PDB-6hnq: TarP-6RboP-(CH2)6NH2

ID or keywords:

Entry

Database: PDB / ID: 6hnq

Title

TarP-6RboP-(CH2)6NH2

Components

Probable ss-1,3-N-acetylglucosaminyltransferase

Keywords

TRANSFERASE / Staphylococcus aureus / wall teichoic acid / glycosyltransferase / GT-A fold

Function / homology

Function and homology information

teichoic acid biosynthetic process / hexosyltransferase activity / Transferases; Glycosyltransferases; Hexosyltransferases / cell wall organization / metal ion binding
Similarity search - Function

Biological species

Staphylococcus aureus subsp. aureus N315 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / Resolution: 2.4 Å

Authors

Guo, Y. / Stehle, T.

Funding support

Germany, 1items

Citation

Journal: Nature / Year: 2018
Title: Methicillin-resistant Staphylococcus aureus alters cell wall glycosylation to evade immunity.
Authors: Gerlach, D. / Guo, Y. / De Castro, C. / Kim, S.H. / Schlatterer, K. / Xu, F.F. / Pereira, C. / Seeberger, P.H. / Ali, S. / Codee, J. / Sirisarn, W. / Schulte, B. / Wolz, C. / Larsen, J. / ...

History

Deposition	Sep 17, 2018	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Oct 24, 2018	Provider: repository / Type: Initial release
Revision 1.1	Nov 21, 2018	Group: Data collection / Database references / Category: citation Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2	Dec 5, 2018	Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.3	Dec 12, 2018	Group: Data collection / Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4	May 15, 2024	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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	6hnq.cif.gz	1.4 MB	Display	PDBx/mmCIF format
PDB format	pdb6hnq.ent.gz	1.2 MB	Display	PDB format
PDBx/mmJSON format	6hnq.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/hn/6hnq ftp://data.pdbj.org/pub/pdb/validation_reports/hn/6hnq	HTTPS FTP

-
Related structure data

Related structure data	6h1jC 6h21C 6h2nC 6h4fC 6h4mC C: citing same article (ref.)
Similar structure data	6h4m-3 6h4m-4 6h4m-2 6h4m-1 6h1j-d 6h21-d 6h2n-d 5ovo-1 5l10-d 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

C: citing same article (ref.)

Similar structure data

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#254 - Feb 2021 Cellulose Synthase similarity (3) #156 - Dec 2012 ABO Blood Type Glycosyltransferases similarity (1)

Deposited unit

B: Probable ss-1,3-N-acetylglucosaminyltransferase

C: Probable ss-1,3-N-acetylglucosaminyltransferase

F: Probable ss-1,3-N-acetylglucosaminyltransferase

O: Probable ss-1,3-N-acetylglucosaminyltransferase

P: Probable ss-1,3-N-acetylglucosaminyltransferase

E: Probable ss-1,3-N-acetylglucosaminyltransferase

G: Probable ss-1,3-N-acetylglucosaminyltransferase

Q: Probable ss-1,3-N-acetylglucosaminyltransferase

A: Probable ss-1,3-N-acetylglucosaminyltransferase

D: Probable ss-1,3-N-acetylglucosaminyltransferase

H: Probable ss-1,3-N-acetylglucosaminyltransferase

I: Probable ss-1,3-N-acetylglucosaminyltransferase

hetero molecules

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

1

B: Probable ss-1,3-N-acetylglucosaminyltransferase

C: Probable ss-1,3-N-acetylglucosaminyltransferase

F: Probable ss-1,3-N-acetylglucosaminyltransferase

hetero molecules

defined by author&software
122 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

O: Probable ss-1,3-N-acetylglucosaminyltransferase

H: Probable ss-1,3-N-acetylglucosaminyltransferase

I: Probable ss-1,3-N-acetylglucosaminyltransferase

hetero molecules

defined by author&software
122 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

P: Probable ss-1,3-N-acetylglucosaminyltransferase

A: Probable ss-1,3-N-acetylglucosaminyltransferase

D: Probable ss-1,3-N-acetylglucosaminyltransferase

hetero molecules

defined by author&software
122 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

E: Probable ss-1,3-N-acetylglucosaminyltransferase

G: Probable ss-1,3-N-acetylglucosaminyltransferase

Q: Probable ss-1,3-N-acetylglucosaminyltransferase

hetero molecules

defined by author&software
122 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	95.410, 211.250, 122.680
Angle α, β, γ (deg.)	90.00, 91.61, 90.00
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Component-ID: _ / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: _

Dom-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	MET	MET	B	A	1 - 327	19 - 345
2	1	MET	MET	C	B	1 - 327	19 - 345
1	2	MET	MET	B	A	1 - 326	19 - 344
2	2	MET	MET	F	C	1 - 326	19 - 344
1	3	MET	MET	B	A	1 - 327	19 - 345
2	3	MET	MET	O	D	1 - 327	19 - 345
1	4	MET	MET	B	A	1 - 327	19 - 345
2	4	MET	MET	P	E	1 - 327	19 - 345
1	5	SER	SER	B	A	0 - 327	18 - 345
2	5	SER	SER	E	F	0 - 327	18 - 345
1	6	MET	MET	B	A	1 - 327	19 - 345
2	6	MET	MET	G	G	1 - 327	19 - 345
1	7	MET	MET	B	A	1 - 327	19 - 345
2	7	MET	MET	Q	H	1 - 327	19 - 345
1	8	SER	SER	B	A	0 - 327	18 - 345
2	8	SER	SER	A	I	0 - 327	18 - 345
1	9	MET	MET	B	A	1 - 327	19 - 345
2	9	MET	MET	D	J	1 - 327	19 - 345
1	10	SER	SER	B	A	0 - 327	18 - 345
2	10	SER	SER	H	K	0 - 327	18 - 345
1	11	MET	MET	B	A	1 - 327	19 - 345
2	11	MET	MET	I	L	1 - 327	19 - 345
1	12	MET	MET	C	B	1 - 327	19 - 345
2	12	MET	MET	F	C	1 - 327	19 - 345
1	13	MET	MET	C	B	1 - 327	19 - 345
2	13	MET	MET	O	D	1 - 327	19 - 345
1	14	MET	MET	C	B	1 - 326	19 - 344
2	14	MET	MET	P	E	1 - 326	19 - 344
1	15	MET	MET	C	B	1 - 327	19 - 345
2	15	MET	MET	E	F	1 - 327	19 - 345
1	16	MET	MET	C	B	1 - 327	19 - 345
2	16	MET	MET	G	G	1 - 327	19 - 345
1	17	MET	MET	C	B	1 - 327	19 - 345
2	17	MET	MET	Q	H	1 - 327	19 - 345
1	18	MET	MET	C	B	1 - 327	19 - 345
2	18	MET	MET	A	I	1 - 327	19 - 345
1	19	MET	MET	C	B	1 - 327	19 - 345
2	19	MET	MET	D	J	1 - 327	19 - 345
1	20	MET	MET	C	B	1 - 327	19 - 345
2	20	MET	MET	H	K	1 - 327	19 - 345
1	21	MET	MET	C	B	1 - 327	19 - 345
2	21	MET	MET	I	L	1 - 327	19 - 345
1	22	MET	MET	F	C	1 - 327	19 - 345
2	22	MET	MET	O	D	1 - 327	19 - 345
1	23	MET	MET	F	C	1 - 327	19 - 345
2	23	MET	MET	P	E	1 - 327	19 - 345
1	24	MET	MET	F	C	1 - 327	19 - 345
2	24	MET	MET	E	F	1 - 327	19 - 345
1	25	MET	MET	F	C	1 - 327	19 - 345
2	25	MET	MET	G	G	1 - 327	19 - 345
1	26	MET	MET	F	C	1 - 327	19 - 345
2	26	MET	MET	Q	H	1 - 327	19 - 345
1	27	MET	MET	F	C	1 - 327	19 - 345
2	27	MET	MET	A	I	1 - 327	19 - 345
1	28	MET	MET	F	C	1 - 327	19 - 345
2	28	MET	MET	D	J	1 - 327	19 - 345
1	29	MET	MET	F	C	1 - 326	19 - 344
2	29	MET	MET	H	K	1 - 326	19 - 344
1	30	MET	MET	F	C	1 - 327	19 - 345
2	30	MET	MET	I	L	1 - 327	19 - 345
1	31	MET	MET	O	D	1 - 327	19 - 345
2	31	MET	MET	P	E	1 - 327	19 - 345
1	32	MET	MET	O	D	1 - 326	19 - 344
2	32	MET	MET	E	F	1 - 326	19 - 344
1	33	MET	MET	O	D	1 - 327	19 - 345
2	33	MET	MET	G	G	1 - 327	19 - 345
1	34	MET	MET	O	D	1 - 327	19 - 345
2	34	MET	MET	Q	H	1 - 327	19 - 345
1	35	MET	MET	O	D	1 - 326	19 - 344
2	35	MET	MET	A	I	1 - 326	19 - 344
1	36	MET	MET	O	D	1 - 327	19 - 345
2	36	MET	MET	D	J	1 - 327	19 - 345
1	37	MET	MET	O	D	1 - 327	19 - 345
2	37	MET	MET	H	K	1 - 327	19 - 345
1	38	MET	MET	O	D	1 - 327	19 - 345
2	38	MET	MET	I	L	1 - 327	19 - 345
1	39	MET	MET	P	E	1 - 326	19 - 344
2	39	MET	MET	E	F	1 - 326	19 - 344
1	40	MET	MET	P	E	1 - 326	19 - 344
2	40	MET	MET	G	G	1 - 326	19 - 344
1	41	MET	MET	P	E	1 - 326	19 - 344
2	41	MET	MET	Q	H	1 - 326	19 - 344
1	42	MET	MET	P	E	1 - 326	19 - 344
2	42	MET	MET	A	I	1 - 326	19 - 344
1	43	MET	MET	P	E	1 - 326	19 - 344
2	43	MET	MET	D	J	1 - 326	19 - 344
1	44	MET	MET	P	E	1 - 327	19 - 345
2	44	MET	MET	H	K	1 - 327	19 - 345
1	45	MET	MET	P	E	1 - 326	19 - 344
2	45	MET	MET	I	L	1 - 326	19 - 344
1	46	MET	MET	E	F	1 - 327	19 - 345
2	46	MET	MET	G	G	1 - 327	19 - 345
1	47	MET	MET	E	F	1 - 327	19 - 345
2	47	MET	MET	Q	H	1 - 327	19 - 345
1	48	SER	SER	E	F	0 - 327	18 - 345
2	48	SER	SER	A	I	0 - 327	18 - 345
1	49	MET	MET	E	F	1 - 327	19 - 345
2	49	MET	MET	D	J	1 - 327	19 - 345
1	50	SER	SER	E	F	0 - 327	18 - 345
2	50	SER	SER	H	K	0 - 327	18 - 345
1	51	MET	MET	E	F	1 - 327	19 - 345
2	51	MET	MET	I	L	1 - 327	19 - 345
1	52	MET	MET	G	G	1 - 327	19 - 345
2	52	MET	MET	Q	H	1 - 327	19 - 345
1	53	MET	MET	G	G	1 - 327	19 - 345
2	53	MET	MET	A	I	1 - 327	19 - 345
1	54	MET	MET	G	G	1 - 327	19 - 345
2	54	MET	MET	D	J	1 - 327	19 - 345
1	55	MET	MET	G	G	1 - 327	19 - 345
2	55	MET	MET	H	K	1 - 327	19 - 345
1	56	MET	MET	G	G	1 - 327	19 - 345
2	56	MET	MET	I	L	1 - 327	19 - 345
1	57	MET	MET	Q	H	1 - 327	19 - 345
2	57	MET	MET	A	I	1 - 327	19 - 345
1	58	MET	MET	Q	H	1 - 327	19 - 345
2	58	MET	MET	D	J	1 - 327	19 - 345
1	59	MET	MET	Q	H	1 - 327	19 - 345
2	59	MET	MET	H	K	1 - 327	19 - 345
1	60	MET	MET	Q	H	1 - 327	19 - 345
2	60	MET	MET	I	L	1 - 327	19 - 345
1	61	MET	MET	A	I	1 - 327	19 - 345
2	61	MET	MET	D	J	1 - 327	19 - 345
1	62	SER	SER	A	I	0 - 327	18 - 345
2	62	SER	SER	H	K	0 - 327	18 - 345
1	63	MET	MET	A	I	1 - 327	19 - 345
2	63	MET	MET	I	L	1 - 327	19 - 345
1	64	MET	MET	D	J	1 - 327	19 - 345
2	64	MET	MET	H	K	1 - 327	19 - 345
1	65	MET	MET	D	J	1 - 327	19 - 345
2	65	MET	MET	I	L	1 - 327	19 - 345
1	66	MET	MET	H	K	1 - 327	19 - 345
2	66	MET	MET	I	L	1 - 327	19 - 345

NCS ensembles :

#1: Protein	Probable ss-1,3-N-acetylglucosaminyltransferase / TarP-6RboP-(CH2)6NH2 Mass: 39888.680 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus subsp. aureus N315 (bacteria) Gene: SA1808 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0H3JNB0
#2: Chemical	ChemComp-FQ8 / [(2~{R},3~{S},4~{S})-2,3,4,5-tetrakis(oxidanyl)pentyl] [(2~{R},3~{R},4~{S})-2,3,4-tris(oxidanyl)-5-[oxidanyl-[(2~{R},3~{S},4~{S})-2,3,4-tris(oxidanyl)-5-phosphonooxy-pentoxy]phosphoryl]oxy-pentyl] hydrogen phosphate Mass: 660.346 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C₁₅H₃₅O₂₂P₃ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: Cl
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1436 / 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: 2.58 Å³/Da / Density % sol: 52.36 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 25% PEG 3350, 250 mM magnesium chloride, 0.1 M sodium citrate, pH 5.7

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00002 Å
Detector	Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jan 30, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.00002 Å / Relative weight: 1
Reflection	Resolution: 2.4→48.5 Å / Num. obs: 188717 / % possible obs: 99.9 % / Redundancy: 6.2 % / Net I/σ(I): 10.84
Reflection shell	Resolution: 2.4→2.46 Å

-
Processing

Software

Name	Version	Classification
REFMAC	5.8.0232	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Resolution: 2.4→48.51 Å / Cor.coef. F_o:F_c: 0.957 / Cor.coef. F_o:F_c free: 0.933 / SU B: 18.836 / SU ML: 0.211 / Cross valid method: THROUGHOUT / ESU R: 0.34 / ESU R Free: 0.232 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.22781	9436	5 %	RANDOM
R_work	0.18372	-	-	-
obs	0.18593	179281	99.94 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 46.749 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.33 Å²	-0 Å²	-0.45 Å²
2-	-	0.27 Å²	0 Å²
3-	-	-	-0.58 Å²

Refinement step

Cycle: 1 / Resolution: 2.4→48.51 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	29279	0	501	1436	31216

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.013	30238
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.017	27344
X-RAY DIFFRACTION	r_angle_refined_deg	1.314	1.661	40837
X-RAY DIFFRACTION	r_angle_other_deg	1.412	1.599	63355
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.597	5	3745
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.515	23.912	1411
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.993	15	5259
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.937	15	104
X-RAY DIFFRACTION	r_chiral_restr	0.061	0.2	4233
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	33238
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	6070
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	5.643	11.031	15060
X-RAY DIFFRACTION	r_mcbond_other	5.643	11.031	15059
X-RAY DIFFRACTION	r_mcangle_it	7.531	14.839	18775
X-RAY DIFFRACTION	r_mcangle_other	7.531	14.839	18776
X-RAY DIFFRACTION	r_scbond_it	7.041	11.926	15178
X-RAY DIFFRACTION	r_scbond_other	7.037	11.926	15178
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	9.32	15.614	22062
X-RAY DIFFRACTION	r_long_range_B_refined	11.458	62.008	127595
X-RAY DIFFRACTION	r_long_range_B_other	11.459	61.892	127070
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

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	B	10296	0.07
1	2	C	10296	0.07
2	1	B	10456	0.07
2	2	F	10456	0.07
3	1	B	10508	0.06
3	2	O	10508	0.06
4	1	B	8197	0.08
4	2	P	8197	0.08
5	1	B	10507	0.06
5	2	E	10507	0.06
6	1	B	10407	0.06
6	2	G	10407	0.06
7	1	B	9258	0.09
7	2	Q	9258	0.09
8	1	B	10455	0.06
8	2	A	10455	0.06
9	1	B	10474	0.06
9	2	D	10474	0.06
10	1	B	10773	0.05
10	2	H	10773	0.05
11	1	B	10276	0.07
11	2	I	10276	0.07
12	1	C	10289	0.06
12	2	F	10289	0.06
13	1	C	10300	0.05
13	2	O	10300	0.05
14	1	C	8190	0.09
14	2	P	8190	0.09
15	1	C	10281	0.06
15	2	E	10281	0.06
16	1	C	10371	0.05
16	2	G	10371	0.05
17	1	C	9260	0.07
17	2	Q	9260	0.07
18	1	C	10243	0.06
18	2	A	10243	0.06
19	1	C	10312	0.06
19	2	D	10312	0.06
20	1	C	10288	0.07
20	2	H	10288	0.07
21	1	C	10287	0.06
21	2	I	10287	0.06
22	1	F	10604	0.06
22	2	O	10604	0.06
23	1	F	8212	0.09
23	2	P	8212	0.09
24	1	F	10437	0.07
24	2	E	10437	0.07
25	1	F	10428	0.06
25	2	G	10428	0.06
26	1	F	9291	0.08
26	2	Q	9291	0.08
27	1	F	10422	0.07
27	2	A	10422	0.07
28	1	F	10454	0.07
28	2	D	10454	0.07
29	1	F	10458	0.07
29	2	H	10458	0.07
30	1	F	10312	0.06
30	2	I	10312	0.06
31	1	O	8234	0.08
31	2	P	8234	0.08
32	1	O	10392	0.06
32	2	E	10392	0.06
33	1	O	10406	0.05
33	2	G	10406	0.05
34	1	O	9322	0.08
34	2	Q	9322	0.08
35	1	O	10374	0.06
35	2	A	10374	0.06
36	1	O	10493	0.05
36	2	D	10493	0.05
37	1	O	10510	0.06
37	2	H	10510	0.06
38	1	O	10330	0.06
38	2	I	10330	0.06
39	1	P	8137	0.09
39	2	E	8137	0.09
40	1	P	8186	0.09
40	2	G	8186	0.09
41	1	P	8134	0.09
41	2	Q	8134	0.09
42	1	P	8095	0.09
42	2	A	8095	0.09
43	1	P	8184	0.08
43	2	D	8184	0.08
44	1	P	8186	0.09
44	2	H	8186	0.09
45	1	P	8181	0.08
45	2	I	8181	0.08
46	1	E	10389	0.06
46	2	G	10389	0.06
47	1	E	9235	0.09
47	2	Q	9235	0.09
48	1	E	10626	0.05
48	2	A	10626	0.05
49	1	E	10407	0.07
49	2	D	10407	0.07
50	1	E	10535	0.06
50	2	H	10535	0.06
51	1	E	10259	0.07
51	2	I	10259	0.07
52	1	G	9292	0.08
52	2	Q	9292	0.08
53	1	G	10379	0.06
53	2	A	10379	0.06
54	1	G	10532	0.04
54	2	D	10532	0.04
55	1	G	10433	0.06
55	2	H	10433	0.06
56	1	G	10336	0.05
56	2	I	10336	0.05
57	1	Q	9198	0.08
57	2	A	9198	0.08
58	1	Q	9282	0.08
58	2	D	9282	0.08
59	1	Q	9267	0.09
59	2	H	9267	0.09
60	1	Q	9308	0.07
60	2	I	9308	0.07
61	1	A	10387	0.06
61	2	D	10387	0.06
62	1	A	10492	0.06
62	2	H	10492	0.06
63	1	A	10218	0.06
63	2	I	10218	0.06
64	1	D	10478	0.06
64	2	H	10478	0.06
65	1	D	10345	0.05
65	2	I	10345	0.05
66	1	H	10289	0.06
66	2	I	10289	0.06

LS refinement shell

Resolution: 2.4→2.462 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.334	696	-
R_work	0.307	13229	-
obs	-	-	99.89 %

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	0.8747	0.0888	0.302	0.0437	0.1082	0.3422	0.0682	0.0879	-0.0113	0.0226	-0.0351	-0.0018	0.0356	0.0128	-0.0331	0.0223	-0.0298	0.0052	0.265	-0.0137	0.2642	-107.9438	-37.8934	479.5777
2	0.519	0.1928	-0.078	0.6445	0.3317	0.279	-0.0168	0.0215	-0.0282	-0.1048	0.1419	-0.0674	-0.0539	0.0577	-0.1251	0.0287	-0.0731	0.022	0.2612	-0.076	0.2841	-55.5306	-14.8138	500.6158
3	0.1955	-0.2924	-0.2282	0.7722	0.4587	0.5229	-0.0938	0.0763	-0.033	0.1289	-0.0011	0.0851	0.0579	0.0143	0.0949	0.0537	-0.0447	0.0207	0.2478	-0.0242	0.2732	-108.5011	-4.4307	528.2333
4	0.3211	0.1722	0.107	0.7327	0.4013	0.3715	-0.108	-0.042	0.0337	-0.1291	0.0393	0.0961	-0.0431	0.0315	0.0687	0.0505	0.0112	-0.0257	0.2313	0.0141	0.2631	-60.7525	-91.7023	453.2128
5	1.7944	0.1127	-0.9367	1.0834	0.7749	1.8225	0.0524	0.0799	0.0755	0.0891	0.1065	-0.006	-0.3688	-0.2407	-0.1588	0.2547	0.1378	0.0511	0.4052	0.159	0.066	-106.8723	-18.4447	565.9233
6	0.7508	-0.3902	-0.3581	0.2042	0.1966	0.2682	0.0719	0.0812	0.0741	-0.0325	-0.0504	-0.0297	0.0168	-0.0767	-0.0215	0.0392	0.0276	-0.0027	0.3208	-0.0047	0.2271	-60.5676	-42.5406	461.1179
7	0.6738	-0.0443	0.2275	0.3101	-0.04	0.223	0.0615	0.0169	0.0613	-0.0243	-0.0296	-0.1498	-0.0074	-0.0738	-0.0318	0.0312	-0.005	0.0076	0.2354	-0.0047	0.2694	-7.3452	-65.3843	440.3377
8	0.707	0.1013	1.1403	0.1551	-0.0307	2.2752	0.1636	-0.1473	-0.1557	-0.0736	0.0777	-0.0825	0.4645	-0.2627	-0.2412	0.1339	-0.0876	-0.0363	0.3647	0.0527	0.1585	-59.09	-78.2608	414.7716
9	0.6628	0.4137	0.3281	0.2667	0.2232	0.214	0.0719	-0.0513	-0.0818	0.035	-0.0402	-0.0275	0.0045	-0.0383	-0.0317	0.0299	-0.0299	0.0004	0.2944	0.0154	0.2597	-108.2993	-54.253	520.8785
10	0.741	0.0648	-0.2947	0.3839	0.1282	0.3115	0.1066	-0.0241	-0.0334	0.0777	-0.0187	-0.1476	0.0196	-0.0614	-0.0879	0.0687	-0.0133	-0.059	0.2028	0.0131	0.2467	-54.9317	-30.7217	541.0139
11	0.6953	-0.0358	-0.2626	0.0322	0.0838	0.3238	0.068	-0.0475	0.0369	-0.0084	-0.0265	0.0025	-0.0035	-0.0025	-0.0415	0.0284	0.0113	-0.0009	0.2672	-0.0022	0.2723	-60.1488	-59.0878	502.2997
12	0.6254	-0.2106	0.1148	0.5726	0.3085	0.4286	-0.0274	-0.0081	0.0718	0.1332	0.1701	-0.0745	0.095	0.0583	-0.1427	0.042	0.0757	-0.0427	0.2466	-0.0752	0.2901	-7.9612	-81.8046	480.5974

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	B	1 - 327
2	X-RAY DIFFRACTION	2	C	1 - 327
3	X-RAY DIFFRACTION	3	F	1 - 327
4	X-RAY DIFFRACTION	4	O	1 - 327
5	X-RAY DIFFRACTION	5	P	1 - 327
6	X-RAY DIFFRACTION	6	E	1 - 327
7	X-RAY DIFFRACTION	7	G	1 - 327
8	X-RAY DIFFRACTION	8	Q	1 - 327
9	X-RAY DIFFRACTION	9	A	1 - 327
10	X-RAY DIFFRACTION	10	D	1 - 327
11	X-RAY DIFFRACTION	11	H	1 - 327
12	X-RAY DIFFRACTION	12	I	1 - 327

-
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