PDB-6h4f: TarP-3RboP

ID or keywords:

Entry

Database: PDB / ID: 6h4f

Title

TarP-3RboP

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 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.18 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	Jul 21, 2018	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Sep 26, 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 / Derived calculations Category: citation / citation_author ...citation / citation_author / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.value
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	Jan 17, 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	6h4f.cif.gz	1.5 MB	Display	PDBx/mmCIF format
PDB format	pdb6h4f.ent.gz	1.2 MB	Display	PDB format
PDBx/mmJSON format	6h4f.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	6h4f_validation.pdf.gz	3.2 MB	Display	wwPDB validaton report
Full document	6h4f_full_validation.pdf.gz	3.2 MB	Display
Data in XML	6h4f_validation.xml.gz	156.2 KB	Display
Data in CIF	6h4f_validation.cif.gz	218.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/h4/6h4f ftp://data.pdbj.org/pub/pdb/validation_reports/h4/6h4f	HTTPS FTP

-
Related structure data

Related structure data	6h1jSC 6h21C 6h2nC 6h4mC 6hnqC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	1jqy-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

6h1jSC

S: Starting model for refinement

C: citing same article (ref.)

Similar structure data

1jqy-d

-
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)	95.610, 217.270, 123.990
Angle α, β, γ (deg.)	90.00, 91.38, 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 - 327	19 - 345
2	2	MET	MET	F	C	1 - 327	19 - 345
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	SER	SER	B	A	0 - 327	18 - 345
2	11	SER	SER	I	L	0 - 327	18 - 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 - 327	19 - 345
2	14	MET	MET	P	E	1 - 327	19 - 345
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 - 327	19 - 345
2	29	MET	MET	H	K	1 - 327	19 - 345
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 - 327	19 - 345
2	39	MET	MET	E	F	1 - 327	19 - 345
1	40	MET	MET	P	E	1 - 327	19 - 345
2	40	MET	MET	G	G	1 - 327	19 - 345
1	41	MET	MET	P	E	1 - 327	19 - 345
2	41	MET	MET	Q	H	1 - 327	19 - 345
1	42	MET	MET	P	E	1 - 327	19 - 345
2	42	MET	MET	A	I	1 - 327	19 - 345
1	43	MET	MET	P	E	1 - 327	19 - 345
2	43	MET	MET	D	J	1 - 327	19 - 345
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 - 327	19 - 345
2	45	MET	MET	I	L	1 - 327	19 - 345
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	SER	SER	E	F	0 - 327	18 - 345
2	51	SER	SER	I	L	0 - 327	18 - 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	SER	SER	A	I	0 - 327	18 - 345
2	63	SER	SER	I	L	0 - 327	18 - 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	SER	SER	H	K	0 - 327	18 - 345
2	66	SER	SER	I	L	0 - 327	18 - 345

NCS ensembles :

-
Protein , 1 types, 12 molecules BCFOPEGQADHI

#1: Protein	Probable ss-1,3-N-acetylglucosaminyltransferase Mass: 39888.680 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (strain N315) (bacteria) Strain: N315 / Gene: SA1808 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0H3JNB0

-
Non-polymers , 5 types, 2366 molecules

#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
#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: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 2332 / 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: 2.69 Å³/Da / Density % sol: 54.27 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.7 Details: 25% PEG 3350, 250 mM magnesium chloride, 0.1 M sodium citrate, pH 5.7. PH range: 5.4-6.0

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
Detector	Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 5, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.18→49.8 Å / Num. obs: 262098 / % possible obs: 100 % / Redundancy: 7 % / R_sym value: 0.137 / Net I/σ(I): 11.9
Reflection shell	Resolution: 2.18→2.22 Å

-
Processing

Software

Name	Version	Classification
REFMAC	5.8.0230	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 6H1J

6h1j

Resolution: 2.18→49.75 Å / Cor.coef. F_o:F_c: 0.966 / Cor.coef. F_o:F_c free: 0.951 / SU B: 10.886 / SU ML: 0.137 / Cross valid method: THROUGHOUT / ESU R: 0.2 / ESU R Free: 0.164 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.20478	13105	5 %	RANDOM
R_work	0.17203	-	-	-
obs	0.17365	248993	99.95 %	-

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: 43.87 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.35 Å²	-0 Å²	0.09 Å²
2-	-	0.15 Å²	0 Å²
3-	-	-	0.2 Å²

Refinement step

Cycle: 1 / Resolution: 2.18→49.75 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	29734	0	507	2332	32573

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.014	30738
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.017	27594
X-RAY DIFFRACTION	r_angle_refined_deg	1.226	1.672	41467
X-RAY DIFFRACTION	r_angle_other_deg	1	1.661	64397
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.031	5	3752
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.065	24.024	1476
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.24	15	5532
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	14.794	15	107
X-RAY DIFFRACTION	r_chiral_restr	0.062	0.2	4250
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	33675
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	5693
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	4.752	8.951	15071
X-RAY DIFFRACTION	r_mcbond_other	4.749	8.95	15070
X-RAY DIFFRACTION	r_mcangle_it	6.146	12.027	18790
X-RAY DIFFRACTION	r_mcangle_other	6.147	12.027	18791
X-RAY DIFFRACTION	r_scbond_it	6.508	10.131	15667
X-RAY DIFFRACTION	r_scbond_other	6.504	10.13	15667
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	8.429	13.089	22674
X-RAY DIFFRACTION	r_long_range_B_refined	9.93	51.623	131289
X-RAY DIFFRACTION	r_long_range_B_other	9.93	51.622	131289
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	10513	0.06
1	2	C	10513	0.06
2	1	B	10598	0.05
2	2	F	10598	0.05
3	1	B	10624	0.06
3	2	O	10624	0.06
4	1	B	9448	0.07
4	2	P	9448	0.07
5	1	B	10688	0.06
5	2	E	10688	0.06
6	1	B	10485	0.06
6	2	G	10485	0.06
7	1	B	9845	0.07
7	2	Q	9845	0.07
8	1	B	10684	0.05
8	2	A	10684	0.05
9	1	B	10498	0.06
9	2	D	10498	0.06
10	1	B	10788	0.05
10	2	H	10788	0.05
11	1	B	10382	0.06
11	2	I	10382	0.06
12	1	C	10569	0.04
12	2	F	10569	0.04
13	1	C	10598	0.04
13	2	O	10598	0.04
14	1	C	9445	0.07
14	2	P	9445	0.07
15	1	C	10543	0.06
15	2	E	10543	0.06
16	1	C	10578	0.05
16	2	G	10578	0.05
17	1	C	9870	0.07
17	2	Q	9870	0.07
18	1	C	10499	0.06
18	2	A	10499	0.06
19	1	C	10537	0.05
19	2	D	10537	0.05
20	1	C	10486	0.06
20	2	H	10486	0.06
21	1	C	10463	0.04
21	2	I	10463	0.04
22	1	F	10713	0.05
22	2	O	10713	0.05
23	1	F	9480	0.07
23	2	P	9480	0.07
24	1	F	10582	0.06
24	2	E	10582	0.06
25	1	F	10535	0.05
25	2	G	10535	0.05
26	1	F	9898	0.07
26	2	Q	9898	0.07
27	1	F	10556	0.06
27	2	A	10556	0.06
28	1	F	10478	0.05
28	2	D	10478	0.05
29	1	F	10546	0.06
29	2	H	10546	0.06
30	1	F	10382	0.06
30	2	I	10382	0.06
31	1	O	9474	0.07
31	2	P	9474	0.07
32	1	O	10606	0.05
32	2	E	10606	0.05
33	1	O	10556	0.05
33	2	G	10556	0.05
34	1	O	9956	0.07
34	2	Q	9956	0.07
35	1	O	10581	0.05
35	2	A	10581	0.05
36	1	O	10513	0.05
36	2	D	10513	0.05
37	1	O	10603	0.06
37	2	H	10603	0.06
38	1	O	10439	0.05
38	2	I	10439	0.05
39	1	P	9406	0.08
39	2	E	9406	0.08
40	1	P	9430	0.07
40	2	G	9430	0.07
41	1	P	9307	0.07
41	2	Q	9307	0.07
42	1	P	9394	0.07
42	2	A	9394	0.07
43	1	P	9438	0.07
43	2	D	9438	0.07
44	1	P	9417	0.07
44	2	H	9417	0.07
45	1	P	9394	0.06
45	2	I	9394	0.06
46	1	E	10523	0.05
46	2	G	10523	0.05
47	1	E	9863	0.07
47	2	Q	9863	0.07
48	1	E	10720	0.05
48	2	A	10720	0.05
49	1	E	10478	0.06
49	2	D	10478	0.06
50	1	E	10712	0.06
50	2	H	10712	0.06
51	1	E	10389	0.06
51	2	I	10389	0.06
52	1	G	9847	0.07
52	2	Q	9847	0.07
53	1	G	10453	0.06
53	2	A	10453	0.06
54	1	G	10592	0.04
54	2	D	10592	0.04
55	1	G	10465	0.06
55	2	H	10465	0.06
56	1	G	10394	0.05
56	2	I	10394	0.05
57	1	Q	9820	0.07
57	2	A	9820	0.07
58	1	Q	9835	0.07
58	2	D	9835	0.07
59	1	Q	9825	0.07
59	2	H	9825	0.07
60	1	Q	9820	0.07
60	2	I	9820	0.07
61	1	A	10442	0.05
61	2	D	10442	0.05
62	1	A	10663	0.05
62	2	H	10663	0.05
63	1	A	10364	0.05
63	2	I	10364	0.05
64	1	D	10473	0.05
64	2	H	10473	0.05
65	1	D	10384	0.05
65	2	I	10384	0.05
66	1	H	10367	0.05
66	2	I	10367	0.05

LS refinement shell

Resolution: 2.18→2.236 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.314	964	-
R_work	0.306	18332	-
obs	-	-	99.9 %

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	0.8213	0.0483	0.3162	0.0968	0.09	0.2567	0.1321	0.1301	-0.0458	0.0725	-0.0742	0.0155	0.0451	0.0022	-0.0579	0.1097	-0.0248	0.0213	0.3031	-0.0455	0.133	-106.7827	-32.2005	484.5335
2	0.5154	0.1607	-0.1347	0.6593	0.3182	0.2647	0.0438	0.015	0.0013	-0.0809	0.0689	-0.1376	-0.0526	0.003	-0.1127	0.1176	-0.0507	0.043	0.257	-0.0762	0.1795	-54.2276	-8.6911	505.0951
3	0.2312	-0.2094	-0.1641	0.8075	0.3499	0.2826	-0.1462	0.0474	0.0206	0.1282	0.0821	0.0814	0.0952	0.0166	0.0642	0.1194	-0.0141	0.0265	0.2626	-0.006	0.1302	-106.8086	2.7601	533.0425
4	0.2497	0.2319	0.0683	0.7585	0.3182	0.2247	-0.1102	-0.0466	-0.0148	-0.1399	0.0403	0.0941	-0.0884	0.0277	0.07	0.129	0.0218	-0.0624	0.2661	-0.0014	0.1174	-59.0241	-88.3998	459.0036
5	1.2446	-0.5821	-0.8767	0.3621	0.0842	1.9858	0.1429	-0.0717	0.1577	0.0198	0.1041	-0.0671	-0.5038	-0.1231	-0.247	0.2479	0.0481	0.083	0.313	-0.006	0.0968	-105.0311	-11.5118	572.1531
6	0.574	-0.3063	-0.318	0.1938	0.1841	0.2352	0.0471	0.0284	0.1183	-0.019	0.0207	-0.0273	0.0373	-0.0305	-0.0678	0.0877	0.0201	-0.033	0.3145	-0.0362	0.1297	-58.9905	-37.1874	465.9514
7	0.7392	-0.0945	0.2039	0.6244	-0.1139	0.0928	0.0048	-0.0323	0.0269	-0.0268	-0.0174	-0.1618	-0.0224	-0.0572	0.0126	0.1228	-0.0134	0.0116	0.2663	-0.0281	0.1255	-5.6747	-60.6124	445.8062
8	0.8448	0.3891	0.7969	0.2725	0.0877	2.1485	0.1417	0.0558	-0.0464	0.0343	0.0374	-0.0209	0.5928	-0.1377	-0.1791	0.2658	-0.1107	-0.0888	0.3639	0.0021	0.0351	-57.6558	-73.8563	418.995
9	0.8046	0.4074	0.4835	0.2727	0.288	0.3954	0.0623	-0.024	-0.109	0.0113	0.011	-0.03	-0.0503	-0.0251	-0.0732	0.0939	-0.0311	-0.0001	0.3118	-0.0242	0.1111	-106.675	-49.0566	526.6399
10	0.7337	0.2077	-0.0544	0.3597	-0.0461	0.2379	0.0592	0.0664	-0.0238	0.0738	-0.013	-0.1134	0.057	-0.0227	-0.0462	0.1103	0.0186	-0.0475	0.2518	-0.0264	0.1471	-53.4343	-24.9303	546.2077
11	0.6708	0.038	-0.2061	0.0915	0.0905	0.2834	0.1027	-0.0958	0.0763	-0.0501	-0.0591	0.0188	-0.0176	-0.0039	-0.0436	0.112	0.0177	-0.0333	0.3104	-0.0414	0.1198	-58.7627	-54.1246	507.7663
12	0.7436	-0.211	0.2849	0.6694	0.2795	0.3372	0.0554	0.0067	0.0144	0.1484	0.0523	-0.1515	0.1089	-0.0017	-0.1078	0.1415	0.0516	-0.0729	0.2604	-0.0571	0.166	-6.3074	-77.2293	486.4192

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

-
Protein , 1 types, 12 molecules BCFOPEGQADHI

-
Non-polymers , 5 types, 2366 molecules

-
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

-Protein , 1 types, 12 molecules BCFOPEGQADHI

-Non-polymers , 5 types, 2366 molecules

-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

-
Protein , 1 types, 12 molecules BCFOPEGQADHI

-
Non-polymers , 5 types, 2366 molecules

-
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