I): 4.722
Reflection shell	Resolution: 2.5→2.64 Å / Redundancy: 4.6 % / R_merge(I) obs: 0.704 / Mean I/σ(I) obs: 1.1 / Num. measured all: 204910 / Num. unique all: 44197 / R_sym value: 0.704 / % possible all: 98.4

-
Phasing

Phasing

Method:

molecular replacement

Phasing MR

Model details: Phaser MODE: MR_AUTO

	Highest resolution	Lowest resolution
Rotation	3.15 Å	19.86 Å
Translation	3.15 Å	19.86 Å

-
Processing

Software

Name	Version	Classification
MOSFLM		data reduction
SCALA	3.2.21	data scaling
PHASER		phasing
REFMAC		refinement
PDB_EXTRACT	3.006	data extraction
MAR345dtb		data collection

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3EY9

3ey9

Resolution: 2.5→30 Å / Cor.coef. F_o:F_c: 0.951 / Cor.coef. F_o:F_c free: 0.944 / WR_factor R_free: 0.2 / WR_factor R_work: 0.187 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.892 / SU B: 12.86 / SU ML: 0.15 / SU R Cruickshank DPI: 0.355 / SU R_free: 0.213 / Isotropic thermal model: Isotropic, TLS refinement / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.344 / ESU R Free: 0.208 / Stereochemistry target values: MAXIMUM LIKELIHOOD

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.198	15217	4.9 %	RANDOM
R_work	0.183	-	-	-
all	0.184	308673	-	-
obs	0.184	308673	99.62 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso max: 173.67 Å² / B_iso mean: 63.922 Å² / B_iso min: 30.08 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.73 Å²	0 Å²	0 Å²
2-	-	-1.08 Å²	0 Å²
3-	-	-	-0.64 Å²

Refine analyze

	Free	Obs
Luzzati coordinate error	0.208 Å	0.344 Å
Luzzati d res low	-	2.5 Å
Luzzati sigma a	0.15 Å	0.208 Å

Refinement step

Cycle: LAST / Resolution: 2.5→30 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	47891	0	1140	1329	50360

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.013	0.022	50096
X-RAY DIFFRACTION	r_angle_refined_deg	1.467	1.988	68168
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.596	5	6366
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.063	24.129	2073
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.179	15	8199
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	22.895	15	287
X-RAY DIFFRACTION	r_chiral_restr	0.095	0.2	7579
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.021	37662
X-RAY DIFFRACTION	r_mcbond_it	0.944	2	31306
X-RAY DIFFRACTION	r_mcangle_it	1.723	3	50203
X-RAY DIFFRACTION	r_scbond_it	1.298	2	18790
X-RAY DIFFRACTION	r_scangle_it	2.072	3	17908

Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	A	1944	TIGHT POSITIONAL	0.02	0.02
1	B	1944	TIGHT POSITIONAL	0.01	0
1	C	1944	TIGHT POSITIONAL	0.02	0
1	D	1944	TIGHT POSITIONAL	0.02	0
1	E	1944	TIGHT POSITIONAL	0.01	0
1	F	1944	TIGHT POSITIONAL	0.01	0
1	G	1944	TIGHT POSITIONAL	0.01	0
1	H	1944	TIGHT POSITIONAL	0.01	0
1	I	1944	TIGHT POSITIONAL	0.01	0
1	J	1944	TIGHT POSITIONAL	0.01	0
1	K	1944	TIGHT POSITIONAL	0.02	0
1	L	1944	TIGHT POSITIONAL	0.02	0
1	A	1636	MEDIUM POSITIONAL	0.02	0.4
1	B	1636	MEDIUM POSITIONAL	0.01	0
1	C	1636	MEDIUM POSITIONAL	0.02	0
1	D	1636	MEDIUM POSITIONAL	0.02	0
1	E	1636	MEDIUM POSITIONAL	0.01	0
1	F	1636	MEDIUM POSITIONAL	0.01	0
1	G	1636	MEDIUM POSITIONAL	0.01	0
1	H	1636	MEDIUM POSITIONAL	0.01	0
1	I	1636	MEDIUM POSITIONAL	0.01	0
1	J	1636	MEDIUM POSITIONAL	0.01	0
1	K	1636	MEDIUM POSITIONAL	0.02	0
1	L	1636	MEDIUM POSITIONAL	0.02	0
1	A	1944	TIGHT THERMAL	0.19	0.5
1	B	1944	TIGHT THERMAL	0.15	0
1	C	1944	TIGHT THERMAL	0.16	0
1	D	1944	TIGHT THERMAL	0.16	0
1	E	1944	TIGHT THERMAL	0.12	0
1	F	1944	TIGHT THERMAL	0.12	0
1	G	1944	TIGHT THERMAL	0.12	0
1	H	1944	TIGHT THERMAL	0.15	0
1	I	1944	TIGHT THERMAL	0.13	0
1	J	1944	TIGHT THERMAL	0.13	0
1	K	1944	TIGHT THERMAL	0.16	0
1	L	1944	TIGHT THERMAL	0.18	0
1	A	1636	MEDIUM THERMAL	0.18	2
1	B	1636	MEDIUM THERMAL	0.14	0
1	C	1636	MEDIUM THERMAL	0.15	0
1	D	1636	MEDIUM THERMAL	0.17	0
1	E	1636	MEDIUM THERMAL	0.12	0
1	F	1636	MEDIUM THERMAL	0.12	0
1	G	1636	MEDIUM THERMAL	0.13	0
1	H	1636	MEDIUM THERMAL	0.13	0
1	I	1636	MEDIUM THERMAL	0.13	0
1	J	1636	MEDIUM THERMAL	0.13	0
1	K	1636	MEDIUM THERMAL	0.16	0
1	L	1636	MEDIUM THERMAL	0.18	0
2	A	80	LOOSE POSITIONAL	0.1	5
2	B	80	LOOSE POSITIONAL	0.1	0.06
2	C	80	LOOSE POSITIONAL	0.1	0
2	D	80	LOOSE POSITIONAL	0.1	0
2	E	80	LOOSE POSITIONAL	0.14	0
2	F	80	LOOSE POSITIONAL	0.11	0
2	G	80	LOOSE POSITIONAL	0.14	0
2	H	80	LOOSE POSITIONAL	0.12	0
2	I	80	LOOSE POSITIONAL	0.09	0
2	J	80	LOOSE POSITIONAL	0.12	0
2	K	80	LOOSE POSITIONAL	0.11	0
2	L	80	LOOSE POSITIONAL	0.09	0
2	A	80	LOOSE THERMAL	8.48	10
2	B	80	LOOSE THERMAL	2.67	0.12
2	C	80	LOOSE THERMAL	4.43	0
2	D	80	LOOSE THERMAL	5.71	0
2	E	80	LOOSE THERMAL	9.92	0
2	F	80	LOOSE THERMAL	6.34	0
2	G	80	LOOSE THERMAL	8.76	0
2	H	80	LOOSE THERMAL	3.53	0
2	I	80	LOOSE THERMAL	1.71	0
2	J	80	LOOSE THERMAL	4.44	0
2	K	80	LOOSE THERMAL	5.81	0
2	L	80	LOOSE THERMAL	5.71	0
3	A	78	LOOSE POSITIONAL	0.6	5
3	B	78	LOOSE POSITIONAL	0.85	0.06
3	C	78	LOOSE POSITIONAL	1.67	0
3	D	78	LOOSE POSITIONAL	0.93	0
3	E	78	LOOSE POSITIONAL	0.56	0
3	F	78	LOOSE POSITIONAL	0.73	0
3	G	78	LOOSE POSITIONAL	0.62	0
3	H	78	LOOSE POSITIONAL	0.87	0
3	I	78	LOOSE POSITIONAL	0.72	0
3	J	78	LOOSE POSITIONAL	0.73	0
3	K	78	LOOSE POSITIONAL	0.94	0
3	L	78	LOOSE POSITIONAL	0.69	0
3	A	78	LOOSE THERMAL	3.45	10
3	B	78	LOOSE THERMAL	2.67	0.13
3	C	78	LOOSE THERMAL	2.3	0
3	D	78	LOOSE THERMAL	3.61	0
3	E	78	LOOSE THERMAL	2.13	0
3	F	78	LOOSE THERMAL	2.07	0
3	G	78	LOOSE THERMAL	2.28	0
3	H	78	LOOSE THERMAL	3.47	0
3	I	78	LOOSE THERMAL	2.69	0
3	J	78	LOOSE THERMAL	2.74	0
3	K	78	LOOSE THERMAL	3.63	0
3	L	78	LOOSE THERMAL	5.02	0
4	A	45	MEDIUM POSITIONAL	0.43	0.4
4	B	45	MEDIUM POSITIONAL	0.66	0.01
4	C	45	MEDIUM POSITIONAL	0.43	0
4	D	45	MEDIUM POSITIONAL	1.34	0
4	E	45	MEDIUM POSITIONAL	0.46	0
4	F	45	MEDIUM POSITIONAL	0.49	0
4	G	45	MEDIUM POSITIONAL	0.49	0
4	H	45	MEDIUM POSITIONAL	0.34	0
4	I	45	MEDIUM POSITIONAL	0.39	0
4	J	45	MEDIUM POSITIONAL	0.48	0
4	K	45	MEDIUM POSITIONAL	0.42	0
4	L	45	MEDIUM POSITIONAL	0.44	0
4	A	45	MEDIUM THERMAL	3.27	2
4	B	45	MEDIUM THERMAL	0.64	0.04
4	C	45	MEDIUM THERMAL	0.6	0
4	D	45	MEDIUM THERMAL	1.04	0
4	E	45	MEDIUM THERMAL	0.52	0
4	F	45	MEDIUM THERMAL	0.55	0
4	G	45	MEDIUM THERMAL	0.57	0
4	H	45	MEDIUM THERMAL	0.72	0
4	I	45	MEDIUM THERMAL	0.53	0
4	J	45	MEDIUM THERMAL	0.55	0
4	K	45	MEDIUM THERMAL	0.89	0
4	L	45	MEDIUM THERMAL	0.58	0

LS refinement shell

Resolution: 2.5→2.564 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.292	1089	-
R_work	0.275	21136	-
all	-	22225	-
obs	-	-	98.21 %

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	1.2984	0.101	0.1857	2.1108	-0.5812	1.0513	0.0425	-0.1876	0.0369	0.0974	-0.0367	0.186	-0.1059	-0.0918	-0.0057	-0.2714	-0.0071	0.0905	-0.1833	-0.0508	-0.2345	23.901	-24.173	-11.211
2	1.9188	-0.2782	0.665	1.4976	-0.6711	1.4756	0.0415	0.0494	-0.3997	-0.4727	-0.0657	0.0484	0.4334	0.0118	0.0241	-0.0719	0.0165	0.0958	-0.2263	-0.0518	-0.0765	29.541	-57.96	-27.833
3	1.7035	0.1609	0.2307	2.6361	-0.3553	1.6248	0.0188	-0.3274	-0.2149	0.2465	-0.1161	-0.1508	0.1246	0.1751	0.0972	-0.2619	0.0172	0.089	-0.0831	0.0739	-0.1422	40.147	-49.49	-1.04
4	1.2697	0.9662	-0.1498	1.7923	0.3688	2.0993	0.0502	-0.1628	-0.1273	-0.0569	-0.1621	-0.4141	0.0202	0.4178	0.1118	-0.2909	0.0001	0.0689	-0.0879	0.0784	-0.1064	55.309	-26.239	-19.716
5	1.6608	0.0012	0.4034	2.1203	-0.2183	2.3364	0.0287	-0.3822	0.5268	0.4809	-0.1239	-0.1846	-0.5732	0.1369	0.0952	0.0996	-0.2077	0.0198	-0.0441	-0.1151	0.0535	49.293	7.893	-3.838
6	1.8609	0.5392	0.1303	3.2797	-0.9925	3.1081	0.0896	-0.4847	-0.0384	0.741	-0.2434	-0.254	-0.3474	0.2746	0.1537	-0.0248	-0.1626	-0.0414	0.095	0.0037	-0.1897	49.02	-19.36	10.12
7	1.4986	0.7551	-0.3364	1.0403	-0.2026	2.0139	0.1064	-0.0022	0.3538	-0.0494	-0.0906	0.0835	-0.3861	-0.0272	-0.0157	-0.153	0.011	0.0734	-0.2477	-0.0208	-0.1239	32.191	-0.776	-31.054
8	1.7313	0.4637	-0.2595	2.0906	-0.5962	1.6822	0.1119	0.0197	0.1268	-0.2254	-0.3554	-0.6724	0.0528	0.3962	0.2435	-0.1692	-0.0246	0.1928	-0.0256	0.1695	0.1287	68.716	-4.488	-41.001
9	2.6279	0.4372	-0.0871	2.3254	-0.6405	2.5736	0.0298	0.4282	0.2303	-0.5479	-0.0619	-0.0396	0.0288	0.0307	0.0322	0.0297	0.0251	0.1334	-0.0885	0.0838	-0.1592	44.774	-1.313	-59.673
10	1.872	0.0133	0.4473	1.1684	-0.4387	1.0522	0.0379	0.2091	-0.1673	-0.4356	-0.1067	-0.0795	0.1369	0.1021	0.0688	-0.109	0.0537	0.0844	-0.2068	-0.0272	-0.2113	36.114	-30.006	-44.762
11	1.4396	-0.14	0.2519	2.113	-0.9243	1.8292	0.0946	-0.0374	-0.092	-0.1522	0.0481	0.6307	0.0081	-0.4652	-0.1428	-0.2125	0.0023	-0.0562	-0.1027	-0.0636	0.021	-0.248	-26.709	-33.939
12	2.4845	0.0072	0.4524	2.1739	-0.3317	2.3085	-0.01	0.3823	0.2009	-0.5083	-0.0234	0.1741	-0.1336	-0.0749	0.0335	0.0128	0.071	-0.0734	-0.136	-0.0074	-0.1819	14.002	-11.818	-56.893
13	1.6868	0.3448	-0.4639	1.714	0.7082	2.5629	0.0387	-0.1084	-0.2183	0.1438	0.1338	-0.3435	0.1787	0.3716	-0.1726	-0.117	0.0882	-0.078	-0.1233	-0.0465	-0.0664	1.559	28.404	-21.682
14	2.805	0.6834	0.4893	2.4579	0.449	2.5568	0.0051	0.4805	0.2326	-0.7451	0.1524	-0.3838	-0.557	0.6564	-0.1574	0.2635	-0.1331	0.1895	0.1069	-0.0103	-0.039	6.585	44.767	-55.718
15	3.6452	0.3647	0.0822	2.6519	0.7081	3.8112	-0.008	0.0957	0.2414	-0.1058	0.2891	-0.6705	-0.4321	1.1381	-0.2811	-0.0573	-0.1917	0.1141	0.3795	-0.2174	0.2336	24.743	47.152	-31.267
16	1.4228	-0.3438	0.4926	1.176	0.3996	2.9624	-0.0302	-0.074	0.3284	-0.0332	0.1483	-0.1861	-0.7453	0.2266	-0.1181	0.1512	-0.0295	0.0465	-0.1465	-0.0811	-0.0452	-3.134	60.518	-18.528
17	1.6085	0.5467	0.1646	1.6287	0.1392	3.1281	0.2538	-0.3523	-0.1087	0.6357	-0.0684	-0.0671	-0.0808	-0.0013	-0.1854	0.3401	0.012	-0.053	0.021	-0.0452	-0.1674	-9.162	44.215	15.389
18	3.1366	0.6407	0.2358	1.871	0.7996	4.552	0.22	-0.273	-0.2408	0.3328	0.0935	-0.6052	-0.1471	0.9658	-0.3134	0.0623	-0.0581	-0.1585	0.2723	-0.1761	0.0907	17.482	47.157	1.091
19	1.7755	-1.0376	0.4548	2.1388	0.8004	2.2914	-0.0101	-0.3066	-0.1793	0.3342	0.0619	0.2806	0.078	-0.4205	-0.0519	-0.0555	0.0568	0.0403	-0.0551	0.0505	-0.1183	-27.589	34.98	-10.738
20	1.9711	-0.5441	0.2432	2.8396	1.0761	2.4115	-0.0008	-0.1419	0.3303	-0.0038	0.0261	0.2487	-0.7278	-0.3195	-0.0254	0.3453	0.299	0.0559	-0.0308	-0.0559	0.014	-32.454	72.715	-8.422
21	3.5515	-0.2483	0.2478	3.1457	1.0591	2.4781	-0.0601	-0.044	-0.0415	-0.1627	-0.2461	0.8096	-0.33	-0.8848	0.3061	0.003	0.3102	-0.0331	0.2822	-0.0785	0.2115	-50.805	52.197	-22.194
22	1.6082	0.2927	0.1774	1.9409	0.756	1.6807	-0.0344	0.1331	0.1347	-0.4051	0.0562	0.1458	-0.3855	-0.1529	-0.0217	0.0637	0.0806	-0.0292	-0.1956	0.0573	-0.1364	-22.651	47.91	-40.272
23	2.5677	-0.7018	-0.2717	2.0256	0.3738	1.8093	0.0414	0.0837	-0.4232	-0.1137	0.0007	0.2705	0.4033	-0.093	-0.0422	0.01	0.0075	-0.1156	-0.2015	-0.0161	-0.005	-16.961	10.309	-42.562
24	3.5097	-0.0611	0.5157	2.8736	0.8065	3.021	0.0773	-0.0112	-0.2736	-0.1398	-0.1471	0.7709	0.1267	-0.7879	0.0697	-0.123	-0.0092	-0.1252	0.0828	0.0055	0.1717	-43.525	24.616	-38.655
25	0.8432	-0.6161	0.7337	1.7359	0.2816	1.8163	0.057	-0.1317	-0.3175	0.1846	0.0383	0.3536	0.2736	-0.2788	-0.0954	-0.1458	-0.1162	-0.0047	-0.1103	0.0536	-0.0366	-20.798	-48.719	35.146
26	2.0455	-1.0144	0.1301	3.4824	-0.3728	2.4248	0.275	0.6042	-0.4215	-0.6158	-0.1492	-0.062	0.5151	0.2974	-0.1259	-0.0051	0.062	-0.0869	0.0813	-0.1963	-0.0575	-3.862	-53.819	1.365
27	1.5408	0.0679	0.6998	4.0682	0.1163	3.3278	0.1672	0.0779	-0.6291	0.0004	0.0558	-0.0315	0.8522	0.1106	-0.2229	0.1871	0.0014	-0.1689	-0.1795	-0.0823	0.1945	-4.848	-73.523	25.292
28	1.0103	0.385	0.4545	1.7107	-0.3839	2.0763	0.0365	0.002	-0.271	0.2201	0.0759	-0.3015	0.2835	0.3157	-0.1123	-0.1106	0.0379	-0.1119	-0.1349	-0.048	-0.0886	11.518	-47.942	39.6
29	1.5214	-0.1457	0.1256	2.2259	-0.2916	2.5732	-0.1805	-0.4867	-0.1718	0.6556	0.2327	0.18	0.0941	-0.2056	-0.0521	0.2911	0.0767	-0.0154	0.0957	0.1035	-0.1888	-5.299	-41.842	73.238
30	1.5192	-0.3047	0.7213	2.6093	0.0067	3.5452	0.0098	-0.1512	-0.5296	0.5495	0.1515	0.2637	0.702	-0.1617	-0.1614	0.3285	-0.0479	-0.085	-0.1241	0.1412	0.1106	-4.511	-68.048	57.254
31	1.5268	0.7808	0.5573	1.8841	-0.0344	1.4234	-0.019	-0.2786	0.1345	0.4416	0.0522	0.2366	-0.0561	-0.1879	-0.0333	-0.121	0.0026	0.01	-0.1064	-0.015	-0.2388	-11.283	-21.074	47.942
32	1.8411	0.165	0.4389	2.3603	0.3159	0.8273	-0.0874	-0.118	0.0181	0.3057	0.1787	-0.6776	0.106	0.2525	-0.0913	-0.0893	0.0258	-0.2213	-0.0224	-0.1225	-0.005	26.652	-20.855	51.451
33	2.4506	0.1906	1.0764	2.802	0.1773	2.3514	-0.2107	0.1231	0.4145	0.0042	0.0623	-0.1635	-0.2991	0.1044	0.1484	-0.181	-0.066	-0.1045	-0.1766	-0.0145	-0.1043	9.254	0.065	37.585
34	1.3703	-0.4642	0.5548	1.6952	0.1888	1.2026	0.0224	0.2348	0.0085	-0.131	0.0221	-0.1522	-0.0345	0.1414	-0.0444	-0.2687	-0.0441	-0.0102	-0.1332	-0.0087	-0.2427	1.931	-26.019	18.561
35	1.3578	0.7015	0.7706	2.4407	0.387	1.402	-0.0268	0.0184	0.1685	-0.0849	-0.0139	0.5428	-0.0045	-0.2507	0.0408	-0.288	-0.039	-0.0451	-0.0373	0.0224	-0.0141	-35.941	-27.12	14.915
36	2.4366	0.3168	1.0675	3.3158	0.1098	2.0275	-0.2018	0.0273	0.4982	-0.0384	0.0315	0.2952	-0.3922	-0.07	0.1702	-0.2035	-0.0005	-0.0878	-0.1667	0.0226	-0.0808	-18.623	-2.587	20.73

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 180
2	X-RAY DIFFRACTION	2	A	181 - 353
3	X-RAY DIFFRACTION	3	A	354 - 539
4	X-RAY DIFFRACTION	4	B	1 - 180
5	X-RAY DIFFRACTION	5	B	181 - 353
6	X-RAY DIFFRACTION	6	B	354 - 535
7	X-RAY DIFFRACTION	7	C	2 - 180
8	X-RAY DIFFRACTION	8	C	181 - 353
9	X-RAY DIFFRACTION	9	C	354 - 535
10	X-RAY DIFFRACTION	10	D	2 - 180
11	X-RAY DIFFRACTION	11	D	181 - 353
12	X-RAY DIFFRACTION	12	D	354 - 533
13	X-RAY DIFFRACTION	13	E	1 - 180
14	X-RAY DIFFRACTION	14	E	181 - 353
15	X-RAY DIFFRACTION	15	E	354 - 536
16	X-RAY DIFFRACTION	16	F	1 - 180
17	X-RAY DIFFRACTION	17	F	181 - 353
18	X-RAY DIFFRACTION	18	F	354 - 535
19	X-RAY DIFFRACTION	19	G	1 - 180
20	X-RAY DIFFRACTION	20	G	181 - 353
21	X-RAY DIFFRACTION	21	G	354 - 533
22	X-RAY DIFFRACTION	22	H	1 - 180
23	X-RAY DIFFRACTION	23	H	181 - 353
24	X-RAY DIFFRACTION	24	H	354 - 536
25	X-RAY DIFFRACTION	25	I	1 - 180
26	X-RAY DIFFRACTION	26	I	181 - 353
27	X-RAY DIFFRACTION	27	I	354 - 535
28	X-RAY DIFFRACTION	28	J	1 - 180
29	X-RAY DIFFRACTION	29	J	181 - 353
30	X-RAY DIFFRACTION	30	J	354 - 534
31	X-RAY DIFFRACTION	31	K	1 - 180
32	X-RAY DIFFRACTION	32	K	181 - 353
33	X-RAY DIFFRACTION	33	K	354 - 535
34	X-RAY DIFFRACTION	34	L	1 - 180
35	X-RAY DIFFRACTION	35	L	181 - 353
36	X-RAY DIFFRACTION	36	L	354 - 535

-
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

-
Protein , 1 types, 12 molecules ABCDEFGHIJKL

-
Non-polymers , 5 types, 1401 molecules

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Phasing

-
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

-Protein , 1 types, 12 molecules ABCDEFGHIJKL

-Non-polymers , 5 types, 1401 molecules

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Phasing

-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

-
Protein , 1 types, 12 molecules ABCDEFGHIJKL

-
Non-polymers , 5 types, 1401 molecules

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Phasing

-
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