PDB-3caz: Crystal structure of a BAR protein from Galdieria sulphuraria

ID or keywords:

Entry

Database: PDB / ID: 3caz

Title

Crystal structure of a BAR protein from Galdieria sulphuraria

Components

BAR protein

Keywords

SIGNALING PROTEIN / BAR protein / thermo-acidophilic red alga /

Protein Structure Initiative / PSI / Center for Eukaryotic Structural Genomics / CESG

Function / homology

Arfaptin homology (AH) domain/BAR domain / AH/BAR domain superfamily / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / Up-down Bundle / Mainly Alpha / BAR protein

Function and homology information

Biological species

Galdieria sulphuraria (eukaryote)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 3.344 Å

Authors

McCoy, J.G. / Bitto, E. / Bingman, C.A. / Wesenberg, G.E. / Phillips Jr., G.N. / Center for Eukaryotic Structural Genomics (CESG)

Citation

Journal: To be Published
Title: Crystal structure of a BAR protein from Galdieria sulphuraria.
Authors: McCoy, J.G. / Bitto, E. / Bingman, C.A. / Wesenberg, G.E. / Phillips Jr., G.N.

History

Deposition	Feb 20, 2008	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 4, 2008	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Oct 25, 2017	Group: Refinement description / Category: software

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	3caz.cif.gz	97.3 KB	Display	PDBx/mmCIF format
PDB format	pdb3caz.ent.gz	79.7 KB	Display	PDB format
PDBx/mmJSON format	3caz.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ca/3caz ftp://data.pdbj.org/pub/pdb/validation_reports/ca/3caz	HTTPS FTP

-
Related structure data

Similar structure data	1uru-1 4atm-1 4tx5-d 4i1q-d 2fic-1 5j9k-d 1i49-d 6ird-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search
Other databases	TargetDB: GO.80055

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#88 - Apr 2007 Clathrin similarity (1)

Deposited unit

A: BAR protein

B: BAR protein

68.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	78.962, 78.962, 456.028
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	178
Space group name H-M	P6₁22

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg label comp-ID: SER / End label comp-ID: GLU / Refine code: 4

Dom-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	A	A	12 - 216	15 - 219
2	B	B	12 - 220	15 - 223

#1: Protein	BAR protein Mass: 34036.277 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Galdieria sulphuraria (eukaryote) / Gene: c501_101305g3.t1 / Plasmid: pVP56k / Production host: Escherichia coli (E. coli) / Strain (production host): B834 P(RARE2) / References: UniProt: D0VWT4*PLUS
Sequence details	THE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT ...THE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT THE TIME OF DEPOSITION.

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 3.01 Å³/Da / Density % sol: 59.2 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, hanging drop Details: Protein solution (10 mg/mL Se-Met protein, 0.05 M Sodium chloride, 0.0003 M TCEP, 0.005 M Bis-Tris pH 7.0) mixed in a 1:1 ratio with the Well solution (27% MPD, 0.12 M Magnesium chloride, 0. ...Details: Protein solution (10 mg/mL Se-Met protein, 0.05 M Sodium chloride, 0.0003 M TCEP, 0.005 M Bis-Tris pH 7.0) mixed in a 1:1 ratio with the Well solution (27% MPD, 0.12 M Magnesium chloride, 0.1 M MES/Acetate pH 5.5), VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal

Density Matthews: 3.01 Å³/Da / Density % sol: 59.2 %

Crystal grow

Temperature: 277 K / Method: vapor diffusion, hanging drop
Details: Protein solution (10 mg/mL Se-Met protein, 0.05 M Sodium chloride, 0.0003 M TCEP, 0.005 M Bis-Tris pH 7.0) mixed in a 1:1 ratio with the Well solution (27% MPD, 0.12 M Magnesium chloride, 0. ...

-
Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 23-ID-D / Wavelength: 0.96411 Å

Detector

Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 18, 2007 / Details: Adjustable focusing mirrors in K-B geometry

Radiation

Monochromator: Si(111) Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.96411 Å / Relative weight: 1

Reflection

Resolution: 3.344→47.168 Å / Num. obs: 13119 / % possible obs: 98.3 % / Redundancy: 12.8 % / R_merge(I) obs: 0.085 / Χ²: 1.053 / Net I/σ(I): 11.425

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. unique all	Χ²	% possible all
3.344-3.47	9.4	0.858	1.622	1255	1.033	98.2
3.47-3.61	12.4	0.626		1302	1.073	99.6
3.61-3.77	13.9	0.398		1253	1.041	99.5
3.77-3.97	13.7	0.26		1288	1.044	99.5
3.97-4.22	13.8	0.177		1274	1.082	99.5
4.22-4.55	13.6	0.127		1304	0.955	99.2
4.55-5	13.4	0.093		1309	1.03	98.6
5-5.73	13.4	0.087		1324	1.037	98.3
5.73-7.22	13.2	0.086		1348	1.123	97.6
7.22-47.168	11.8	0.046		1462	1.112	94.1

-
Phasing

Phasing

Method:

SAD

Phasing MAD set

R cullis centric: 0 / Highest resolution: 3.35 Å / Lowest resolution: 47.17 Å / Power centric: 0

ID	R cullis acentric	Power acentric	Reflection acentric	Reflection centric
ISO_1	0	0	9687	3361
ANO_1	0.872	0.845	9620	0

Phasing MAD set shell

R cullis centric: 0 / Power centric: 0

ID	Resolution (Å)	R cullis acentric	Power acentric	Reflection acentric	Reflection centric
ISO_1	14.31-47.17	0	0	68	139
ISO_1	10.36-14.31	0	0	154	168
ISO_1	8.53-10.36	0	0	221	168
ISO_1	7.42-8.53	0	0	278	170
ISO_1	6.65-7.42	0	0	320	152
ISO_1	6.08-6.65	0	0	355	174
ISO_1	5.64-6.08	0	0	406	156
ISO_1	5.28-5.64	0	0	434	167
ISO_1	4.98-5.28	0	0	476	161
ISO_1	4.73-4.98	0	0	505	183
ISO_1	4.51-4.73	0	0	543	164
ISO_1	4.32-4.51	0	0	559	166
ISO_1	4.15-4.32	0	0	572	183
ISO_1	4-4.15	0	0	633	164
ISO_1	3.87-4	0	0	640	181
ISO_1	3.74-3.87	0	0	652	176
ISO_1	3.63-3.74	0	0	705	156
ISO_1	3.53-3.63	0	0	707	193
ISO_1	3.44-3.53	0	0	712	164
ISO_1	3.35-3.44	0	0	747	176
ANO_1	14.31-47.17	0.526	2.632	68	0
ANO_1	10.36-14.31	0.604	2.074	154	0
ANO_1	8.53-10.36	0.613	1.894	221	0
ANO_1	7.42-8.53	0.596	1.886	278	0
ANO_1	6.65-7.42	0.57	2.044	320	0
ANO_1	6.08-6.65	0.579	1.988	355	0
ANO_1	5.64-6.08	0.685	1.547	406	0
ANO_1	5.28-5.64	0.741	1.325	434	0
ANO_1	4.98-5.28	0.848	1.061	476	0
ANO_1	4.73-4.98	0.883	0.837	505	0
ANO_1	4.51-4.73	0.894	0.688	543	0
ANO_1	4.32-4.51	0.953	0.615	559	0
ANO_1	4.15-4.32	0.955	0.475	572	0
ANO_1	4-4.15	0.97	0.413	633	0
ANO_1	3.87-4	0.985	0.293	640	0
ANO_1	3.74-3.87	0.988	0.225	652	0
ANO_1	3.63-3.74	0.994	0.167	705	0
ANO_1	3.53-3.63	0.997	0.138	707	0
ANO_1	3.44-3.53	0.999	0.115	705	0
ANO_1	3.35-3.44	1	0.117	687	0

Phasing MAD set site

ID	Cartn x (Å)	Cartn y (Å)	Cartn z (Å)	Atom type symbol	B iso	Occupancy
1	42.053	3.25	10.833	SE	130.87	1.8
2	19.397	7.401	27.508	SE	146.41	1.85
3	44.511	-9.601	6.245	SE	195.43	1.89
4	46.15	4.592	8.954	SE	151	1.93
5	23.549	8.402	28.834	SE	165.28	2.13
6	15.526	19.101	31.966	SE	238.26	1.82

Phasing dm

Method: Solvent flattening and Histogram matching / Reflection: 13048

Phasing dm shell

Resolution (Å)	Delta phi final	FOM	Reflection
10.54-100	75.8	0.641	503
8.27-10.54	76.8	0.875	501
7.12-8.27	76.5	0.846	512
6.43-7.12	68.6	0.817	511
5.94-6.43	67.6	0.809	505
5.57-5.94	64	0.817	501
5.27-5.57	70	0.83	503
5.04-5.27	65.3	0.876	502
4.84-5.04	71.3	0.91	504
4.66-4.84	70.6	0.887	513
4.51-4.66	74.4	0.905	512
4.37-4.51	79.7	0.869	509
4.25-4.37	74	0.873	530
4.13-4.25	79.7	0.859	518
4.03-4.13	80.2	0.858	533
3.94-4.03	85.6	0.844	548
3.85-3.94	86.8	0.816	580
3.76-3.85	82.7	0.791	558
3.68-3.76	85.9	0.807	592
3.61-3.68	85.7	0.744	575
3.54-3.61	83.8	0.711	629
3.48-3.54	90.5	0.705	613
3.41-3.48	87.6	0.666	619
3.35-3.41	94	0.589	677

-
Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
SHARP		phasing
DM	5	phasing
REFMAC	5.2.0019	refinement
PDB_EXTRACT	3	data extraction
MAR345	CCD	data collection
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

SAD / Resolution: 3.344→47.168 Å / Cor.coef. F_o:F_c: 0.952 / Cor.coef. F_o:F_c free: 0.95 / WR_factor R_free: 0.286 / WR_factor R_work: 0.232 / SU B: 58.864 / SU ML: 0.398 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0 / ESU R Free: 0.452 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.252	648	4.941 %	RANDOM
R_work	0.215	-	-	-
obs	0.217	13115	99.101 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 74.648 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.209 Å²	0.604 Å²	0 Å²
2-	-	1.209 Å²	0 Å²
3-	-	-	-1.813 Å²

Refinement step

Cycle: LAST / Resolution: 3.344→47.168 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3437	0	0	0	3437

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.006	0.022	3501
X-RAY DIFFRACTION	r_angle_refined_deg	0.904	1.942	4710
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.917	5	413
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.599	25.187	187
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	19.415	15	686
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.282	15	20
X-RAY DIFFRACTION	r_chiral_restr	0.074	0.2	501
X-RAY DIFFRACTION	r_gen_planes_refined	0.002	0.02	2632
X-RAY DIFFRACTION	r_nbd_refined	0.213	0.2	1729
X-RAY DIFFRACTION	r_nbtor_refined	0.297	0.2	2390
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.121	0.2	92
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.175	0.2	62
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.194	0.2	5
X-RAY DIFFRACTION	r_mcbond_it	0.216	1.5	2115
X-RAY DIFFRACTION	r_mcangle_it	0.385	2	3348
X-RAY DIFFRACTION	r_scbond_it	0.38	3	1554
X-RAY DIFFRACTION	r_scangle_it	0.642	4.5	1362

Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 1696 / Refine-ID: X-RAY DIFFRACTION

Type	Rms dev position (Å)	Weight position
MEDIUM POSITIONAL	0.48	0.5
MEDIUM THERMAL	0.14	2

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
3.344-3.431	0.4	47	0.36	885	955	97.592
3.431-3.525	0.298	42	0.316	847	891	99.776
3.525-3.627	0.385	56	0.278	844	901	99.889
3.627-3.738	0.283	36	0.27	833	869	100
3.738-3.86	0.281	38	0.25	803	842	99.881
3.86-3.996	0.24	38	0.234	789	827	100
3.996-4.146	0.28	45	0.221	758	804	99.876
4.146-4.315	0.271	30	0.211	723	754	99.867
4.315-4.506	0.279	32	0.214	699	735	99.456
4.506-4.725	0.261	37	0.209	676	717	99.442
4.725-4.98	0.206	38	0.18	653	697	99.139
4.98-5.28	0.214	30	0.186	611	647	99.073
5.28-5.643	0.366	28	0.24	589	624	98.878
5.643-6.092	0.44	30	0.246	525	562	98.754
6.092-6.669	0.263	31	0.258	496	534	98.689
6.669-7.449	0.299	27	0.221	454	490	98.163
7.449-8.588	0.223	19	0.178	430	458	98.035
8.588-10.485	0.116	22	0.136	367	390	99.744
10.485-14.689	0.239	13	0.164	302	319	98.746
14.689-47.168	0.196	9	0.312	183	218	88.073

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	0.6272	-2.4505	0.6804	19.934	-14.5543	14.3977	0.1787	-1.1574	0.2568	-0.6744	-0.1546	0.2186	-0.9406	0.4849	-0.0241	0.8689	0.0133	-0.035	0.1894	0.2534	0.5001	3.3023	70.7933	-7.8481
2	0.4745	-3.1867	1.4626	29.9726	-21.5058	20.4321	-0.268	-0.3865	-0.3169	0.0572	0.2573	-1.5633	-0.0478	0.4478	0.0106	0.5094	0.1201	-0.1674	0.1618	0.4272	0.5403	5.3161	48.1636	5.5501
3	9.0656	-6.6805	9.7257	40.7192	-41.3651	43.1052	-0.9104	-0.0599	-0.2608	-1.9582	0.3109	-1.2565	2.2734	0.085	0.5995	0.9242	0.3561	0.0315	0.2625	0.2767	0.3516	6.3667	25.9749	24.1063
4	3.242	-5.3865	9.0654	8.9496	-15.0619	25.3488	-0.8545	-1.3323	-2.3293	-1.366	2.3689	0.2759	3.894	-1.8027	-1.5144	1.0896	0.0087	-0.4073	1.1703	0.4158	1.7095	2.1959	12.681	33.404
5	5.6987	-3.2944	9.8639	13.8465	-24.4464	46.4941	0.0693	1.0824	-0.8359	-2.0822	0.19	-0.8547	3.0423	-0.9496	-0.2593	1.4045	0.1283	-0.3305	0.3497	0.3386	0.8126	-0.7871	26.4147	12.4395
6	50.8988	10.6195	-1.8751	3.2842	8.2116	69.3255	-0.4838	2.8745	-1.9406	-2.1772	0.8165	-1.9479	2.1805	-1.3444	-0.3327	1.1611	0.0945	-0.0728	0.0128	0.4399	0.664	0.6934	43.7034	-4.3383
7	33.9923	29.7755	4.6433	32.7809	-18.4049	76.0164	0.4126	4.3875	-3.8331	-3.3957	0.1438	-1.9344	2.9259	1.077	-0.5564	1.1768	0.477	-0.0509	0.0736	0.3001	0.476	5.192	54.2929	-9.6089
8	3.6482	8.5574	-6.0329	32.8098	-21.6849	15.2735	-0.3503	0.4615	-0.3378	-1.1283	0.187	-2.0258	0.8619	0.6365	0.1633	0.7089	0.0152	0.1203	0.4118	0.3187	0.7073	12.8343	80.9018	-23.1126
9	12.5107	7.9261	2.3186	21.5563	-5.0891	9.1298	-0.2946	1.6389	-0.1322	-0.8773	1.7164	0.4703	0.1019	-0.9147	-1.4217	1.0097	-0.025	0.127	0.4113	0.2694	0.3896	6.3898	82.9367	-28.0091
10	10.9505	13.9449	-14.3227	40.3459	-30.8256	26.5327	-0.7559	1.0578	0.3116	-1.5507	1.7589	1.3398	0.3206	-2.4606	-1.0029	0.8174	-0.1122	-0.1072	0.285	0.3	0.4517	-1.8982	65.3409	-13.863
11	2.876	0.6151	0.7546	13.0998	-11.055	9.8991	-0.3625	0.5235	0.0308	-0.9121	0.6481	-0.3338	0.6134	-0.5394	-0.2856	0.7989	-0.0256	-0.225	0.2599	0.4485	0.4262	-6.1517	44.5149	5.574
12	13.3594	-0.0503	-16.8167	4.474	-5.2922	31.4671	-0.4015	-2.1488	0.173	-0.3327	0.2856	1.9918	1.6107	-0.8875	0.1159	0.9211	-0.3279	-0.3383	0.5035	0.6471	0.7948	-9.6701	24.479	27.8543
13	3.0971	-0.9805	2.8147	15.8047	-3.2225	2.9088	-0.857	1.6085	-0.2193	-0.7273	0.0008	-0.9165	0.1189	1.9206	0.8562	1.2962	0.7901	-0.0079	0.6276	0.384	0.6825	19.3568	8.6349	45.6626
14	2.0054	2.1382	2.0222	8.8662	-6.3859	13.1172	-0.6036	0.3156	1.4642	0.0692	0.347	-1.5923	0.3581	1.2316	0.2566	0.5703	0.2465	-0.0019	0.2729	0.3659	0.6828	11.4389	27.5102	33.8934
15	2.989	-6.133	7.1452	12.6356	-14.0583	24.1745	-0.9894	-0.2259	0.7169	-0.4117	1.0899	-0.7812	-0.3226	0.2859	-0.1006	0.6503	0.0002	-0.1785	0.2925	0.371	0.4576	0.7048	47.7086	15.63
16	0.0006	0.1325	-0.0548	31.8152	-13.1585	5.4422	0.6604	-1.1176	2.4515	-0.8734	1.6622	1.0123	-1.4314	-1.7472	-2.3226	1.0244	-0.0031	-0.0272	1.5309	0.3441	0.9719	-9.7456	58.6984	4.6116
17	4.2897	-6.9689	12.1583	11.7715	-21.4691	41.01	-0.4143	-0.5831	0.91	1.3513	0.7206	0.3659	-1.0632	-2.1367	-0.3063	0.6361	0.1764	0.045	0.4116	0.5068	0.7756	-5.5737	45.5369	25.5521
18	19.8937	-4.9836	8.225	29.4317	-9.3687	33.6849	-0.7195	-1.3307	2.4065	1.2849	0.7112	-0.599	-0.5648	-1.3036	0.0083	0.6689	0.2706	-0.1682	0.1182	0.2774	0.5098	4.5925	29.9232	42.4896
19	15.5979	-16.7306	12.6983	20.175	-12.7378	10.6871	-0.3503	-0.5703	1.0195	0.1264	0.2601	-1.4101	-0.6002	0.2122	0.0902	0.9069	0.3493	-0.1529	0.4878	0.38	0.7275	29.2174	8.0818	58.4315
20	30.7771	-19.9449	16.6447	20.2321	-12.431	9.3718	1.0402	-0.7171	-0.5461	-0.8228	-0.1992	-0.2538	-0.2115	0.1671	-0.841	1.2627	0.4172	-0.2355	1.0679	0.2279	0.5447	28.62	-0.0691	66.3535
21	24.5345	-17.4311	20.9253	26.2065	-28.9142	32.1233	0.6675	-2.1739	-0.9688	-1.4192	1.0748	1.5944	2.4307	-2.0908	-1.7423	1.045	0.3429	-0.1296	0.3903	0.2025	0.5611	11.9359	11.248	51.635
22	14.5637	-9.7269	9.4642	11.7932	-13.5143	16.946	-0.1706	-1.0201	-0.0385	-0.0823	1.1507	0.0965	0.9913	-1.3881	-0.9801	0.6876	0.0358	-0.11	0.1629	0.3146	0.2963	-0.9383	26.2245	33.2724
23	15.7592	-6.7557	6.2656	6.9123	-1.0317	3.1724	-0.5901	0.6482	0.0219	-1.8851	0.3188	0.8934	1.322	-3.7235	0.2713	0.7586	-0.1843	-0.1818	0.835	0.5656	0.6372	-13.7641	42.6622	12.1413
24	42.996	-7.7998	4.6846	1.415	-0.8498	0.5104	-2.2458	-1.5276	-1.7059	2.0775	-0.0743	0.6033	-2.4692	-1.8226	2.3202	2.3479	-0.5726	0.0122	1.8474	0.517	0.9887	-12.7277	37.5646	-3.1615

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	X-RAY DIFFRACTION	1	A	A	12 - 23	15 - 26
2	X-RAY DIFFRACTION	2	A	A	24 - 46	27 - 49
3	X-RAY DIFFRACTION	3	A	A	47 - 60	50 - 63
4	X-RAY DIFFRACTION	4	A	A	61 - 72	64 - 75
5	X-RAY DIFFRACTION	5	A	A	73 - 97	76 - 100
6	X-RAY DIFFRACTION	6	A	A	98 - 106	101 - 109
7	X-RAY DIFFRACTION	7	A	A	107 - 114	110 - 117
8	X-RAY DIFFRACTION	8	A	A	115 - 147	118 - 150
9	X-RAY DIFFRACTION	9	A	A	148 - 162	151 - 165
10	X-RAY DIFFRACTION	10	A	A	163 - 177	166 - 180
11	X-RAY DIFFRACTION	11	A	A	178 - 201	181 - 204
12	X-RAY DIFFRACTION	12	A	A	202 - 216	205 - 219
13	X-RAY DIFFRACTION	13	B	B	12 - 23	15 - 26
14	X-RAY DIFFRACTION	14	B	B	24 - 44	27 - 47
15	X-RAY DIFFRACTION	15	B	B	45 - 60	48 - 63
16	X-RAY DIFFRACTION	16	B	B	61 - 72	64 - 75
17	X-RAY DIFFRACTION	17	B	B	73 - 97	76 - 100
18	X-RAY DIFFRACTION	18	B	B	98 - 107	101 - 110
19	X-RAY DIFFRACTION	19	B	B	108 - 146	111 - 149
20	X-RAY DIFFRACTION	20	B	B	147 - 163	150 - 166
21	X-RAY DIFFRACTION	21	B	B	164 - 177	167 - 180
22	X-RAY DIFFRACTION	22	B	B	178 - 199	181 - 202
23	X-RAY DIFFRACTION	23	B	B	200 - 216	203 - 219
24	X-RAY DIFFRACTION	24	B	B	217 - 221	220 - 224

-
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

-
Phasing

-
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

-Phasing

-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

-
Phasing

-
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