PDB-7ag7: Crystal structure of SFP aldolase YihT from Salmonella enterica i...

ID or keywords:

Entry

Database: PDB / ID: 7ag7

Title

Crystal structure of SFP aldolase YihT from Salmonella enterica in complex with sulfate bound at the active site

Components

Sulfofructosephosphate aldolase

Keywords

LYASE / sulfofructose / sulfoquinovose / SFP aldolase / sulfoglycolysis

Function / homology

Function and homology information

sulfofructosephosphate aldolase / 6-deoxy-6-sulfofructose-1-phosphate aldolase activity / 6-sulfoquinovose(1-) catabolic process
Similarity search - Function

Biological species

Salmonella typhimurium (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.8 Å

Authors

Sharma, M. / Davies, G.J.

Funding support

United Kingdom, 1items

Citation

Journal: Acs Cent.Sci. / Year: 2021
Title: Molecular Basis of Sulfosugar Selectivity in Sulfoglycolysis.
Authors: Sharma, M. / Abayakoon, P. / Epa, R. / Jin, Y. / Lingford, J.P. / Shimada, T. / Nakano, M. / Mui, J.W. / Ishihama, A. / Goddard-Borger, E.D. / Davies, G.J. / Williams, S.J.

History

Deposition	Sep 21, 2020	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Apr 14, 2021	Provider: repository / Type: Initial release
Revision 1.1	Jan 31, 2024	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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	7ag7.cif.gz	674.9 KB	Display	PDBx/mmCIF format
PDB format	pdb7ag7.ent.gz	548.4 KB	Display	PDB format
PDBx/mmJSON format	7ag7.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	7ag7_validation.pdf.gz	4.2 MB	Display	wwPDB validaton report
Full document	7ag7_full_validation.pdf.gz	4.2 MB	Display
Data in XML	7ag7_validation.xml.gz	127.1 KB	Display
Data in CIF	7ag7_validation.cif.gz	186.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ag/7ag7 ftp://data.pdbj.org/pub/pdb/validation_reports/ag/7ag7	HTTPS FTP

-
Related structure data

Related structure data	7ag1C 7ag4C 7ag6C 7aghC 7agkC 7ne2C 1to3S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	7ag1-1 6a1m-1 6a0d-1 2c6q-2 6a4g-1 6a13-1 5zzy-1 6a39-1 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

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	#50 - Feb 2004 Glycolytic Enzymes similarity (3)

Deposited unit

A: Sulfofructosephosphate aldolase

B: Sulfofructosephosphate aldolase

C: Sulfofructosephosphate aldolase

D: Sulfofructosephosphate aldolase

E: Sulfofructosephosphate aldolase

F: Sulfofructosephosphate aldolase

G: Sulfofructosephosphate aldolase

H: Sulfofructosephosphate aldolase

I: Sulfofructosephosphate aldolase

J: Sulfofructosephosphate aldolase

K: Sulfofructosephosphate aldolase

L: Sulfofructosephosphate aldolase

hetero molecules

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

1

B: Sulfofructosephosphate aldolase

J: Sulfofructosephosphate aldolase

hetero molecules

A: Sulfofructosephosphate aldolase

C: Sulfofructosephosphate aldolase

hetero molecules

defined by author
Evidence: gel filtration, homotetramer in solution
137 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

D: Sulfofructosephosphate aldolase

I: Sulfofructosephosphate aldolase

hetero molecules

K: Sulfofructosephosphate aldolase

L: Sulfofructosephosphate aldolase

hetero molecules

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

3

E: Sulfofructosephosphate aldolase

G: Sulfofructosephosphate aldolase

hetero molecules

F: Sulfofructosephosphate aldolase

hetero molecules

H: Sulfofructosephosphate aldolase

hetero molecules

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

Unit cell

Length a, b, c (Å)	85.207, 107.233, 126.855
Angle α, β, γ (deg.)	107.420, 95.930, 110.550
Int Tables number	1
Space group name H-M	P1

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	TYR	TYR	LYS	LYS	A	A	4 - 290	24 - 310
2	1	TYR	TYR	LYS	LYS	B	B	4 - 290	24 - 310
1	2	TYR	TYR	LYS	LYS	A	A	4 - 290	24 - 310
2	2	TYR	TYR	LYS	LYS	C	C	4 - 290	24 - 310
1	3	TYR	TYR	ARG	ARG	A	A	4 - 291	24 - 311
2	3	TYR	TYR	ARG	ARG	D	D	4 - 291	24 - 311
1	4	TYR	TYR	LYS	LYS	A	A	4 - 290	24 - 310
2	4	TYR	TYR	LYS	LYS	E	E	4 - 290	24 - 310
1	5	THR	THR	LYS	LYS	A	A	10 - 290	30 - 310
2	5	THR	THR	LYS	LYS	F	F	10 - 290	30 - 310
1	6	TYR	TYR	ALA	ALA	A	A	4 - 289	24 - 309
2	6	TYR	TYR	ALA	ALA	G	G	4 - 289	24 - 309
1	7	THR	THR	LYS	LYS	A	A	5 - 290	25 - 310
2	7	THR	THR	LYS	LYS	H	H	5 - 290	25 - 310
1	8	TYR	TYR	LYS	LYS	A	A	4 - 290	24 - 310
2	8	TYR	TYR	LYS	LYS	I	I	4 - 290	24 - 310
1	9	TYR	TYR	LYS	LYS	A	A	4 - 290	24 - 310
2	9	TYR	TYR	LYS	LYS	J	J	4 - 290	24 - 310
1	10	TYR	TYR	LYS	LYS	A	A	4 - 290	24 - 310
2	10	TYR	TYR	LYS	LYS	K	K	4 - 290	24 - 310
1	11	TYR	TYR	LYS	LYS	A	A	4 - 290	24 - 310
2	11	TYR	TYR	LYS	LYS	L	L	4 - 290	24 - 310
1	12	ASN	ASN	LYS	LYS	B	B	2 - 290	22 - 310
2	12	ASN	ASN	LYS	LYS	C	C	2 - 290	22 - 310
1	13	MET	MET	LYS	LYS	B	B	1 - 290	21 - 310
2	13	MET	MET	LYS	LYS	D	D	1 - 290	21 - 310
1	14	MET	MET	LYS	LYS	B	B	1 - 290	21 - 310
2	14	MET	MET	LYS	LYS	E	E	1 - 290	21 - 310
1	15	THR	THR	LYS	LYS	B	B	10 - 290	30 - 310
2	15	THR	THR	LYS	LYS	F	F	10 - 290	30 - 310
1	16	ASN	ASN	ALA	ALA	B	B	3 - 289	23 - 309
2	16	ASN	ASN	ALA	ALA	G	G	3 - 289	23 - 309
1	17	THR	THR	LYS	LYS	B	B	5 - 290	25 - 310
2	17	THR	THR	LYS	LYS	H	H	5 - 290	25 - 310
1	18	ASN	ASN	LYS	LYS	B	B	3 - 290	23 - 310
2	18	ASN	ASN	LYS	LYS	I	I	3 - 290	23 - 310
1	19	ASN	ASN	LYS	LYS	B	B	3 - 290	23 - 310
2	19	ASN	ASN	LYS	LYS	J	J	3 - 290	23 - 310
1	20	ASN	ASN	LYS	LYS	B	B	3 - 290	23 - 310
2	20	ASN	ASN	LYS	LYS	K	K	3 - 290	23 - 310
1	21	ASN	ASN	LYS	LYS	B	B	3 - 290	23 - 310
2	21	ASN	ASN	LYS	LYS	L	L	3 - 290	23 - 310
1	22	ASN	ASN	LYS	LYS	C	C	2 - 290	22 - 310
2	22	ASN	ASN	LYS	LYS	D	D	2 - 290	22 - 310
1	23	ASN	ASN	LYS	LYS	C	C	2 - 290	22 - 310
2	23	ASN	ASN	LYS	LYS	E	E	2 - 290	22 - 310
1	24	THR	THR	LYS	LYS	C	C	10 - 290	30 - 310
2	24	THR	THR	LYS	LYS	F	F	10 - 290	30 - 310
1	25	ASN	ASN	ALA	ALA	C	C	3 - 289	23 - 309
2	25	ASN	ASN	ALA	ALA	G	G	3 - 289	23 - 309
1	26	THR	THR	LYS	LYS	C	C	5 - 290	25 - 310
2	26	THR	THR	LYS	LYS	H	H	5 - 290	25 - 310
1	27	ASN	ASN	LYS	LYS	C	C	3 - 290	23 - 310
2	27	ASN	ASN	LYS	LYS	I	I	3 - 290	23 - 310
1	28	ASN	ASN	LYS	LYS	C	C	3 - 290	23 - 310
2	28	ASN	ASN	LYS	LYS	J	J	3 - 290	23 - 310
1	29	ASN	ASN	LYS	LYS	C	C	3 - 290	23 - 310
2	29	ASN	ASN	LYS	LYS	K	K	3 - 290	23 - 310
1	30	ASN	ASN	LYS	LYS	C	C	3 - 290	23 - 310
2	30	ASN	ASN	LYS	LYS	L	L	3 - 290	23 - 310
1	31	HIS	HIS	LYS	LYS	D	D	0 - 290	20 - 310
2	31	HIS	HIS	LYS	LYS	E	E	0 - 290	20 - 310
1	32	THR	THR	LYS	LYS	D	D	10 - 290	30 - 310
2	32	THR	THR	LYS	LYS	F	F	10 - 290	30 - 310
1	33	ASN	ASN	ALA	ALA	D	D	3 - 289	23 - 309
2	33	ASN	ASN	ALA	ALA	G	G	3 - 289	23 - 309
1	34	THR	THR	LYS	LYS	D	D	5 - 290	25 - 310
2	34	THR	THR	LYS	LYS	H	H	5 - 290	25 - 310
1	35	ASN	ASN	LYS	LYS	D	D	3 - 290	23 - 310
2	35	ASN	ASN	LYS	LYS	I	I	3 - 290	23 - 310
1	36	ASN	ASN	LYS	LYS	D	D	3 - 290	23 - 310
2	36	ASN	ASN	LYS	LYS	J	J	3 - 290	23 - 310
1	37	ASN	ASN	LYS	LYS	D	D	3 - 290	23 - 310
2	37	ASN	ASN	LYS	LYS	K	K	3 - 290	23 - 310
1	38	ASN	ASN	LYS	LYS	D	D	3 - 290	23 - 310
2	38	ASN	ASN	LYS	LYS	L	L	3 - 290	23 - 310
1	39	THR	THR	LYS	LYS	E	E	10 - 290	30 - 310
2	39	THR	THR	LYS	LYS	F	F	10 - 290	30 - 310
1	40	ASN	ASN	ALA	ALA	E	E	3 - 289	23 - 309
2	40	ASN	ASN	ALA	ALA	G	G	3 - 289	23 - 309
1	41	THR	THR	LYS	LYS	E	E	5 - 290	25 - 310
2	41	THR	THR	LYS	LYS	H	H	5 - 290	25 - 310
1	42	ASN	ASN	LYS	LYS	E	E	3 - 290	23 - 310
2	42	ASN	ASN	LYS	LYS	I	I	3 - 290	23 - 310
1	43	ASN	ASN	LYS	LYS	E	E	3 - 290	23 - 310
2	43	ASN	ASN	LYS	LYS	J	J	3 - 290	23 - 310
1	44	ASN	ASN	LYS	LYS	E	E	3 - 290	23 - 310
2	44	ASN	ASN	LYS	LYS	K	K	3 - 290	23 - 310
1	45	ASN	ASN	LYS	LYS	E	E	3 - 290	23 - 310
2	45	ASN	ASN	LYS	LYS	L	L	3 - 290	23 - 310
1	46	THR	THR	ALA	ALA	F	F	10 - 289	30 - 309
2	46	THR	THR	ALA	ALA	G	G	10 - 289	30 - 309
1	47	THR	THR	ARG	ARG	F	F	10 - 291	30 - 311
2	47	THR	THR	ARG	ARG	H	H	10 - 291	30 - 311
1	48	THR	THR	LYS	LYS	F	F	10 - 290	30 - 310
2	48	THR	THR	LYS	LYS	I	I	10 - 290	30 - 310
1	49	THR	THR	LYS	LYS	F	F	10 - 290	30 - 310
2	49	THR	THR	LYS	LYS	J	J	10 - 290	30 - 310
1	50	THR	THR	LYS	LYS	F	F	10 - 290	30 - 310
2	50	THR	THR	LYS	LYS	K	K	10 - 290	30 - 310
1	51	THR	THR	LYS	LYS	F	F	10 - 290	30 - 310
2	51	THR	THR	LYS	LYS	L	L	10 - 290	30 - 310
1	52	THR	THR	ALA	ALA	G	G	5 - 289	25 - 309
2	52	THR	THR	ALA	ALA	H	H	5 - 289	25 - 309
1	53	ASN	ASN	ALA	ALA	G	G	3 - 289	23 - 309
2	53	ASN	ASN	ALA	ALA	I	I	3 - 289	23 - 309
1	54	ASN	ASN	ALA	ALA	G	G	3 - 289	23 - 309
2	54	ASN	ASN	ALA	ALA	J	J	3 - 289	23 - 309
1	55	ASN	ASN	ALA	ALA	G	G	3 - 289	23 - 309
2	55	ASN	ASN	ALA	ALA	K	K	3 - 289	23 - 309
1	56	ASN	ASN	ALA	ALA	G	G	3 - 289	23 - 309
2	56	ASN	ASN	ALA	ALA	L	L	3 - 289	23 - 309
1	57	THR	THR	LYS	LYS	H	H	5 - 290	25 - 310
2	57	THR	THR	LYS	LYS	I	I	5 - 290	25 - 310
1	58	THR	THR	LYS	LYS	H	H	5 - 290	25 - 310
2	58	THR	THR	LYS	LYS	J	J	5 - 290	25 - 310
1	59	THR	THR	LYS	LYS	H	H	5 - 290	25 - 310
2	59	THR	THR	LYS	LYS	K	K	5 - 290	25 - 310
1	60	THR	THR	LYS	LYS	H	H	5 - 290	25 - 310
2	60	THR	THR	LYS	LYS	L	L	5 - 290	25 - 310
1	61	ASN	ASN	ARG	ARG	I	I	3 - 291	23 - 311
2	61	ASN	ASN	ARG	ARG	J	J	3 - 291	23 - 311
1	62	ASN	ASN	ARG	ARG	I	I	3 - 291	23 - 311
2	62	ASN	ASN	ARG	ARG	K	K	3 - 291	23 - 311
1	63	ASN	ASN	ARG	ARG	I	I	3 - 291	23 - 311
2	63	ASN	ASN	ARG	ARG	L	L	3 - 291	23 - 311
1	64	ASN	ASN	ARG	ARG	J	J	3 - 291	23 - 311
2	64	ASN	ASN	ARG	ARG	K	K	3 - 291	23 - 311
1	65	ASN	ASN	ARG	ARG	J	J	3 - 291	23 - 311
2	65	ASN	ASN	ARG	ARG	L	L	3 - 291	23 - 311
1	66	ASN	ASN	ARG	ARG	K	K	3 - 291	23 - 311
2	66	ASN	ASN	ARG	ARG	L	L	3 - 291	23 - 311

NCS ensembles :

#1: Protein	Sulfofructosephosphate aldolase / SFP aldolase Mass: 34076.262 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria) Strain: LT2 / SGSC1412 / ATCC 700720 / Gene: yihT, STM4022 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: Q9L7R9, sulfofructosephosphate aldolase
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO₄ / Feature type: SUBJECT OF INVESTIGATION
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1870 / 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: 3.44 Å³/Da / Density % sol: 64.32 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 25% PEG 3350, 0.2 M Na2SO4, 0.1M BisTris propane pH7.5

-
Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

Diamond

/ Beamline: I03 / Wavelength: 0.97625 Å

Detector

Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Sep 14, 2019

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97625 Å / Relative weight: 1

Reflection

Resolution: 1.8→53.71 Å / Num. obs: 352557 / % possible obs: 97.5 % / Redundancy: 2.2 % / CC_1/2: 0.998 / R_merge(I) obs: 0.043 / R_pim(I) all: 0.034 / R_rim(I) all: 0.055 / Net I/σ(I): 9.2 / Num. measured all: 786014 / Scaling rejects: 30

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. measured all	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all	Net I/σ(I) obs	% possible all
1.8-1.83	2.1	0.324	36708	17222	0.841	0.272	0.425	2.3	96.1
9.86-53.71	2.2	0.024	4779	2171	0.998	0.019	0.031	19.4	98.7

-
Processing

Software

Name	Version	Classification
REFMAC	5.8.0266	refinement
Aimless	0.7.4	data scaling
PDB_EXTRACT	3.25	data extraction
xia2		data reduction
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1TO3

1to3

Resolution: 1.8→53.01 Å / Cor.coef. F_o:F_c: 0.955 / Cor.coef. F_o:F_c free: 0.949 / SU B: 2.592 / SU ML: 0.079 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.125 / ESU R Free: 0.11 / 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	0.2073	17503	5 %	RANDOM
R_work	0.193	-	-	-
obs	0.1937	335012	97.47 %	-

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: 88.65 Å² / B_iso mean: 26.46 Å² / B_iso min: 11.56 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.94 Å²	-0.32 Å²	-0.46 Å²
2-	-	1.09 Å²	-0.11 Å²
3-	-	-	0.1 Å²

Refinement step

Cycle: final / Resolution: 1.8→53.01 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	25659	0	60	1870	27589
B_iso mean	-	-	25.01	29.25	-
Num. residues	-	-	-	-	3461

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.013	26155
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	25227
X-RAY DIFFRACTION	r_angle_refined_deg	1.457	1.627	35488
X-RAY DIFFRACTION	r_angle_other_deg	1.466	1.58	57768
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.371	5	3477
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	32.169	21.971	1253
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.847	15	4328
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.417	15	196
X-RAY DIFFRACTION	r_chiral_restr	0.078	0.2	3482
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	30258
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	5774

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	8976	0.06
1	2	B	8976	0.06
2	1	A	9117	0.05
2	2	C	9117	0.05
3	1	A	9098	0.06
3	2	D	9098	0.06
4	1	A	8995	0.06
4	2	E	8995	0.06
5	1	A	7836	0.05
5	2	F	7836	0.05
6	1	A	8987	0.07
6	2	G	8987	0.07
7	1	A	8906	0.06
7	2	H	8906	0.06
8	1	A	9100	0.06
8	2	I	9100	0.06
9	1	A	9038	0.05
9	2	J	9038	0.05
10	1	A	9107	0.05
10	2	K	9107	0.05
11	1	A	9094	0.06
11	2	L	9094	0.06
12	1	B	9004	0.06
12	2	C	9004	0.06
13	1	B	9127	0.05
13	2	D	9127	0.05
14	1	B	9090	0.04
14	2	E	9090	0.04
15	1	B	7793	0.05
15	2	F	7793	0.05
16	1	B	8980	0.06
16	2	G	8980	0.06
17	1	B	8865	0.05
17	2	H	8865	0.05
18	1	B	9057	0.04
18	2	I	9057	0.04
19	1	B	9040	0.04
19	2	J	9040	0.04
20	1	B	9004	0.06
20	2	K	9004	0.06
21	1	B	8978	0.05
21	2	L	8978	0.05
22	1	C	9088	0.06
22	2	D	9088	0.06
23	1	C	9036	0.06
23	2	E	9036	0.06
24	1	C	7805	0.05
24	2	F	7805	0.05
25	1	C	8971	0.07
25	2	G	8971	0.07
26	1	C	8891	0.05
26	2	H	8891	0.05
27	1	C	9102	0.05
27	2	I	9102	0.05
28	1	C	9014	0.06
28	2	J	9014	0.06
29	1	C	9166	0.05
29	2	K	9166	0.05
30	1	C	9109	0.05
30	2	L	9109	0.05
31	1	D	9260	0.04
31	2	E	9260	0.04
32	1	D	7801	0.06
32	2	F	7801	0.06
33	1	D	9073	0.06
33	2	G	9073	0.06
34	1	D	8916	0.05
34	2	H	8916	0.05
35	1	D	9155	0.05
35	2	I	9155	0.05
36	1	D	9121	0.05
36	2	J	9121	0.05
37	1	D	9130	0.07
37	2	K	9130	0.07
38	1	D	9083	0.06
38	2	L	9083	0.06
39	1	E	7804	0.05
39	2	F	7804	0.05
40	1	E	9009	0.06
40	2	G	9009	0.06
41	1	E	8899	0.04
41	2	H	8899	0.04
42	1	E	9091	0.04
42	2	I	9091	0.04
43	1	E	9058	0.04
43	2	J	9058	0.04
44	1	E	9049	0.06
44	2	K	9049	0.06
45	1	E	9022	0.05
45	2	L	9022	0.05
46	1	F	7772	0.06
46	2	G	7772	0.06
47	1	F	7802	0.05
47	2	H	7802	0.05
48	1	F	7829	0.04
48	2	I	7829	0.04
49	1	F	7840	0.04
49	2	J	7840	0.04
50	1	F	7818	0.04
50	2	K	7818	0.04
51	1	F	7819	0.05
51	2	L	7819	0.05
52	1	G	8929	0.05
52	2	H	8929	0.05
53	1	G	9117	0.06
53	2	I	9117	0.06
54	1	G	9077	0.06
54	2	J	9077	0.06
55	1	G	9045	0.07
55	2	K	9045	0.07
56	1	G	9016	0.07
56	2	L	9016	0.07
57	1	H	8919	0.04
57	2	I	8919	0.04
58	1	H	8906	0.04
58	2	J	8906	0.04
59	1	H	8922	0.05
59	2	K	8922	0.05
60	1	H	8891	0.05
60	2	L	8891	0.05
61	1	I	9158	0.05
61	2	J	9158	0.05
62	1	I	9174	0.06
62	2	K	9174	0.06
63	1	I	9149	0.05
63	2	L	9149	0.05
64	1	J	9095	0.06
64	2	K	9095	0.06
65	1	J	9076	0.06
65	2	L	9076	0.06
66	1	K	9116	0.06
66	2	L	9116	0.06

LS refinement shell

Resolution: 1.8→1.847 Å / R_factor R_free error: 0 / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.282	1279	-
R_work	0.258	24499	-
all	-	25778	-
obs	-	-	96.03 %

-
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