PDB-6xk2: Crystal structure of Ribokinase from Cryptococcus neoformans var....

ID or keywords:

Entry

Database: PDB / ID: 6xk2

Title

Crystal structure of Ribokinase from Cryptococcus neoformans var. grubii serotype A in complex with ADP

Components

Ribokinase

Keywords

TRANSFERASE / SSGCID / Cryptococcus neoformans / Ribokinase / phosphorylation / ATP / ADP / D-ribose / D-ribose 5-phosphate / structural genomics / Seattle Structural Genomics Center for Infectious Disease

Function / homology

Function and homology information

ribokinase / ribokinase activity / D-ribose catabolic process / ATP binding / metal ion binding / nucleus / cytoplasm
Similarity search - Function

Biological species

Cryptococcus neoformans var. grubii serotype A (fungus)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.5 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Citation

Journal: to be published
Title: Crystal structure of Ribokinase from Cryptococcus neoformans var. grubii serotype A in complex with ADP
Authors: Abendroth, J. / Davies, D.R. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.

History

Deposition	Jun 25, 2020	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 15, 2020	Provider: repository / Type: Initial release
Revision 1.1	Oct 18, 2023	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 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	6xk2.cif.gz	477.5 KB	Display	PDBx/mmCIF format
PDB format	pdb6xk2.ent.gz	390.7 KB	Display	PDB format
PDBx/mmJSON format	6xk2.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/xk/6xk2 ftp://data.pdbj.org/pub/pdb/validation_reports/xk/6xk2	HTTPS FTP

-
Related structure data

Related structure data	6cw5S S: Starting model for refinement
Similar structure data	4xda-2 6wjz-d 5c3z-d 4xck-2 3i3y-1 2fv7-2 5byf-d 4pvv-1 3i3y-2 5c41-1 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Other databases	TargetTrack: CrneC.01141.a

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Ribokinase

B: Ribokinase

C: Ribokinase

D: Ribokinase

hetero molecules

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

1

A: Ribokinase

D: Ribokinase

hetero molecules

defined by author&software
Evidence: gel filtration
71.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Ribokinase

C: Ribokinase

hetero molecules

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

Unit cell

Length a, b, c (Å)	77.170, 84.570, 98.270
Angle α, β, γ (deg.)	90.000, 95.270, 90.000
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	(chain A and (resid 4 through 5 or (resid 6...
2	1	(chain B and (resid 4 through 5 or (resid 6...
3	1	(chain C and (resid 4 through 5 or (resid 6...
4	1	(chain D and (resid 4 through 88 or (resid 89...

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Selection details	Auth asym-ID	Auth seq-ID
1	1	1	(chain A and (resid 4 through 5 or (resid 6...	A	4 - 5
1	2	1	(chain A and (resid 4 through 5 or (resid 6...	A	6
1	3	1	(chain A and (resid 4 through 5 or (resid 6...	A	2 - 323
1	4	1	(chain A and (resid 4 through 5 or (resid 6...	A	2 - 323
1	5	1	(chain A and (resid 4 through 5 or (resid 6...	A	2 - 323
1	6	1	(chain A and (resid 4 through 5 or (resid 6...	A	2 - 323
2	1	1	(chain B and (resid 4 through 5 or (resid 6...	B	4 - 5
2	2	1	(chain B and (resid 4 through 5 or (resid 6...	B	6
2	3	1	(chain B and (resid 4 through 5 or (resid 6...	B	4 - 323
2	4	1	(chain B and (resid 4 through 5 or (resid 6...	B	4 - 323
2	5	1	(chain B and (resid 4 through 5 or (resid 6...	B	4 - 323
2	6	1	(chain B and (resid 4 through 5 or (resid 6...	B	4 - 323
3	1	1	(chain C and (resid 4 through 5 or (resid 6...	C	4 - 5
3	2	1	(chain C and (resid 4 through 5 or (resid 6...	C	6
3	3	1	(chain C and (resid 4 through 5 or (resid 6...	C	4 - 401
3	4	1	(chain C and (resid 4 through 5 or (resid 6...	C	4 - 401
3	5	1	(chain C and (resid 4 through 5 or (resid 6...	C	4 - 401
4	1	1	(chain D and (resid 4 through 88 or (resid 89...	D	4 - 88
4	2	1	(chain D and (resid 4 through 88 or (resid 89...	D	89 - 90
4	3	1	(chain D and (resid 4 through 88 or (resid 89...	D	4 - 400
4	4	1	(chain D and (resid 4 through 88 or (resid 89...	D	4 - 400
4	5	1	(chain D and (resid 4 through 88 or (resid 89...	D	4 - 400
4	6	1	(chain D and (resid 4 through 88 or (resid 89...	D	4 - 400

#1: Protein	Ribokinase / RK Mass: 35086.723 Da / Num. of mol.: 4 / Fragment: CrneC.01141.a.B12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cryptococcus neoformans var. grubii serotype A (strain H99 / ATCC 208821 / CBS 10515 / FGSC 9487) (fungus) Strain: H99 / ATCC 208821 / CBS 10515 / FGSC 9487 / Gene: CNAG_02296 / Plasmid: CrneC.01141.a.B12 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) Strain (production host): BL21(DE3) / References: UniProt: J9VQ51, ribokinase
#2: Chemical	ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE Mass: 427.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₀H₁₅N₅O₁₀P₂ / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 167 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.28 Å³/Da / Density % sol: 45.94 %
Crystal grow	Temperature: 285 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: Microlytic MCSG-1 screen D12: 20% (w/V) PDG 3350, 200mM ammonium chloride; CrneC.01141.a.B12.PW38396 at 19.46mg/ml + 2.5mM ADP + 2.5mM MgCl2; tray 299998 D12; cryo: 20% EG + 2.5mM ADP/MgCl2; puck pjn0-4

-
Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 21-ID-F / Wavelength: 0.97872 Å

Detector

Type: RAYONIX MX-300 / Detector: CCD / Date: Apr 12, 2018 / Details: C(111)

Radiation

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

Radiation wavelength

Wavelength: 0.97872 Å / Relative weight: 1

Reflection

Resolution: 2.5→37.05 Å / Num. obs: 43388 / % possible obs: 99.1 % / Redundancy: 3.413 % / B_iso Wilson estimate: 58.322 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.046 / R_rim(I) all: 0.055 / Χ²: 1.029 / Net I/σ(I): 17.97 / Num. measured all: 148087 / Scaling rejects: 12

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. possible	Num. unique obs	CC_1/2	R_rim(I) all	% possible all
2.5-2.56	3.427	0.575	2.09	11007	3215	3212	0.8	0.682	99.9
2.56-2.64	3.427	0.426	2.79	10658	3119	3110	0.873	0.506	99.7
2.64-2.71	3.417	0.336	3.47	10491	3073	3070	0.909	0.399	99.9
2.71-2.8	3.423	0.249	4.51	10035	2939	2932	0.963	0.296	99.8
2.8-2.89	3.428	0.179	6.15	9917	2900	2893	0.978	0.213	99.8
2.89-2.99	3.403	0.136	8.1	9430	2772	2771	0.987	0.162	100
2.99-3.1	3.431	0.109	9.96	9196	2692	2680	0.992	0.129	99.6
3.1-3.23	3.418	0.085	12.71	8767	2574	2565	0.994	0.101	99.7
3.23-3.37	3.421	0.067	16.59	8480	2500	2479	0.996	0.079	99.2
3.37-3.54	3.406	0.052	20.64	8007	2365	2351	0.997	0.062	99.4
3.54-3.73	3.411	0.042	25.56	7626	2258	2236	0.998	0.049	99
3.73-3.95	3.415	0.036	29.22	7274	2149	2130	0.999	0.042	99.1
3.95-4.23	3.417	0.032	32.61	6741	2002	1973	0.998	0.038	98.6
4.23-4.56	3.392	0.028	36.82	6279	1880	1851	0.999	0.033	98.5
4.56-5	3.4	0.025	39.31	5800	1735	1706	0.999	0.03	98.3
5-5.59	3.419	0.026	38.1	5238	1561	1532	0.999	0.031	98.1
5.59-6.46	3.403	0.027	37.54	4648	1399	1366	0.999	0.032	97.6
6.46-7.91	3.401	0.021	45.5	3891	1172	1144	0.999	0.024	97.6
7.91-11.18	3.378	0.016	50.87	3044	927	901	1	0.019	97.2
11.18-37.05	3.206	0.016	50.88	1558	531	486	0.999	0.02	91.5

-
Processing

Software

Name	Version	Classification
XDS		data reduction
XSCALE		data scaling
PHENIX	1.18.2	refinement
PDB_EXTRACT	3.25	data extraction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: apo structure, 6cw5

6cw5

Resolution: 2.5→37.05 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 26.63 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2304	1941	4.48 %	0
R_work	0.1811	41396	-	-
obs	0.1833	43337	99.1 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso max: 147.25 Å² / B_iso mean: 65.7744 Å² / B_iso min: 34.2 Å²

Refinement step

Cycle: final / Resolution: 2.5→37.05 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9027	0	123	167	9317
B_iso mean	-	-	62.28	54.46	-
Num. residues	-	-	-	-	1266

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	9333
X-RAY DIFFRACTION	f_angle_d	0.827	12762
X-RAY DIFFRACTION	f_dihedral_angle_d	14.991	3241
X-RAY DIFFRACTION	f_chiral_restr	0.048	1510
X-RAY DIFFRACTION	f_plane_restr	0.006	1705

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Number	Refine-ID	Rms	Type
1	1	A	5225	X-RAY DIFFRACTION	6.196	TORSIONAL
1	2	B	5225	X-RAY DIFFRACTION	6.196	TORSIONAL
1	3	C	5225	X-RAY DIFFRACTION	6.196	TORSIONAL
1	4	D	5225	X-RAY DIFFRACTION	6.196	TORSIONAL

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / Total num. of bins used: 14

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
2.5-2.56	0.32	150	0.277	2933	3083	100
2.56-2.63	0.3214	148	0.2617	2930	3078	100
2.63-2.71	0.3036	132	0.254	2988	3120	100
2.71-2.8	0.3245	139	0.2407	2940	3079	100
2.8-2.9	0.2904	150	0.2342	2956	3106	100
2.9-3.01	0.2751	143	0.2148	2968	3111	100
3.01-3.15	0.2586	121	0.2196	2966	3087	99
3.15-3.32	0.2906	133	0.2103	2972	3105	100
3.32-3.52	0.2575	132	0.1896	2979	3111	99
3.52-3.79	0.1952	129	0.1776	2936	3065	99
3.79-4.18	0.2235	143	0.1656	2955	3098	99
4.18-4.78	0.1796	130	0.1408	2967	3097	99
4.78-6.02	0.22	136	0.1584	2953	3089	98
6.02-37.05	0.1847	155	0.1493	2953	3108	97

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	4.8403	0.3021	-3.2146	1.9878	-0.6221	4.1737	0.0056	-0.0846	-0.0611	-0.1234	-0.1374	-0.1346	0.0046	0.4851	0.1043	0.3441	-0.0028	-0.0296	0.3344	-0.0126	0.3212	-5.1721	-27.4283	-25.3242
2	4.298	-0.2437	-1.3899	2.6909	0.4764	4.3105	0.1286	0.6756	0.3409	-0.4692	-0.0322	0.4939	-0.542	-0.3542	-0.1797	0.424	0.0328	-0.0496	0.4521	0.116	0.4487	-22.056	-19.4523	-27.1262
3	2.6373	-0.2827	0.1283	1.4412	0.4311	3.9859	0.2925	0.4055	0.957	-0.2318	0.0982	0.3998	-0.8278	-0.222	-0.2568	0.7523	0.046	0.138	0.3501	0.0782	0.901	-21.4727	-6.0682	-18.8371
4	4.4061	0.6947	0.8182	3.3423	-0.6631	3.7469	0.1185	-0.3487	0.4732	0.1641	-0.0225	-0.0899	-0.0313	0.2431	-0.1159	0.4461	-0.0245	0.0516	0.3857	-0.1037	0.3463	-10.9859	-18.3083	-8.5934
5	5.4007	0.1168	1.3954	0.4521	0.4246	2.8704	0.0083	-0.1105	-0.6029	0.0391	0.1917	0.0304	0.2093	0.3779	-0.2186	0.3675	0.071	-0.0303	0.3465	-0.1199	0.5361	-39.449	-15.8723	5.1649
6	7.5396	-0.1458	0.1735	1.0579	1.1925	2.3698	0.0626	0.6997	-0.1562	-0.1345	0.002	0.1756	-0.0457	0.6761	-0.0001	0.3791	-0.0097	0.0093	0.4257	-0.0506	0.5013	-43.525	-9.6387	-3.1921
7	3.8628	-1.0135	2.3375	1.3485	0.5499	3.5853	-0.0913	0.3341	0.8752	-0.1749	-0.11	-0.1251	-0.4118	0.5156	0.0898	0.4586	-0.0311	0.0394	0.3655	0.0399	0.602	-47.213	-0.6847	-1.8837
8	3.2377	-0.7799	1.7227	1.7724	0.7995	3.3991	-0.0944	0.1005	-0.0192	0.1341	0.1307	-0.3087	0.1464	0.1671	-0.1146	0.3326	0.0343	-0.0155	0.3425	-0.0535	0.4845	-43.8636	-8.858	6.997
9	1.9586	-0.2672	0.91	1.2322	0.9445	1.5091	0.1904	-0.3401	-0.2161	0.1525	-0.005	0.4281	-0.3172	-0.6179	0.3732	0.5042	0.0859	0.0304	0.477	-0.01	0.6577	-62.8875	-1.0649	5.8737
10	3.8893	-0.1863	0.7298	3.3008	1.1703	4.0677	0.1984	-0.2574	-0.9406	0.1694	-0.1632	0.5459	0.3976	-0.3059	-0.0439	0.3792	-0.0331	0.0403	0.3885	0.0275	0.7675	-60.924	-17.4251	4.5411
11	2.8414	-1.3898	-0.9101	0.9841	0.9742	1.3409	0.115	0.2878	-1.5383	0.0767	-0.1813	0.8239	0.2738	-0.1998	0.1293	0.6466	-0.1144	-0.0685	0.5523	-0.1024	1.4423	-60.2857	-32.9465	1.2973
12	2.8632	0.6198	0.0316	3.3987	0.3082	2.0222	0.118	0.9121	-1.1261	-0.2729	-0.1488	0.1327	0.147	-0.0108	0.031	0.445	0.0597	-0.0697	0.5523	-0.2717	0.7679	-51.9782	-21.7356	-11.8586
13	7.2588	-2.565	-1.4509	6.6992	0.9209	1.1407	0.7623	1.054	0.1296	-0.5277	-0.3614	-1.1436	0.1068	-0.0203	-0.4388	0.4792	0.101	0.0507	0.6807	0.013	0.734	-43.8232	-12.3823	-15.4409
14	9.3995	0.8495	2.8954	2.2808	-0.0675	1.9479	0.151	-0.6535	-0.9189	0.1031	-0.0129	0.1565	0.0977	-0.1338	-0.1215	0.4511	0.0827	0.0113	0.4944	0.06	0.4927	-30.1027	-15.9223	18.7432
15	6.6072	1.4663	1.1741	3.4806	0.2623	1.7215	0.1142	-0.3626	0.4411	0.2773	-0.1653	-0.0672	-0.2374	-0.0719	0.0166	0.4323	0.0666	0.0393	0.5391	-0.0211	0.3544	-20.1222	-5.9687	23.5164
16	8.7085	1.8288	3.3015	3.0594	0.8169	2.0387	0.2842	0.16	-0.1927	-0.1669	-0.1334	0.0914	-0.0059	0.1626	-0.1241	0.4878	0.1184	0.0152	0.5323	0.0311	0.3147	-23.5874	-11.781	15.6547
17	2.9731	-0.6102	1.7478	4.3353	-0.0583	4.2746	0.2767	0.2327	-0.1442	-0.4054	-0.4432	-0.7301	0.038	0.7213	-0.0276	0.3765	0.0633	-0.002	0.7103	-0.0163	0.6446	-6.6252	-15.2016	17.7229
18	1.9086	0.6542	-0.1116	3.1022	-0.6755	4.2724	0.5207	-0.3222	-2.6407	-0.0821	-0.3099	-0.5754	0.9905	0.3757	0.0775	0.7036	0.1444	-0.248	0.5773	0.1431	1.4969	-13.4408	-30.4487	24.0392
19	7.5422	-2.1001	-0.9762	1.5763	0.1144	4.1595	0.5477	-0.1963	-1.9335	0.3459	-0.1068	-0.1146	0.8093	0.1868	-0.2787	0.8274	0.0702	-0.2132	0.8378	0.3277	1.4234	-14.3422	-32.4288	30.1118
20	0.5298	0.5394	0.2425	1.5691	-0.2313	2.2029	-0.6614	-1.5614	-1.2298	0.8403	0.5959	-0.0094	0.4444	-0.1021	-0.1723	0.7061	-0.0492	0.028	1.1488	0.5076	0.8212	-25.3211	-23.7243	37.1428
21	0.5691	0.0791	1.5065	2.1449	0.4687	3.9757	0.7712	-1.8039	-1.6337	0.3822	-0.1505	-0.1822	0.0341	0.3088	0.0093	0.6549	-0.067	-0.1152	0.9947	0.216	0.4416	-14.4698	-16.8852	35.325
22	0.6449	-0.1567	0.9297	0.9758	0.7201	2.8904	0.0284	-0.8112	-0.5478	0.9775	-0.1894	0.2836	0.3932	0.1638	-0.4832	0.81	0.0208	-0.0426	1.3533	0.5473	0.5292	-21.8577	-18.7	39.153
23	4.6434	1.8182	0.5877	2.8104	-1.839	4.1065	0.3129	-1.0827	0.239	0.4695	-0.2093	0.179	-0.9091	-0.1841	-0.1231	0.7788	-0.0988	0.0982	1.0753	0.1206	0.4852	-25.1096	-9.6874	37.7028
24	7.683	-0.5287	-3.3751	0.3402	0.0534	3.244	0.3522	0.7345	0.1352	0.0049	-0.3752	-0.1292	-0.1809	-0.2131	-0.0439	0.4353	-0.0128	-0.0042	0.4795	0.123	0.4778	10.765	-25.7652	-42.4386
25	7.9655	-3.6517	-3.2864	2.3417	1.8025	2.1215	-0.3796	-0.1721	-1.1453	0.1345	-0.4913	0.6424	0.5147	0.1102	0.6224	0.5623	-0.0118	0.0093	0.6074	0.1443	0.8714	17.7085	-38.0727	-41.8554
26	4.3096	-0.9163	-1.1603	3.0663	0.1809	2.0314	0.2639	0.8261	0.6859	-0.4388	-0.3578	-0.4475	-0.0876	0.2472	0.1496	0.5414	0.0371	0.1338	0.6341	0.2517	0.5522	11.3121	-25.9978	-37.5969
27	2.3821	0.6692	-0.4571	3.3504	0.0503	4.4676	0.3386	-1.2128	-0.8354	0.233	-0.1162	-0.2528	0.446	0.7165	-0.1097	0.4952	0.0161	-0.094	1.0231	0.2728	0.6323	30.2344	-29.7883	-36.5068
28	4.9479	1.3343	-0.729	4.4255	-0.2392	4.7354	0.1212	-0.4493	0.4692	-0.0765	-0.3241	-0.5374	-0.6423	0.7298	0.138	0.4252	-0.0975	0.0099	0.6685	0.112	0.5251	33.7136	-15.0615	-47.0848
29	6.0488	0.55	0.9131	2.4413	0.2255	2.7691	0.1205	0.5143	0.2527	-0.0898	-0.2199	-0.1687	-0.0845	0.8012	0.169	0.4428	0.0748	0.0732	0.7756	0.1523	0.4253	29.1086	-22.9875	-57.4355
30	3.4195	-1.2178	0.6479	5.271	0.671	0.2771	0.575	0.1174	-0.4177	-0.7418	-0.2743	0.9005	0.865	-0.657	-0.2596	0.8218	0.1115	-0.0961	0.6181	-0.0055	0.7442	17.5808	-32.9127	-60.3732

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 2 through 116 )	A	2 - 116
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 117 through 208 )	A	117 - 208
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 209 through 247 )	A	209 - 247
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 248 through 323 )	A	248 - 323
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 4 through 34 )	B	4 - 34
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 35 through 53 )	B	35 - 53
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 54 through 78 )	B	54 - 78
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 79 through 116 )	B	79 - 116
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 117 through 131 )	B	117 - 131
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 132 through 197 )	B	132 - 197
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 198 through 233 )	B	198 - 233
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 234 through 305 )	B	234 - 305
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 306 through 323 )	B	306 - 323
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 4 through 34 )	C	4 - 34
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 35 through 78 )	C	35 - 78
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 79 through 116 )	C	79 - 116
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 117 through 152 )	C	117 - 152
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 153 through 224 )	C	153 - 224
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 225 through 247 )	C	225 - 247
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 248 through 270 )	C	248 - 270
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 271 through 288 )	C	271 - 288
22	X-RAY DIFFRACTION	22	chain 'C' and (resid 289 through 305 )	C	289 - 305
23	X-RAY DIFFRACTION	23	chain 'C' and (resid 306 through 323 )	C	306 - 323
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 4 through 53 )	D	4 - 53
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 54 through 78 )	D	54 - 78
26	X-RAY DIFFRACTION	26	chain 'D' and (resid 79 through 111 )	D	79 - 111
27	X-RAY DIFFRACTION	27	chain 'D' and (resid 112 through 152 )	D	112 - 152
28	X-RAY DIFFRACTION	28	chain 'D' and (resid 153 through 224 )	D	153 - 224
29	X-RAY DIFFRACTION	29	chain 'D' and (resid 225 through 304 )	D	225 - 304
30	X-RAY DIFFRACTION	30	chain 'D' and (resid 305 through 323 )	D	305 - 323

-
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