PDB-8bgo: N,N-diacetylchitobiose deacetylase from Pyrococcus chitonophagus ...

ID or keywords:

Entry

Database: PDB / ID: 8bgo

Title

N,N-diacetylchitobiose deacetylase from Pyrococcus chitonophagus with substrate N,N-diacetylchitobiose

Components

Diacetylchitobiose deacetylase

Keywords

HYDROLASE / hyperthermophile

Function / homology

N-acetylglucosaminyl phosphatidylinositol deacetylase-related / Putative deacetylase LmbE-like domain superfamily / GlcNAc-PI de-N-acetylase / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides / metal ion binding / Diacetylchitobiose deacetylase

Function and homology information

Biological species

Thermococcus chitonophagus (archaea)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.08 Å

Authors

Rypniewski, W. / Bejger, M. / Biniek-Antosiak, K.

Funding support

Poland, 1items

Citation

Journal: Int J Mol Sci / Year: 2022
Title: Structural, Thermodynamic and Enzymatic Characterization of N , N -Diacetylchitobiose Deacetylase from Pyrococcus chitonophagus.
Authors: Biniek-Antosiak, K. / Bejger, M. / Sliwiak, J. / Baranowski, D. / Mohammed, A.S.A. / Svergun, D.I. / Rypniewski, W.

History

Deposition	Oct 28, 2022	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jan 11, 2023	Provider: repository / Type: Initial release
Revision 1.1	Feb 7, 2024	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / 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

-
Download

PDBx/mmCIF format	8bgo.cif.gz	652.5 KB	Display	PDBx/mmCIF format
PDB format	pdb8bgo.ent.gz	541.5 KB	Display	PDB format
PDBx/mmJSON format	8bgo.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	8bgo_validation.pdf.gz	3.3 MB	Display	wwPDB validaton report
Full document	8bgo_full_validation.pdf.gz	3.3 MB	Display
Data in XML	8bgo_validation.xml.gz	107.9 KB	Display
Data in CIF	8bgo_validation.cif.gz	144.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/bg/8bgo ftp://data.pdbj.org/pub/pdb/validation_reports/bg/8bgo	HTTPS FTP

-
Related structure data

Related structure data	8bgnSC 8bgpC 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

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Diacetylchitobiose deacetylase

H: Diacetylchitobiose deacetylase

K: Diacetylchitobiose deacetylase

B: Diacetylchitobiose deacetylase

E: Diacetylchitobiose deacetylase

L: Diacetylchitobiose deacetylase

G: Diacetylchitobiose deacetylase

C: Diacetylchitobiose deacetylase

I: Diacetylchitobiose deacetylase

J: Diacetylchitobiose deacetylase

F: Diacetylchitobiose deacetylase

D: Diacetylchitobiose deacetylase

hetero molecules

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

1

A: Diacetylchitobiose deacetylase

B: Diacetylchitobiose deacetylase

E: Diacetylchitobiose deacetylase

C: Diacetylchitobiose deacetylase

F: Diacetylchitobiose deacetylase

D: Diacetylchitobiose deacetylase

hetero molecules

defined by author&software
Evidence: SAXS
192 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

H: Diacetylchitobiose deacetylase

K: Diacetylchitobiose deacetylase

L: Diacetylchitobiose deacetylase

G: Diacetylchitobiose deacetylase

I: Diacetylchitobiose deacetylase

J: Diacetylchitobiose deacetylase

hetero molecules

defined by author&software
192 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	79.164, 151.662, 167.092
Angle α, β, γ (deg.)	90.000, 93.330, 90.000
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Component-ID: _ / Refine code: _

Dom-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	MET	MET	ILE	ILE	A	A	1 - 267	5 - 271
2	1	MET	MET	ILE	ILE	H	B	1 - 267	5 - 271
1	2	PHE	PHE	LEU	LEU	A	A	2 - 266	6 - 270
2	2	PHE	PHE	LEU	LEU	K	C	2 - 266	6 - 270
1	3	MET	MET	LEU	LEU	A	A	1 - 266	5 - 270
2	3	MET	MET	LEU	LEU	B	D	1 - 266	5 - 270
1	4	PHE	PHE	LEU	LEU	A	A	2 - 266	6 - 270
2	4	PHE	PHE	LEU	LEU	E	E	2 - 266	6 - 270
1	5	MET	MET	LEU	LEU	A	A	1 - 266	5 - 270
2	5	MET	MET	LEU	LEU	L	F	1 - 266	5 - 270
1	6	MET	MET	LEU	LEU	A	A	1 - 266	5 - 270
2	6	MET	MET	LEU	LEU	G	G	1 - 266	5 - 270
1	7	MET	MET	LEU	LEU	A	A	1 - 266	5 - 270
2	7	MET	MET	LEU	LEU	C	H	1 - 266	5 - 270
1	8	MET	MET	LEU	LEU	A	A	1 - 266	5 - 270
2	8	MET	MET	LEU	LEU	I	I	1 - 266	5 - 270
1	9	PHE	PHE	LEU	LEU	A	A	2 - 266	6 - 270
2	9	PHE	PHE	LEU	LEU	J	J	2 - 266	6 - 270
1	10	MET	MET	LEU	LEU	A	A	1 - 266	5 - 270
2	10	MET	MET	LEU	LEU	F	K	1 - 266	5 - 270
1	11	PHE	PHE	LEU	LEU	A	A	2 - 266	6 - 270
2	11	PHE	PHE	LEU	LEU	D	L	2 - 266	6 - 270
1	12	PHE	PHE	LEU	LEU	H	B	2 - 266	6 - 270
2	12	PHE	PHE	LEU	LEU	K	C	2 - 266	6 - 270
1	13	MET	MET	LEU	LEU	H	B	1 - 266	5 - 270
2	13	MET	MET	LEU	LEU	B	D	1 - 266	5 - 270
1	14	PHE	PHE	LEU	LEU	H	B	2 - 266	6 - 270
2	14	PHE	PHE	LEU	LEU	E	E	2 - 266	6 - 270
1	15	MET	MET	LEU	LEU	H	B	1 - 266	5 - 270
2	15	MET	MET	LEU	LEU	L	F	1 - 266	5 - 270
1	16	MET	MET	LEU	LEU	H	B	1 - 266	5 - 270
2	16	MET	MET	LEU	LEU	G	G	1 - 266	5 - 270
1	17	MET	MET	LEU	LEU	H	B	1 - 266	5 - 270
2	17	MET	MET	LEU	LEU	C	H	1 - 266	5 - 270
1	18	MET	MET	LEU	LEU	H	B	1 - 266	5 - 270
2	18	MET	MET	LEU	LEU	I	I	1 - 266	5 - 270
1	19	PHE	PHE	LEU	LEU	H	B	2 - 266	6 - 270
2	19	PHE	PHE	LEU	LEU	J	J	2 - 266	6 - 270
1	20	MET	MET	LEU	LEU	H	B	1 - 266	5 - 270
2	20	MET	MET	LEU	LEU	F	K	1 - 266	5 - 270
1	21	PHE	PHE	LEU	LEU	H	B	2 - 266	6 - 270
2	21	PHE	PHE	LEU	LEU	D	L	2 - 266	6 - 270
1	22	PHE	PHE	LEU	LEU	K	C	2 - 266	6 - 270
2	22	PHE	PHE	LEU	LEU	B	D	2 - 266	6 - 270
1	23	PHE	PHE	ILE	ILE	K	C	2 - 267	6 - 271
2	23	PHE	PHE	ILE	ILE	E	E	2 - 267	6 - 271
1	24	PHE	PHE	LEU	LEU	K	C	2 - 266	6 - 270
2	24	PHE	PHE	LEU	LEU	L	F	2 - 266	6 - 270
1	25	PHE	PHE	LEU	LEU	K	C	2 - 266	6 - 270
2	25	PHE	PHE	LEU	LEU	G	G	2 - 266	6 - 270
1	26	PHE	PHE	LEU	LEU	K	C	2 - 266	6 - 270
2	26	PHE	PHE	LEU	LEU	C	H	2 - 266	6 - 270
1	27	PHE	PHE	LEU	LEU	K	C	2 - 266	6 - 270
2	27	PHE	PHE	LEU	LEU	I	I	2 - 266	6 - 270
1	28	PHE	PHE	ILE	ILE	K	C	2 - 267	6 - 271
2	28	PHE	PHE	ILE	ILE	J	J	2 - 267	6 - 271
1	29	PHE	PHE	LEU	LEU	K	C	2 - 266	6 - 270
2	29	PHE	PHE	LEU	LEU	F	K	2 - 266	6 - 270
1	30	PHE	PHE	ILE	ILE	K	C	2 - 267	6 - 271
2	30	PHE	PHE	ILE	ILE	D	L	2 - 267	6 - 271
1	31	PHE	PHE	LEU	LEU	B	D	2 - 266	6 - 270
2	31	PHE	PHE	LEU	LEU	E	E	2 - 266	6 - 270
1	32	PHE	PHE	ILE	ILE	B	D	-1 - 267	3 - 271
2	32	PHE	PHE	ILE	ILE	L	F	-1 - 267	3 - 271
1	33	PHE	PHE	LEU	LEU	B	D	-1 - 266	3 - 270
2	33	PHE	PHE	LEU	LEU	G	G	-1 - 266	3 - 270
1	34	PHE	PHE	LEU	LEU	B	D	-1 - 266	3 - 270
2	34	PHE	PHE	LEU	LEU	C	H	-1 - 266	3 - 270
1	35	PHE	PHE	ILE	ILE	B	D	-1 - 267	3 - 271
2	35	PHE	PHE	ILE	ILE	I	I	-1 - 267	3 - 271
1	36	PHE	PHE	LEU	LEU	B	D	2 - 266	6 - 270
2	36	PHE	PHE	LEU	LEU	J	J	2 - 266	6 - 270
1	37	PHE	PHE	ILE	ILE	B	D	-1 - 267	3 - 271
2	37	PHE	PHE	ILE	ILE	F	K	-1 - 267	3 - 271
1	38	PHE	PHE	LEU	LEU	B	D	2 - 266	6 - 270
2	38	PHE	PHE	LEU	LEU	D	L	2 - 266	6 - 270
1	39	PHE	PHE	LEU	LEU	E	E	2 - 266	6 - 270
2	39	PHE	PHE	LEU	LEU	L	F	2 - 266	6 - 270
1	40	PHE	PHE	LEU	LEU	E	E	2 - 266	6 - 270
2	40	PHE	PHE	LEU	LEU	G	G	2 - 266	6 - 270
1	41	PHE	PHE	LEU	LEU	E	E	2 - 266	6 - 270
2	41	PHE	PHE	LEU	LEU	C	H	2 - 266	6 - 270
1	42	PHE	PHE	LEU	LEU	E	E	2 - 266	6 - 270
2	42	PHE	PHE	LEU	LEU	I	I	2 - 266	6 - 270
1	43	PHE	PHE	ILE	ILE	E	E	2 - 267	6 - 271
2	43	PHE	PHE	ILE	ILE	J	J	2 - 267	6 - 271
1	44	PHE	PHE	LEU	LEU	E	E	2 - 266	6 - 270
2	44	PHE	PHE	LEU	LEU	F	K	2 - 266	6 - 270
1	45	PHE	PHE	ILE	ILE	E	E	2 - 267	6 - 271
2	45	PHE	PHE	ILE	ILE	D	L	2 - 267	6 - 271
1	46	PHE	PHE	LEU	LEU	L	F	-1 - 266	3 - 270
2	46	PHE	PHE	LEU	LEU	G	G	-1 - 266	3 - 270
1	47	PHE	PHE	LEU	LEU	L	F	-1 - 266	3 - 270
2	47	PHE	PHE	LEU	LEU	C	H	-1 - 266	3 - 270
1	48	PHE	PHE	ILE	ILE	L	F	-1 - 267	3 - 271
2	48	PHE	PHE	ILE	ILE	I	I	-1 - 267	3 - 271
1	49	PHE	PHE	LEU	LEU	L	F	2 - 266	6 - 270
2	49	PHE	PHE	LEU	LEU	J	J	2 - 266	6 - 270
1	50	PHE	PHE	ILE	ILE	L	F	-1 - 267	3 - 271
2	50	PHE	PHE	ILE	ILE	F	K	-1 - 267	3 - 271
1	51	PHE	PHE	LEU	LEU	L	F	2 - 266	6 - 270
2	51	PHE	PHE	LEU	LEU	D	L	2 - 266	6 - 270
1	52	ASP	ASP	ILE	ILE	G	G	-3 - 267	1 - 271
2	52	ASP	ASP	ILE	ILE	C	H	-3 - 267	1 - 271
1	53	PHE	PHE	LEU	LEU	G	G	-1 - 266	3 - 270
2	53	PHE	PHE	LEU	LEU	I	I	-1 - 266	3 - 270
1	54	PHE	PHE	LEU	LEU	G	G	2 - 266	6 - 270
2	54	PHE	PHE	LEU	LEU	J	J	2 - 266	6 - 270
1	55	PHE	PHE	LEU	LEU	G	G	-1 - 266	3 - 270
2	55	PHE	PHE	LEU	LEU	F	K	-1 - 266	3 - 270
1	56	PHE	PHE	LEU	LEU	G	G	2 - 266	6 - 270
2	56	PHE	PHE	LEU	LEU	D	L	2 - 266	6 - 270
1	57	PHE	PHE	LEU	LEU	C	H	-1 - 266	3 - 270
2	57	PHE	PHE	LEU	LEU	I	I	-1 - 266	3 - 270
1	58	PHE	PHE	LEU	LEU	C	H	2 - 266	6 - 270
2	58	PHE	PHE	LEU	LEU	J	J	2 - 266	6 - 270
1	59	PHE	PHE	LEU	LEU	C	H	-1 - 266	3 - 270
2	59	PHE	PHE	LEU	LEU	F	K	-1 - 266	3 - 270
1	60	PHE	PHE	LEU	LEU	C	H	2 - 266	6 - 270
2	60	PHE	PHE	LEU	LEU	D	L	2 - 266	6 - 270
1	61	PHE	PHE	LEU	LEU	I	I	2 - 266	6 - 270
2	61	PHE	PHE	LEU	LEU	J	J	2 - 266	6 - 270
1	62	PHE	PHE	ILE	ILE	I	I	-1 - 267	3 - 271
2	62	PHE	PHE	ILE	ILE	F	K	-1 - 267	3 - 271
1	63	PHE	PHE	LEU	LEU	I	I	2 - 266	6 - 270
2	63	PHE	PHE	LEU	LEU	D	L	2 - 266	6 - 270
1	64	PHE	PHE	LEU	LEU	J	J	2 - 266	6 - 270
2	64	PHE	PHE	LEU	LEU	F	K	2 - 266	6 - 270
1	65	PHE	PHE	ILE	ILE	J	J	2 - 267	6 - 271
2	65	PHE	PHE	ILE	ILE	D	L	2 - 267	6 - 271
1	66	PHE	PHE	LEU	LEU	F	K	2 - 266	6 - 270
2	66	PHE	PHE	LEU	LEU	D	L	2 - 266	6 - 270

NCS ensembles :

#1: Protein

Diacetylchitobiose deacetylase

Mass: 31432.088 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Thermococcus chitonophagus (archaea) / Gene: A3L04_02905, CHITON_0574 / Production host:

Escherichia coli (E. coli) / References: UniProt: A0A160VQZ8, EC: 3.5.1.136

#2: Polysaccharide

2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 12 / Source method: obtained synthetically

Descriptor	Type	Program
DGlcpNAcb1-4DGlcpNAcb1-ROH	Glycam Condensed Sequence	GMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1	WURCS	PDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}	LINUCS	PDB-CARE

#3: Chemical

ChemComp-ZN / ZINC ION

Mass: 65.409 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Zn

#4: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 62 / Source method: isolated from a natural source / Formula: H₂O

Has ligand of interest

Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.68 Å³/Da / Density % sol: 54.18 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop Details: 0.2M ammonium chloride, 0.1M MES pH6.0, 20% v/v PEG 6000,

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9797 Å
Detector	Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 10, 2018
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9797 Å / Relative weight: 1
Reflection	Resolution: 3.08→48.38 Å / Num. obs: 72565 / % possible obs: 99.3 % / Redundancy: 6.7 % / R_merge(I) obs: 0.077 / Net I/σ(I): 14.6
Reflection shell	Resolution: 3.08→3.19 Å / R_merge(I) obs: 0.657 / Mean I/σ(I) obs: 2 / Num. unique obs: 6943 / % possible all: 94.75

-
Processing

Software

Name	Version	Classification
XDS	5.8.0253	data reduction
XSCALE	3.27	data scaling
Coot		model building
PHASER		phasing
REFMAC	5	refinement

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 8BGN

8bgn

Resolution: 3.08→48.38 Å / Cor.coef. F_o:F_c: 0.966 / Cor.coef. F_o:F_c free: 0.949 / SU B: 20.383 / SU ML: 0.339 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.407 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2147	1000	1.4 %	RANDOM
R_work	0.168	-	-	-
obs	0.1687	71565	99.27 %	-

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 max: 230.85 Å² / B_iso mean: 93.303 Å² / B_iso min: 44.72 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-3.11 Å²	-0 Å²	-2.93 Å²
2-	-	3.19 Å²	0 Å²
3-	-	-	0.26 Å²

Refinement step

Cycle: final / Resolution: 3.08→48.38 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	26314	0	360	62	26736
B_iso mean	-	-	138.49	63.33	-
Num. residues	-	-	-	-	3216

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.013	27441
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	25516
X-RAY DIFFRACTION	r_angle_refined_deg	1.523	1.653	37218
X-RAY DIFFRACTION	r_angle_other_deg	1.199	1.594	59288
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.681	5	3204
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	31.967	22.151	1460
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.468	15	4694
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.245	15	168
X-RAY DIFFRACTION	r_chiral_restr	0.071	0.2	3570
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	30040
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	5872

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	8826	0.08
1	2	H	8826	0.08
2	1	A	8667	0.08
2	2	K	8667	0.08
3	1	A	8703	0.08
3	2	B	8703	0.08
4	1	A	8655	0.07
4	2	E	8655	0.07
5	1	A	8651	0.08
5	2	L	8651	0.08
6	1	A	8635	0.09
6	2	G	8635	0.09
7	1	A	8646	0.08
7	2	C	8646	0.08
8	1	A	8677	0.08
8	2	I	8677	0.08
9	1	A	8715	0.08
9	2	J	8715	0.08
10	1	A	8738	0.08
10	2	F	8738	0.08
11	1	A	8621	0.08
11	2	D	8621	0.08
12	1	H	8718	0.07
12	2	K	8718	0.07
13	1	H	8711	0.08
13	2	B	8711	0.08
14	1	H	8692	0.07
14	2	E	8692	0.07
15	1	H	8703	0.08
15	2	L	8703	0.08
16	1	H	8709	0.08
16	2	G	8709	0.08
17	1	H	8722	0.07
17	2	C	8722	0.07
18	1	H	8735	0.08
18	2	I	8735	0.08
19	1	H	8731	0.08
19	2	J	8731	0.08
20	1	H	8721	0.07
20	2	F	8721	0.07
21	1	H	8728	0.07
21	2	D	8728	0.07
22	1	K	8699	0.07
22	2	B	8699	0.07
23	1	K	8731	0.07
23	2	E	8731	0.07
24	1	K	8695	0.08
24	2	L	8695	0.08
25	1	K	8678	0.08
25	2	G	8678	0.08
26	1	K	8717	0.07
26	2	C	8717	0.07
27	1	K	8655	0.08
27	2	I	8655	0.08
28	1	K	8791	0.06
28	2	J	8791	0.06
29	1	K	8626	0.08
29	2	F	8626	0.08
30	1	K	8717	0.07
30	2	D	8717	0.07
31	1	B	8689	0.07
31	2	E	8689	0.07
32	1	B	8769	0.08
32	2	L	8769	0.08
33	1	B	8734	0.08
33	2	G	8734	0.08
34	1	B	8743	0.08
34	2	C	8743	0.08
35	1	B	8780	0.09
35	2	I	8780	0.09
36	1	B	8744	0.07
36	2	J	8744	0.07
37	1	B	8765	0.08
37	2	F	8765	0.08
38	1	B	8661	0.08
38	2	D	8661	0.08
39	1	E	8604	0.08
39	2	L	8604	0.08
40	1	E	8679	0.08
40	2	G	8679	0.08
41	1	E	8678	0.07
41	2	C	8678	0.07
42	1	E	8671	0.08
42	2	I	8671	0.08
43	1	E	8737	0.07
43	2	J	8737	0.07
44	1	E	8614	0.08
44	2	F	8614	0.08
45	1	E	8701	0.07
45	2	D	8701	0.07
46	1	L	8715	0.09
46	2	G	8715	0.09
47	1	L	8689	0.09
47	2	C	8689	0.09
48	1	L	8737	0.09
48	2	I	8737	0.09
49	1	L	8681	0.08
49	2	J	8681	0.08
50	1	L	8773	0.08
50	2	F	8773	0.08
51	1	L	8618	0.09
51	2	D	8618	0.09
52	1	G	8851	0.09
52	2	C	8851	0.09
53	1	G	8699	0.1
53	2	I	8699	0.1
54	1	G	8677	0.08
54	2	J	8677	0.08
55	1	G	8708	0.09
55	2	F	8708	0.09
56	1	G	8717	0.08
56	2	D	8717	0.08
57	1	C	8708	0.09
57	2	I	8708	0.09
58	1	C	8698	0.08
58	2	J	8698	0.08
59	1	C	8713	0.08
59	2	F	8713	0.08
60	1	C	8709	0.07
60	2	D	8709	0.07
61	1	I	8682	0.08
61	2	J	8682	0.08
62	1	I	8720	0.1
62	2	F	8720	0.1
63	1	I	8644	0.09
63	2	D	8644	0.09
64	1	J	8698	0.08
64	2	F	8698	0.08
65	1	J	8727	0.08
65	2	D	8727	0.08
66	1	F	8636	0.08
66	2	D	8636	0.08

LS refinement shell

Resolution: 3.08→3.157 Å / R_factor R_free error: 0

	R_factor	Num. reflection	% reflection
R_free	0.384	69	-
R_work	0.336	4976	-
obs	-	-	92.91 %

-
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