PDB-2y7a: Crystal structure of unliganded GTB P156L

ID or keywords:

Entry

Database: PDB / ID: 2y7a

Title

Crystal structure of unliganded GTB P156L

Components

ABO GLYCOSYLTRANSFERASE

Keywords

TRANSFERASE /

ABO BLOOD GROUP

Function / homology

Function and homology information

fucosylgalactoside 3-alpha-galactosyltransferase / glycoprotein-fucosylgalactoside alpha-N-acetylgalactosaminyltransferase / glycoprotein-fucosylgalactoside alpha-N-acetylgalactosaminyltransferase activity /

fucosylgalactoside 3-alpha-galactosyltransferase activity / ABO blood group biosynthesis /

hexosyltransferase activity / lipid glycosylation / Golgi cisterna membrane / protein glycosylation /

antigen binding ...
Similarity search - Function

Biological species

HOMO SAPIENS (human)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 2.06 Å

Authors

Weadge, J. / Palcic, M.M. / Henriksen, A.

Citation

Journal: To be Published
Title: Structural and Biochemical Characterization of the Human Blood Group a and B Galactosyltransferases Possessing the Pro156Leu Mutation
Authors: Weadge, J. / Palcic, M.M. / Henriksen, A.

History

Deposition	Jan 31, 2011	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Feb 15, 2012	Provider: repository / Type: Initial release
Revision 1.1	Oct 3, 2012	Group: Derived calculations
Revision 1.2	Jul 12, 2017	Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.3	Dec 20, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	2y7a.cif.gz	465.9 KB	Display	PDBx/mmCIF format
PDB format	pdb2y7a.ent.gz	385.9 KB	Display	PDB format
PDBx/mmJSON format	2y7a.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/y7/2y7a ftp://data.pdbj.org/pub/pdb/validation_reports/y7/2y7a	HTTPS FTP

-
Related structure data

Related structure data	1zizS S: Starting model for refinement
Similar structure data	1r82-2 1lzj-2 2rit-2 6bjl-2 1r81-2 3sxd-2 1wt2-2 5nue-2 4frh-1 3sx8-2 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

1zizS

S: Starting model for refinement

Similar structure data

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#156 - Dec 2012 ABO Blood Type Glycosyltransferases similarity (9) #254 - Feb 2021 Cellulose Synthase similarity (2) #141 - Sep 2011 O-GlcNAc Transferase similarity (1)

Deposited unit

A: ABO GLYCOSYLTRANSFERASE

B: ABO GLYCOSYLTRANSFERASE

C: ABO GLYCOSYLTRANSFERASE

D: ABO GLYCOSYLTRANSFERASE

hetero molecules

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

1

A: ABO GLYCOSYLTRANSFERASE

B: ABO GLYCOSYLTRANSFERASE

hetero molecules

defined by author&software
69.8 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: ABO GLYCOSYLTRANSFERASE

D: ABO GLYCOSYLTRANSFERASE

defined by author&software
69.4 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

D: ABO GLYCOSYLTRANSFERASE

C: ABO GLYCOSYLTRANSFERASE

defined by author&software
69.4 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	63.730, 78.290, 143.740
Angle α, β, γ (deg.)	90.00, 88.96, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	ABO GLYCOSYLTRANSFERASE Mass: 34676.098 Da / Num. of mol.: 4 / Fragment: RESIDUES 54-344 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q70V26, UniProt: P16442*PLUS, fucosylgalactoside 3-alpha-galactosyltransferase
#2: Chemical	ChemComp-MN / MANGANESE (II) ION Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#3: Chemical	ChemComp-UDP / URIDINE-5'-DIPHOSPHATE / Uridine diphosphate Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₉H₁₄N₂O₁₂P₂ / Comment: UDP*YM
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 376 / Source method: isolated from a natural source / Formula: H₂O
Compound details	ENGINEERED RESIDUE IN CHAIN A, PRO 146 TO LEU ENGINEERED RESIDUE IN CHAIN B, PRO 146 TO LEU ...ENGINEERED RESIDUE IN CHAIN A, PRO 146 TO LEU ENGINEERED RESIDUE IN CHAIN B, PRO 146 TO LEU ENGINEERED RESIDUE IN CHAIN C, PRO 146 TO LEU ENGINEERED RESIDUE IN CHAIN D, PRO 146 TO LEU
Sequence details	N-TERMINAL DISCREPANCIES ENGINEERED TO CONSTRUCT EXPRESSION PLASMID.

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.72 Å³/Da / Density % sol: 54.8 % / Description: NONE
Crystal grow	pH: 7 Details: 5 MM MOPS PH 7, 1 MM MNCL2, 1 MM DTT, 0.1 M AMSO4, 10% (W/V) PEG 3350.

-
Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418

Detector

Type: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Details: MIRRORS

Radiation

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

Radiation wavelength

Wavelength: 1.5418 Å / Relative weight: 1

Reflection twin

Crystal-ID	ID	Operator	Domain-ID	Fraction
1	1	H, K, L	1	0.55
1	1	h,-k,-l	2	0.45

Reflection

Resolution: 2.06→143.76 Å / Num. obs: 75523 / % possible obs: 93.2 % / Observed criterion σ(I): 0 / Redundancy: 2.5 % / B_iso Wilson estimate: 29.955 Å² / R_merge(I) obs: 0.07 / Net I/σ(I): 12.6

Reflection shell

Resolution: 2.06→2.16 Å / Redundancy: 2.8 % / R_merge(I) obs: 0.35 / Mean I/σ(I) obs: 2.6 / % possible all: 77.6

-
Processing

Software

Name	Version	Classification
REFMAC	5.5.0109	refinement
MOSFLM		data reduction
SCALA		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ZIZ

1ziz

Resolution: 2.06→143.76 Å / Cor.coef. F_o:F_c: 0.935 / Cor.coef. F_o:F_c free: 0.92 / SU B: 9.629 / SU ML: 0.113 / Cross valid method: THROUGHOUT / ESU R: 0.049 / ESU R Free: 0.039 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DISORDERED REGIONS AND SIDECHAINS WERE NOT MODELED.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.24453	4047	5.1 %	RANDOM
R_work	0.21567	-	-	-
obs	0.21716	75523	91 %	-

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 mean: 39.362 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	7.46 Å²	0 Å²	-6.98 Å²
2-	-	-27.82 Å²	0 Å²
3-	-	-	20.35 Å²

Refinement step

Cycle: LAST / Resolution: 2.06→143.76 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8969	0	26	376	9371

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.022	9253
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	0.984	1.952	12570
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.289	5	1097
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.235	22.648	438
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.213	15	1529
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	13.104	15	74
X-RAY DIFFRACTION	r_chiral_restr	0.071	0.2	1370
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.021	7063
X-RAY DIFFRACTION	r_gen_planes_other
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	0.164	1.5	5502
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	0.295	2	8936
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	0.504	3	3751
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	0.79	4.5	3634
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.061→2.114 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.3	174	-
R_work	0.297	2951	-
obs	-	-	48.82 %

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	6.7791	-6.8043	3.7399	-2.5962	1.6671	-0.7683	0.1026	-0.4293	-0.1546	0.4572	0.32	-0.0165	0.2435	-0.1271	-0.4226	0.3232	-0.0851	0.0714	0.3144	-0.0487	0.3065	-5.598	31.062	-9.991
2	6.1848	1.5886	4.9253	0.2122	2.1143	6.71	-0.0665	0.3894	0.1572	-0.2273	0.0471	-0.1768	-0.0498	0.1513	0.0194	0.2994	0.007	0.1566	0.3601	0.0152	0.2283	-8.496	29.942	-26.816
3	1.999	1.1097	0.9253	1.8325	0.6348	0.0758	0.0434	0.1353	0.0265	-0.1541	0.0138	-0.0755	-0.0132	0.0727	-0.0572	0.1305	0.031	0.0805	0.2734	0.0075	0.0995	-9.187	17.278	-23.24
4	0.2027	-18.7594	-4.2383	29.3121	-17.9336	19.2946	-0.0824	-0.6044	0.0618	0.5282	0.1033	-0.4394	-0.4745	0.0775	-0.021	0.2084	-0.062	0.0686	0.3563	-0.0457	0.2278	-1.73	23.793	-7.556
5	3.4321	0.9886	0.6986	1.4794	0.7624	1.7934	0.1576	0.0872	-0.4311	-0.0229	-0.1249	-0.2092	0.3027	0.1137	-0.0327	0.1442	-0.005	0.0424	0.2935	-0.0329	0.1403	5.586	-1.628	-9.783
6	3.0058	-0.7569	2.6001	4.7107	-0.5689	1.5626	0.2424	0.29	-0.0514	-0.3613	-0.0712	-0.4426	0.0337	0.2869	-0.1712	0.1379	-0.0052	0.1187	0.3774	-0.0891	0.2247	9.414	9.251	-14.674
7	3.3398	-0.5055	3.5294	8.2496	-13.2228	10.4822	0.0743	-0.017	0.0131	0.3793	-0.2172	-0.0488	-0.4736	-0.0609	0.1429	0.0963	-0.0132	0.0791	0.2999	0.0049	0.1171	5.7	8.419	-4.609
8	1.6727	-0.3951	0.8034	6.6005	0.4993	1.1979	0.1125	0.0183	-0.1165	-0.0243	-0.0452	-0.5676	0.1087	0.1908	-0.0673	0.1625	0.0157	0.0665	0.3571	0.012	0.2121	12.315	2.671	-5.162
9	-5.9628	-1.0607	-9.1167	-0.4422	-4.3541	2.1371	-0.0237	0.3759	0.1075	-0.2857	-0.0408	0.1443	0.6515	0.2107	0.0645	0.4014	0.0701	0.0271	0.4952	0.0016	0.3787	1.503	-8.334	-2.108
10	2.4865	2.3182	2.878	6.5152	3.8548	6.8494	0.21	-0.2213	-0.1416	0.3338	-0.0645	-0.1519	0.5005	-0.2386	-0.1455	0.1164	0.0285	0.0603	0.3085	0.0214	0.1293	-4.16	-2.799	-0.93
11	3.9024	0.4418	-2.9795	10.3344	0.4392	9.4715	-0.0663	-0.7032	0.015	0.5118	-0.0961	-0.0644	0.0819	0.258	0.1624	0.1248	-0.0254	0.0461	0.2877	-0.0053	0.0972	-1.445	8.414	1.631
12	0.4168	-0.6316	-0.235	6.9619	-1.0308	3.3347	-0.0076	0.0411	-0.0916	0.0798	0.0626	-0.1396	0.3409	0.1251	-0.055	0.0955	-0.0142	0.066	0.2988	-0.0609	0.1628	0.996	3.092	-13.363
13	2.8805	0.7234	2.3176	0.1397	-0.89	1.8208	-0.0219	-0.0068	-0.0766	-0.0842	-0.0543	-0.1233	-0.0892	0.1536	0.0761	0.1404	-0.0084	0.0878	0.2317	-0.0059	0.0989	0.541	12.4	-18.028
14	2.0771	-1.6077	-2.3419	-0.1409	0.1979	4.1218	0.0796	-0.014	0.0273	-0.1817	0.0778	0.0231	-0.1238	0.2986	-0.1574	0.148	-0.0434	0.0661	0.2982	-0.0002	0.1028	-10.186	2.713	-23.001
15	1.583	0.6015	-0.1793	2.3679	0.1586	0.9669	-0.0845	0.0901	-0.1916	-0.2541	0.0942	0.0445	0.1408	-0.0517	-0.0097	0.1077	0.0046	0.053	0.2549	-0.0123	0.0906	-16.725	-3.648	-18.37
16	4.5683	8.978	2.1495	14.8046	4.3291	1.0871	0.1679	-0.1672	0.0708	0.3458	-0.1766	0.238	0.1117	-0.0245	0.0087	0.0797	0.0277	0.0949	0.3009	0.0113	0.1098	-13.243	-2.225	-4.034
17	1.1895	-0.3446	-1.7541	11.0671	-5.3383	17.0974	-0.0574	-0.092	0.0068	-0.3753	-0.214	-0.5405	-0.108	0.8543	0.2714	0.0985	-0.0249	0.0775	0.3402	-0.0206	0.1626	-16.473	-16.505	-7.938
18	2.4558	-1.1502	-1.1909	6.1894	1.8515	3.1254	-0.0006	-0.0344	-0.0974	0.0982	0.0119	0.008	0.2272	0.0485	-0.0114	0.1205	0.0004	0.0278	0.2636	-0.0042	0.0767	-14.288	-5.057	-14.858
19	1.2411	-0.9925	-0.363	0.7339	-0.5342	1.4965	-0.0313	0.1759	-0.1094	-0.0265	-0.0457	0.015	0.0866	-0.046	0.077	0.097	-0.0204	0.0297	0.2534	-0.0629	0.0744	-7.156	6.397	-21.466
20	3.4911	2.0882	-1.2142	1.1906	2.5414	3.6863	-0.072	0.1513	-0.0784	0.042	0.211	-0.2296	0.2978	0.1038	-0.139	0.2524	0.0259	0.0783	0.3672	-0.0481	0.0736	1.452	4.811	-29.084
21	6.6422	-1.9583	0.1553	0.1701	1.617	0.2064	0.0114	0.0288	0.1053	0.0333	-0.0414	0.1916	-0.0934	-0.1077	0.0301	0.2761	-0.0062	0.058	0.2637	0.0085	0.2807	-27.13	2.644	-19.569
22	23.8931	0.1131	-5.9921	7.351	0.9992	20.4693	-0.3713	0.8757	-0.4872	-0.3592	-0.2472	0.2006	0.243	-0.422	0.6185	0.337	0.0246	0.1172	0.3237	-0.0522	0.1255	-16.483	8.506	-31.307
23	19.0246	21.753	8.9914	-3.7958	3.4809	25.1138	-0.0875	1.488	-1.7566	-0.1353	0.7983	-0.7546	1.3256	1.3706	-0.7108	0.4728	0.0334	0.1501	0.4953	-0.0521	0.1897	-19.031	20.91	-33.19
24	2.2005	0.0865	-0.145	2.2111	0.2892	0.5039	0.0328	0.0916	-0.2379	-0.1848	-0.0425	-0.0824	-0.02	-0.07	0.0097	0.0858	0.0241	0.039	0.2538	0.0001	0.0471	-21.098	18.962	-21.687
25	2.6686	-3.1414	-1.275	13.0432	2.1176	1.3566	-0.1282	-0.2189	-0.3751	0.2746	0.0774	0.3627	0.3255	0.1171	0.0508	0.152	0.0251	0.0552	0.3155	0.047	0.136	-30.685	18.896	-7.889
26	6.9443	0.0162	2.7733	2.3442	2.1922	5.1434	0.0382	0.0236	1.0844	-0.7337	-0.2462	0.286	-0.8643	-0.2613	0.2081	0.3588	0.0198	0.083	0.3347	0.0154	0.2935	-39.76	42.254	-11.813
27	1.9962	0.2974	-0.2783	4.2492	1.8614	3.004	0.0784	-0.0348	0.1041	0.0564	-0.1074	0.1892	0.0247	-0.1904	0.029	0.0501	-0.0004	0.0833	0.2959	0.0127	0.1089	-39.33	29.924	-10.108
28	4.1272	0.8883	0.9418	6.621	1.3716	2.3338	0.2413	-0.0806	0.258	-0.0641	-0.2071	0.4906	-0.1036	-0.2948	-0.0342	0.099	0.0006	0.1169	0.3298	-0.013	0.1569	-43.03	30.528	-5
29	3.1845	0.8131	0.3026	5.7752	-1.6704	2.0098	-0.0752	-0.1459	0.3391	0.4773	0.0529	-0.1077	-0.4902	0.0112	0.0222	0.1812	0.0102	0.0692	0.2949	-0.0378	0.1693	-25.978	42.74	-2.976
30	0.9249	-0.6659	1.1199	1.2164	0.782	4.5508	-0.0266	-0.1762	0.1785	0.4401	0.1188	-0.0327	0.0769	0.0472	-0.0922	0.1815	-0.0188	0.0607	0.3105	0.0225	0.138	-29.151	27.385	-0.849
31	1.7248	1.7246	1.6028	5.9328	4.9305	8.8853	-0.0511	0.2237	0.0871	-0.3919	0.1322	0.3825	-0.4193	0.1235	-0.0811	0.0926	0.0189	0.0489	0.2669	0.0424	0.1081	-34.81	31.484	-19.113
32	1.7653	0.4738	-0.9382	1.6756	0.8366	0.6255	0.0261	-0.024	0.1618	0.0023	0.0605	-0.0176	-0.0319	0.045	-0.0866	0.1107	0.0241	0.0581	0.2484	0.0118	0.0422	-22.913	28.879	-18.146
33	2.4207	0.8879	0.3418	3.1902	1.4992	2.9326	-0.0551	0.2012	0.2226	-0.4289	0.1665	-0.3555	-0.4609	0.3587	-0.1114	0.159	-0.0295	0.0919	0.2634	0.0313	0.1202	-11.263	43.772	-20.268
34	5.7583	1.1843	-0.6291	1.4133	-0.0213	1.3605	0.0242	0.0453	0.1888	-0.1392	0.0613	0.0081	-0.1814	0.0692	-0.0855	0.1147	0.0179	0.0658	0.2161	0.0017	0.0781	-15.297	36.98	-18.774
35	3.2554	5.9038	-1.1219	15.7269	-0.7155	4.7958	0.2914	-0.6204	-0.1477	0.5037	-0.3152	-0.3924	0.2045	0.2269	0.0238	0.0735	-0.0064	0.0192	0.2727	0.0084	0.0776	-19.511	31.578	-3.325
36	6.3565	4.9323	-1.5378	4.5232	-2.1236	-2.1487	0.2481	-0.2884	0.4111	0.3331	-0.1455	0.5268	-0.0724	-0.1201	-0.1026	0.2039	0.0096	0.0777	0.3713	-0.0136	0.1586	-16.119	46.241	-3.408
37	3.6745	0.734	0.0253	4.5893	1.0623	2.3889	0.0666	-0.0353	0.1947	-0.069	-0.1533	0.1626	-0.0971	-0.1329	0.0867	0.0981	0.0106	0.0638	0.2536	0.0294	0.0794	-16.637	45.341	-12.065
38	2.1616	0.3761	0.7708	1.2448	0.4371	1.0612	-0.0747	0.1502	-0.0427	0.0151	0.0762	0.0268	-0.1716	-0.0097	-0.0015	0.0966	-0.0139	0.0561	0.2085	0.0201	0.0642	-18.3	29.59	-17.666
39	14.6509	-0.1717	4.3051	16.6742	-17.5402	11.7135	-0.1982	-0.6067	0.0734	0.6143	0.0223	0.302	-0.8794	-0.1249	0.1758	0.4011	0.0002	-0.069	0.3305	0.0208	0.1233	-31.017	38.115	-30.059
40	1.3825	2.0179	0.8938	0.1106	-0.264	9.4605	0.0485	-0.0593	0.0294	-0.2321	-0.0002	0.1209	-0.0595	0.0508	-0.0483	0.2472	-0.0416	0.0409	0.2981	0.0633	0.1146	-31.5	30.398	-28.752
41	-0.4937	0.6077	0.2898	0.1219	-0.2415	0.2949	-0.0075	-0.0511	-0.0416	-0.0382	-0.0246	-0.2676	-0.064	0.1552	0.032	0.2818	0.0052	0.0717	0.4347	-0.0166	0.3573	-7.773	-30.894	-45.359
42	3.3837	0.7287	0.0603	3.6266	0.4178	1.1527	-0.2426	0.1173	-0.1849	-0.2687	0.2179	-0.1603	0.0409	0.1188	0.0247	0.1987	-0.044	0.0897	0.2935	0.0049	0.1032	-9.045	-19.385	-48.865
43	-2.6181	12.2808	5.023	27.1267	-3.1872	2.3114	0.3666	0.3185	-0.1577	-1.5148	-0.1096	0.1415	0.4432	0.6006	-0.2569	0.4211	-0.0554	0.2352	0.5072	-0.1047	0.4537	-0.773	-22.756	-64.634
44	4.843	1.136	3.465	5.2941	-0.4115	2.753	-0.0504	0.4951	0.435	0.3013	-0.1292	-0.0967	-0.3566	0.2855	0.1796	0.4123	-0.1102	0.1665	0.4706	-0.0436	0.2599	7.646	1.558	-59.037
45	1.0212	2.6421	3.9675	10.6251	2.6699	5.8311	-0.1293	-0.0019	0.0508	0.1108	0.1669	-0.2782	-0.0054	0.1718	-0.0375	0.2109	-0.0652	0.1587	0.4923	-0.0904	0.1965	9.267	-12.512	-55.671
46	4.821	-2.6555	-0.2509	-2.5389	-0.9445	4.1201	0.1333	-0.1759	0.3387	-0.5951	-0.1416	0.0241	0.1242	0.0177	0.0083	0.3747	-0.0237	0.1805	0.4711	-0.0702	0.2169	7.276	-4.801	-65.974
47	5.3638	-1.3903	0.2821	15.2427	-2.5251	2.8354	0.2154	-0.129	0.1667	0.6682	-0.1077	-0.1333	-0.1548	0.2772	-0.1077	0.3108	-0.0307	0.1366	0.448	-0.024	0.1456	11.786	-6.863	-66.259
48	13.2937	-2.0164	-1.0043	22.7592	14.5171	13.1133	0.1386	0.1347	-0.0315	-0.0741	0.1308	-0.5715	0.0364	-0.0017	-0.2694	0.2959	-0.0474	0.0499	0.4159	0.043	0.2139	-5.144	-0.127	-69.721
49	1.8839	-0.0097	-0.5077	1.095	-1.2664	2.2031	0.0064	0.0977	0.0085	-0.1221	0.109	-0.0121	-0.102	-0.0426	-0.1155	0.3504	-0.0599	0.0387	0.3993	-0.0157	0.2487	-0.122	-7.074	-64.652
50	6.9957	-0.0104	0.873	-1.6307	-0.7606	8.0415	-0.2389	0.0503	-0.5171	-0.1035	0.1678	-0.6655	-0.4633	-0.0135	0.0711	0.3901	-0.0807	0.1776	0.3664	-0.1153	0.3528	3.047	-13.796	-50.736
51	1.0295	-1.061	1.4548	-4.5661	-3.4787	-4.2621	0.1799	0.3143	-0.0685	-0.2088	-0.0691	0.3166	0.0172	-0.1427	-0.1107	0.4159	-0.1429	0.0884	0.3935	-0.0035	0.2279	-8.609	-9.978	-54.99
52	19.1576	5.965	-6.2416	18.7954	10.819	5.4754	-0.6433	-0.7669	0.1001	-0.9231	0.7328	0.2759	-0.1685	0.7115	-0.0895	0.3402	-0.0003	0.0315	0.3358	0.0222	0.2993	-10.063	-1.477	-41.966
53	1.1774	0.0839	-1.1903	0.9374	-0.5384	0.2042	-0.0218	-0.019	-0.3189	0.3562	-0.1414	-0.2548	-0.3011	-0.2092	0.1632	0.4555	0.0343	0.0456	0.4079	0.0189	0.508	-20.671	6.662	-50.281
54	16.0672	5.0822	-1.618	-1.9487	3.8286	4.9594	0.2291	-0.4512	1.5052	0.1196	-0.3893	0.5324	-0.2767	-0.147	0.1603	0.307	-0.0704	0.0806	0.3542	0.0191	0.5557	-19.511	-1.553	-48.548
55	1.9323	-1.592	-3.4443	0.8	-0.3595	-1.9836	0.2083	0.1863	-0.0524	-0.3583	-0.1686	-0.0927	-0.0616	-0.2874	-0.0397	0.3382	-0.0795	0.0203	0.4229	0.0028	0.2409	-10.288	-4.149	-62.979
56	11.241	-0.697	1.8516	5.0551	-8.1583	3.3213	-0.7495	-0.1444	-0.2418	0.5221	0.298	-0.1465	-0.0908	0.2841	0.4516	0.394	0.0965	0.0331	0.4158	-0.0671	0.261	-15.863	9.545	-66.069
57	2.3324	-2.4791	1.8646	-0.4143	-1.2726	3.9726	-0.009	0.1027	0.2871	0.047	0.0339	-0.1637	-0.2582	0.0706	-0.0249	0.3358	-0.0856	-0.0456	0.355	0.0175	0.325	-13.21	9.502	-57.658
58	-16.976	11.516	4.1553	8.7028	-8.9174	-1.8971	0.8552	0.5357	-0.5354	0.4385	-0.7445	-0.0003	-0.3483	-0.8579	-0.1107	0.5322	-0.0659	-0.0243	0.5791	0.2272	0.4624	-19.613	-2.71	-58.357
59	2.9574	0.6646	2.4121	1.6301	1.8909	5.017	-0.473	0.3971	-0.1437	-0.2357	0.6264	-0.1076	-0.3365	0.6122	-0.1534	0.3459	-0.0934	0.0798	0.3559	-0.0063	0.0965	-4.761	-6.679	-46.622
60	1.3459	-0.7162	1.4332	4.1972	-0.4834	7.0968	-0.1368	0.2379	-0.3336	0.0712	0.18	-0.7087	-0.3577	0.0764	-0.0432	0.2209	-0.0163	0.0637	0.3029	-0.0886	0.1738	1.44	-8.362	-42.392
61	4.9037	-3.3524	3.8118	1.6962	-6.456	-1.0508	-0.0836	-0.0417	-0.0359	0.0788	-0.128	0.4575	-0.1743	-0.229	0.2116	0.4293	0.0263	0.0434	0.3607	-0.0248	0.4179	-27.972	73.584	-53.484
62	3.4229	4.0864	0.7547	6.1567	1.1155	-1.0942	0.1951	-0.3122	-0.048	0.2466	-0.2152	-0.4172	-0.0128	-0.223	0.0201	0.3322	-0.0066	0.1086	0.5334	-0.0095	0.33	-19.081	65.115	-39.786
63	5.6425	2.1658	-2.8802	6.1712	-0.0658	1.9965	-0.1991	-0.1312	-0.1546	-0.1013	0.1404	0.0676	-0.0964	0.0956	0.0587	0.2023	-0.041	0.0371	0.3165	-0.0144	0.0595	-17.857	53.465	-46.295
64	-1.8521	6.1565	4.3919	17.3373	10.4369	6.9874	0.3685	-0.0261	-0.1147	0.7247	-0.3789	-0.4224	0.2102	-0.3344	0.0105	0.3658	-0.0696	0.0062	0.3516	0.1134	0.4209	-28.932	64.449	-53.413
65	1.7279	-4.5456	1.8676	9.6012	-11.1782	4.588	0.0067	-0.3642	0.7437	-0.6801	-0.1395	-0.1835	0.1585	-0.3082	0.1329	0.5261	0.0322	0.0252	0.4773	0.0343	0.203	-31.188	56.408	-62.984
66	-4.4558	8.0879	3.1787	4.5782	2.541	7.7994	0.0812	-0.0261	-0.4967	0.2111	-0.0197	-0.4069	0.5713	0.7635	-0.0615	0.4341	-0.0606	0.1299	0.518	0.1224	0.5598	-39.978	33.9	-58.577
67	8.761	-1.0418	2.9159	-3.6039	-3.2456	6.7662	0.1211	0.5052	0.5019	-0.0137	-0.4177	0.3577	0.1874	-0.3674	0.2966	0.4161	-0.1135	0.0249	0.4249	0.0536	0.3011	-41.289	47.422	-54.136
68	3.1474	1.7723	-0.4046	3.5979	2.5409	8.7294	0.0192	0.0082	-0.0307	-0.1092	-0.1392	0.0417	-0.0613	-0.2031	0.12	0.2965	-0.0099	0.0108	0.3543	0.1083	0.2094	-36.352	52.264	-61.917
69	3.6167	-2.7156	-0.784	9.1081	1.8537	3.4209	-0.1776	0.034	-0.3097	0.2525	0.1397	0.4566	0.4486	-0.2285	0.038	0.3377	-0.0144	0.0716	0.4501	0.0322	0.2808	-43.777	42.925	-64.348
70	4.7841	-4.3697	2.4835	5.9185	-3.093	0.6521	0.2484	0.4118	-0.5203	-0.1415	-0.2553	-0.1415	0.0152	0.1443	0.0069	0.535	0.0311	0.0794	0.4912	-0.0713	0.4106	-30.91	30.525	-66.533
71	1.5394	2.341	-6.6625	18.4975	-6.6541	9.6605	0.2537	0.3497	0.083	-0.7857	0.0235	0.009	-0.1274	0.9696	-0.2773	0.5241	0.1394	0.0075	0.7526	-0.2061	0.1857	-26.708	37.386	-69.954
72	1.0165	5.4845	7.7693	-5.6527	3.6453	24.6344	0.1774	1.0411	-0.838	-0.4243	-0.5003	0.0709	-0.0037	2.219	0.3229	0.5387	-0.0995	0.0321	0.7833	0.0319	0.3417	-29.077	43.551	-74.003
73	0.554	-0.1474	-1.1837	0.6439	-0.3204	3.2541	0.0091	0.0837	-0.0298	-0.1766	0.0496	0.0145	0.0744	-0.1523	-0.0587	0.3348	-0.0962	0.0203	0.4109	0.0775	0.289	-32.16	46.8	-57.956
74	1.6009	1.5074	-0.6309	0.6165	-0.4006	0.4639	-0.2178	0.1312	0.199	-0.1287	0.2653	0.078	0.0865	0.0555	-0.0475	0.2674	-0.0443	0.0613	0.3491	0.0061	0.1251	-22.289	45.883	-51.028
75	2.2069	-2.1388	0.311	1.3317	0.2271	2.8883	-0.043	-0.1661	-0.2071	0.2611	0.0944	-0.1653	0.386	0.3698	-0.0513	0.357	-0.0132	0.1405	0.4558	-0.0666	0.4893	-10.628	30.892	-51.225
76	2.2261	-1.9663	1.543	4.8882	-3.0747	1.7597	-0.0422	0.3172	-0.3364	-0.1437	0.0114	-0.4029	0.1402	0.0697	0.0308	0.3224	-0.0965	0.1091	0.399	-0.1028	0.2788	-15.279	38.562	-51.379
77	0.295	-4.6206	-0.4624	12.6593	3.3781	0.8198	0.2812	0.1172	0.2523	-0.4973	-0.2553	-0.5737	0.0612	0.1384	-0.0259	0.3528	-0.0522	0.1396	0.5217	0.0213	0.3343	-19.156	41.949	-67.156
78	2.219	-3.2187	-3.9812	5.6898	4.1275	5.8183	-0.0601	-0.0625	0.3242	-0.0134	0.2429	0.4326	0.8754	-0.052	-0.1828	0.4928	-0.0389	0.0398	0.4043	-0.0877	0.3242	-16.485	25.702	-61.607
79	2.5969	0.5849	0.0025	1.1518	0.2103	2.3588	-0.2812	0.3585	-0.3419	-0.2822	0.202	-0.2656	0.0964	0.1197	0.0792	0.2318	-0.047	0.1041	0.2917	0.0417	0.157	-19.545	42.023	-52.904
80	3.8516	-2.0987	-0.0355	1.1747	-3.5434	4.78	-0.2131	-0.1741	0.0378	-0.0822	0.2286	0.3026	0.283	0.0005	-0.0155	0.2924	-0.0308	0.0463	0.3573	0.0675	0.1534	-31.443	43.81	-41.445

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	62 - 68
2	X-RAY DIFFRACTION	2	A	69 - 80
3	X-RAY DIFFRACTION	3	A	81 - 107
4	X-RAY DIFFRACTION	4	A	108 - 113
5	X-RAY DIFFRACTION	5	A	114 - 130
6	X-RAY DIFFRACTION	6	A	131 - 145
7	X-RAY DIFFRACTION	7	A	146 - 151
8	X-RAY DIFFRACTION	8	A	152 - 172
9	X-RAY DIFFRACTION	9	A	173 - 186
10	X-RAY DIFFRACTION	10	A	187 - 198
11	X-RAY DIFFRACTION	11	A	199 - 205
12	X-RAY DIFFRACTION	12	A	206 - 215
13	X-RAY DIFFRACTION	13	A	216 - 226
14	X-RAY DIFFRACTION	14	A	227 - 240
15	X-RAY DIFFRACTION	15	A	241 - 275
16	X-RAY DIFFRACTION	16	A	276 - 289
17	X-RAY DIFFRACTION	17	A	290 - 297
18	X-RAY DIFFRACTION	18	A	298 - 312
19	X-RAY DIFFRACTION	19	A	313 - 327
20	X-RAY DIFFRACTION	20	A	328 - 345
21	X-RAY DIFFRACTION	21	B	65 - 73
22	X-RAY DIFFRACTION	22	B	74 - 79
23	X-RAY DIFFRACTION	23	B	80 - 84
24	X-RAY DIFFRACTION	24	B	85 - 107
25	X-RAY DIFFRACTION	25	B	108 - 120
26	X-RAY DIFFRACTION	26	B	121 - 131
27	X-RAY DIFFRACTION	27	B	132 - 158
28	X-RAY DIFFRACTION	28	B	159 - 175
29	X-RAY DIFFRACTION	29	B	181 - 197
30	X-RAY DIFFRACTION	30	B	198 - 208
31	X-RAY DIFFRACTION	31	B	209 - 220
32	X-RAY DIFFRACTION	32	B	221 - 236
33	X-RAY DIFFRACTION	33	B	237 - 255
34	X-RAY DIFFRACTION	34	B	256 - 271
35	X-RAY DIFFRACTION	35	B	272 - 283
36	X-RAY DIFFRACTION	36	B	284 - 292
37	X-RAY DIFFRACTION	37	B	293 - 309
38	X-RAY DIFFRACTION	38	B	310 - 324
39	X-RAY DIFFRACTION	39	B	325 - 330
40	X-RAY DIFFRACTION	40	B	331 - 345
41	X-RAY DIFFRACTION	41	C	66 - 82
42	X-RAY DIFFRACTION	42	C	83 - 108
43	X-RAY DIFFRACTION	43	C	109 - 116
44	X-RAY DIFFRACTION	44	C	117 - 133
45	X-RAY DIFFRACTION	45	C	134 - 144
46	X-RAY DIFFRACTION	46	C	145 - 158
47	X-RAY DIFFRACTION	47	C	159 - 175
48	X-RAY DIFFRACTION	48	C	188 - 197
49	X-RAY DIFFRACTION	49	C	198 - 215
50	X-RAY DIFFRACTION	50	C	216 - 223
51	X-RAY DIFFRACTION	51	C	224 - 233
52	X-RAY DIFFRACTION	52	C	234 - 239
53	X-RAY DIFFRACTION	53	C	240 - 258
54	X-RAY DIFFRACTION	54	C	259 - 264
55	X-RAY DIFFRACTION	55	C	265 - 285
56	X-RAY DIFFRACTION	56	C	286 - 291
57	X-RAY DIFFRACTION	57	C	292 - 307
58	X-RAY DIFFRACTION	58	C	308 - 313
59	X-RAY DIFFRACTION	59	C	314 - 331
60	X-RAY DIFFRACTION	60	C	332 - 345
61	X-RAY DIFFRACTION	61	D	65 - 71
62	X-RAY DIFFRACTION	62	D	72 - 82
63	X-RAY DIFFRACTION	63	D	83 - 100
64	X-RAY DIFFRACTION	64	D	101 - 108
65	X-RAY DIFFRACTION	65	D	109 - 120
66	X-RAY DIFFRACTION	66	D	121 - 132
67	X-RAY DIFFRACTION	67	D	133 - 140
68	X-RAY DIFFRACTION	68	D	141 - 150
69	X-RAY DIFFRACTION	69	D	151 - 169
70	X-RAY DIFFRACTION	70	D	170 - 188
71	X-RAY DIFFRACTION	71	D	189 - 195
72	X-RAY DIFFRACTION	72	D	196 - 200
73	X-RAY DIFFRACTION	73	D	201 - 221
74	X-RAY DIFFRACTION	74	D	222 - 238
75	X-RAY DIFFRACTION	75	D	239 - 255
76	X-RAY DIFFRACTION	76	D	256 - 270
77	X-RAY DIFFRACTION	77	D	271 - 287
78	X-RAY DIFFRACTION	78	D	288 - 301
79	X-RAY DIFFRACTION	79	D	302 - 327
80	X-RAY DIFFRACTION	80	D	328 - 345

-
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