PDB-5br9: Crystal structure of an uncharacterized protein with similarity t...

ID or keywords:

Entry

Database: PDB / ID: 5br9

Title

Crystal structure of an uncharacterized protein with similarity to peptidase YEAZ from Pseudomonas aeruginosa

Components

Uncharacterized protein

Keywords

UNKNOWN FUNCTION / SSGCID / Pseudomonas aeruginosa / Uncharacterized protein / peptidase YEAZ / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease

Function / homology

Function and homology information

tRNA threonylcarbamoyladenosine modification
Similarity search - Function

Biological species

Pseudomonas aeruginosa (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 2.35 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Citation

Journal: to be published
Title: Crystal structure of an uncharacterized protein with similarity to peptidase YEAZ from Pseudomonas aeruginosa
Authors: Abendroth, J. / Fairman, J.W. / Lorimer, D.D. / Edwards, T.E.

History

Deposition	May 29, 2015	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 15, 2015	Provider: repository / Type: Initial release
Revision 1.1	Sep 27, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Source and taxonomy Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_src_gen / pdbx_initial_refinement_model / pdbx_prerelease_seq / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	5br9.cif.gz	425 KB	Display	PDBx/mmCIF format
PDB format	pdb5br9.ent.gz	348.6 KB	Display	PDB format
PDBx/mmJSON format	5br9.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	5br9_validation.pdf.gz	450.5 KB	Display	wwPDB validaton report
Full document	5br9_full_validation.pdf.gz	455 KB	Display
Data in XML	5br9_validation.xml.gz	40.2 KB	Display
Data in CIF	5br9_validation.cif.gz	57.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/br/5br9 ftp://data.pdbj.org/pub/pdb/validation_reports/br/5br9	HTTPS FTP

-
Related structure data

Related structure data	3r6mS S: Starting model for refinement
Similar structure data	3wya-d 3zrc-3 4w9g-2 4c57-1 5ixk-d 1rzo-1 5lfp-d 1nj4-d 3zcz-3 4w9i-3 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
Other databases	TargetTrack: PsaeA.17385.a

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Uncharacterized protein

B: Uncharacterized protein

C: Uncharacterized protein

D: Uncharacterized protein

E: Uncharacterized protein

126 kDa, 5 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Uncharacterized protein

D: Uncharacterized protein

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

2

B: Uncharacterized protein

C: Uncharacterized protein

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

3

E: Uncharacterized protein

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

Unit cell

Length a, b, c (Å)	80.350, 201.940, 162.900
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	20
Space group name H-M	C222₁

#1: Protein	Uncharacterized protein Mass: 25234.791 Da / Num. of mol.: 5 / Fragment: PsaeA.17385.a.B1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228) (bacteria) Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / Gene: PA3685 / Plasmid: PsaeA.17385.a.B1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9HXV5
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 384 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

Uncharacterized protein

Mass: 25234.791 Da / Num. of mol.: 5 / Fragment: PsaeA.17385.a.B1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Pseudomonas aeruginosa (strain ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228) (bacteria)
Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / Gene: PA3685 / Plasmid: PsaeA.17385.a.B1 / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9HXV5

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 384 / 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: 2.63 Å³/Da / Density % sol: 53 %
Crystal grow	Temperature: 290 K / Method: vapor diffusion, sitting drop Details: Microlytics MCSG1 A3: 10% PEG 8000, 200mM NaCl, 100mM Na2HPO4/ KH2PO4 pH 6.2; PsaeA.17385.a.B1.PS02242 at 20mg/ml; cryo: 20% EG in 2 steps; tray 260042a3, puck ges3-7

-
Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

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

Detector

Type: RAYONIX MX-225 / Detector: CCD / Date: Mar 12, 2015

Radiation

Monochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97872 Å / Relative weight: 1

Reflection

Resolution: 2.35→50 Å / Num. all: 55527 / Num. obs: 55353 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 5 % / B_iso Wilson estimate: 38 Å² / R_merge F obs: 0.998 / R_merge(I) obs: 0.071 / R_rim(I) all: 0.079 / Χ²: 0.978 / Net I/σ(I): 16.65 / Num. measured all: 277630

Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)	Highest resolution (Å)	Redundancy (%)	R_merge F obs	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. possible	Num. unique obs	R_rim(I) all	% possible all
2.35-2.41		5.1	0.832	0.537	2.98	20475	4047	4045	0.6	100
2.41-2.48			0.887	0.429	3.67	20044	3963	3960	0.479	99.9
2.48-2.55			0.926	0.343	4.55	19428	3851	3848	0.383	99.9
2.55-2.63			0.935	0.304	5.17	18831	3723	3716	0.34	99.8
2.63-2.71			0.958	0.242	6.38	18532	3661	3656	0.27	99.9
2.71-2.81			0.968	0.205	7.43	17638	3497	3489	0.229	99.8
2.81-2.91			0.98	0.162	9.5	17173	3400	3395	0.18	99.9
2.91-3.03			0.987	0.129	11.61	16539	3269	3267	0.144	99.9
3.03-3.17			0.992	0.1	14.58	15846	3145	3139	0.112	99.8
3.17-3.32			0.995	0.077	18.47	15152	3011	3009	0.086	99.9
3.32-3.5			0.996	0.065	21.61	14560	2887	2885	0.072	99.9
3.5-3.72			0.998	0.054	25.9	13468	2697	2690	0.06	99.7
3.72-3.97			0.998	0.046	29.5	12756	2562	2553	0.051	99.6
3.97-4.29			0.998	0.04	33.24	11788	2379	2368	0.044	99.5
4.29-4.7			0.998	0.036	36.68	10941	2224	2204	0.041	99.1
4.7-5.25			0.998	0.036	36.47	9851	2003	1998	0.04	99.8
5.25-6.07			0.998	0.039	34.48	8679	1782	1775	0.044	99.6
6.07-7.43			0.999	0.032	37.36	7344	1517	1513	0.036	99.7
7.43-10.51			0.999	0.027	43.69	5666	1200	1176	0.03	98
	10.51		0.999	0.026	42.93	2919	709	667	0.029	94.1

-
Phasing

Phasing	Method: molecular replacement

-
Processing

Software

Name	Classification
XDS	data reduction
XSCALE	data scaling
BALBES	phasing
MOLREP	phasing
PHASER	phasing
PHENIX	refinement
Coot	model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 3r6m

3r6m

Resolution: 2.35→48.222 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.05 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2057	2766	5 %	Random selection
R_work	0.1609	52579	-	-
obs	0.1632	55345	99.69 %	-

Solvent computation

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

Displacement parameters

B_iso max: 131.31 Å² / B_iso mean: 45.8076 Å² / B_iso min: 16.78 Å²

Refinement step

Cycle: final / Resolution: 2.35→48.222 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7909	0	0	384	8293
B_iso mean	-	-	-	42.35	-
Num. residues	-	-	-	-	1081

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	8255
X-RAY DIFFRACTION	f_angle_d	1.07	11310
X-RAY DIFFRACTION	f_chiral_restr	0.047	1285
X-RAY DIFFRACTION	f_plane_restr	0.006	1491
X-RAY DIFFRACTION	f_dihedral_angle_d	14.895	4902

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 (%)
2.35-2.3905	0.2869	131	0.2288	2601	2732	100
2.3905-2.434	0.2664	142	0.2116	2600	2742	100
2.434-2.4808	0.2562	145	0.1831	2585	2730	100
2.4808-2.5315	0.2384	121	0.1842	2640	2761	100
2.5315-2.5865	0.2224	125	0.1859	2634	2759	100
2.5865-2.6467	0.247	139	0.1762	2586	2725	100
2.6467-2.7128	0.2554	140	0.1825	2603	2743	100
2.7128-2.7862	0.252	146	0.1953	2586	2732	100
2.7862-2.8682	0.2608	146	0.1944	2628	2774	100
2.8682-2.9607	0.2323	135	0.1952	2610	2745	100
2.9607-3.0665	0.256	137	0.188	2608	2745	100
3.0665-3.1893	0.225	153	0.1814	2628	2781	100
3.1893-3.3344	0.2153	148	0.1702	2599	2747	100
3.3344-3.5101	0.2589	105	0.1704	2690	2795	100
3.5101-3.73	0.1974	124	0.1594	2625	2749	100
3.73-4.0178	0.1846	156	0.1406	2633	2789	100
4.0178-4.4219	0.1653	131	0.1213	2644	2775	100
4.4219-5.0612	0.1449	158	0.1208	2639	2797	99
5.0612-6.3743	0.1885	144	0.1481	2682	2826	100
6.3743-48.2324	0.1739	140	0.1528	2758	2898	98

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	3.2166	1.1946	-2.3569	2.8394	0.8932	3.19	0.0798	0.1649	0.2154	-0.2185	0.0993	-0.112	0.0753	0.1534	-0.1321	0.2747	0.0623	0.0447	0.3337	0.0166	0.1527	2.485	55.2713	-19.5124
2	8.7065	1.2752	2.7391	2.4409	-3.0957	6.4479	-0.2218	-1.0751	-0.4141	1.0774	0.6248	-0.3106	-0.0182	0.196	-0.3711	0.306	0.035	-0.0072	0.5136	-0.0216	0.1573	9.1266	53.8147	-15.6655
3	5.7703	-1.9707	0.1334	9.5891	-1.4724	1.6785	-0.4688	-0.2997	-0.3575	0.6495	0.4883	-0.7806	0.5158	0.3779	0.0424	0.3432	0.097	0.0463	0.4623	0.0157	0.2074	3.8351	50.7499	-9.7718
4	2.152	1.2745	-1.0449	0.8185	-1.0277	2.4834	-0.3029	-0.1339	-0.2528	-0.0094	0.273	-0.0606	0.4374	0.2933	0.047	0.3127	0.0878	0.0521	0.3082	0.0211	0.2092	-3.7048	48.221	-19.6102
5	2.5019	-1.1807	-1.3942	1.4103	1.2646	1.8323	-0.2126	-0.1357	-0.0897	-0.0296	0.2282	-0.0754	0.0018	0.2886	-0.0364	0.1991	-0.0142	-0.0254	0.3336	0.0256	0.1652	8.0084	50.3829	-33.4035
6	4.0109	-1.6321	-0.713	3.7121	1.0211	2.9131	0.1816	0.2975	-0.235	-0.5551	-0.1444	0.6812	0.0218	-0.3198	-0.0001	0.2983	-0.0471	-0.0418	0.3263	0.0579	0.1493	6.6652	47.8324	-40.8527
7	1.9741	-5.9603	0.4505	3.5039	-0.3555	4.1875	0.2497	0.1102	1.5975	-0.5172	-0.4669	-0.5057	-0.2329	-0.0818	0.0213	0.3519	-0.0792	0.1229	0.4984	-0.0349	0.2506	15.4441	51.9586	-47.3283
8	2.2771	-1.7705	-1.1356	1.8366	0.2933	2.1215	-0.0463	-0.0244	0.1166	-0.0639	0.1053	-0.1734	-0.1159	0.2546	-0.0623	0.1701	-0.0588	0.001	0.2914	-0.0158	0.176	13.6812	49.5661	-34.1874
9	2.7233	0.581	0.5825	3.0432	-0.3701	4.6213	0.1638	0.4383	-0.3899	0.9783	-0.0002	0.3679	0.6914	-0.2543	-0.147	0.5155	0.0222	-0.008	0.4633	-0.0348	0.2527	-9.2542	47.726	-29.2224
10	3.2903	-0.4483	-0.6802	3.0588	1.6295	6.8625	-0.048	0.249	-0.3022	0.0403	0.1191	-0.1524	0.321	0.5441	-0.0327	0.2835	-0.0128	-0.0457	0.3522	-0.0233	0.2192	32.0913	32.0953	-7.1822
11	1.7222	0.049	0.688	3.6629	1.8604	5.1949	-0.0035	0.1634	-0.0607	0.0546	-0.05	-0.2534	0.1892	0.4205	-0.0368	0.1859	0.013	-0.0051	0.2971	0.0066	0.1899	27.3388	31.3545	-24.1288
12	2.159	2.0816	0.9669	5.5186	0.6998	1.6515	-0.0782	0.5589	-0.0624	-0.4296	0.1023	-0.2223	-0.2673	0.2922	-0.0138	0.2462	0.0028	-0.0005	0.4787	-0.009	0.2104	23.2184	31.463	-33.4938
13	0.823	0.3535	0.1646	4.5499	2.4468	6.7765	-0.0028	0.032	-0.0656	0.1493	-0.1189	-0.0303	-0.024	-0.0493	0.1049	0.1506	0.013	0.0034	0.3092	0.016	0.2034	26.2373	29.9143	-23.3241
14	7.4853	2.5398	2.5405	6.2278	3.2456	9.0532	0.2801	-0.6788	0.0257	-0.0055	-0.533	0.5676	-0.0051	-0.3853	-0.0184	0.2972	-0.0884	-0.0144	0.2223	0.0437	0.2949	16.4709	32.7378	13.4234
15	7.405	-0.1191	2.5445	3.2851	-0.8754	2.7678	-0.396	0.3742	0.0839	-0.3801	0.1022	1.0399	-0.7529	0.0702	0.3039	0.2735	-0.0474	-0.0801	0.2298	0.0085	0.4817	9.3931	35.9266	10.1372
16	3.8657	2.7156	2.974	4.2463	4.0074	3.925	-0.0169	0.2024	-0.2186	-0.7319	-0.1889	0.9632	-0.3739	-0.7482	0.2138	0.4264	-0.0759	-0.1486	0.3008	0.0433	0.4439	12.9195	40.4703	4.2595
17	3.6363	0.9877	-0.743	3.5242	-0.2665	1.4639	-0.1154	0.2716	-0.3512	-0.319	0.102	0.0767	0.1424	-0.0738	0.0566	0.2325	-0.0715	-0.0313	0.2152	0.0149	0.2283	20.6935	30.475	5.9326
18	2.9417	2.3636	0.789	3.6145	0.1783	0.5241	0.0115	-0.1873	-0.1996	0.2434	0.0247	0.2249	0.0661	-0.0446	-0.0424	0.2244	0.0017	0.0454	0.2121	0.0294	0.3828	9.4551	17.0377	14.0025
19	8.085	-0.2392	4.2405	6.1149	3.2976	4.3574	-0.1554	-0.7654	-0.5	0.4912	0.0453	0.4735	0.1553	-0.4873	-0.0379	0.238	-0.0606	0.1193	0.2707	0.0873	0.5318	0.4175	9.6873	15.3264
20	3.2923	3.077	0.2035	4.684	-0.1278	0.2187	-0.1178	0.0707	-0.1817	0.1593	0.0291	0.203	0.1018	0.0159	0.1488	0.2792	-0.0375	0.0259	0.2451	0.0061	0.3314	12.1464	20.8944	13.2897
21	7.4633	3.3398	2.3352	4.066	-1.8588	8.402	-0.0675	-0.0218	-0.4395	-0.3423	0.3275	0.2075	0.175	-0.0818	-0.1576	0.3272	0.0381	0.0375	0.1556	0.0703	0.4192	-17.8689	35.3449	-9.5888
22	2.4258	0.9099	-2.679	0.7424	-1.1096	2.9054	-0.4285	0.0718	-0.0825	-0.6031	0.1565	0.4408	-0.14	0.636	-0.1791	0.6322	-0.0378	0.01	0.4795	0.0366	0.4623	-21.1786	33.6225	-18.2819
23	2.0902	-0.6506	-3.839	5.8033	0.4928	9.0562	0.112	0.5415	-0.4563	-0.3041	-0.3514	0.8162	-0.1002	-0.9362	-0.0576	0.3292	0.05	-0.0944	0.2828	0.0058	0.495	-22.0947	41.6061	-16.1442
24	5.6107	-1.6375	1.3207	6.5904	-0.4968	3.7441	0.0586	-0.1257	-0.3771	0.0056	-0.0542	0.0737	0.2546	-0.0073	0.0152	0.3336	0.0339	0.1132	0.1857	0.0792	0.2559	-12.6374	37.6773	-7.8939
25	8.8521	1.4332	-0.783	3.5994	-3.1349	3.8802	0.0823	0.8344	-0.9187	-0.5426	0.1278	-0.2521	0.6314	0.7475	-0.072	0.4524	0.1869	0.0574	0.3722	-0.0105	0.3371	-6.4641	40.5657	-13.7681
26	2.3896	-1.6963	0.8485	8.8196	-0.194	1.506	0.2372	0.0004	-0.6657	-0.4564	-0.0441	0.0886	0.1654	-0.0625	-0.2097	0.2777	0.0275	-0.0426	0.2496	0.0304	0.4397	-10.0663	17.237	-6.3193
27	1.4056	-0.867	0.3273	8.5463	-0.4839	1.5431	0.2315	-0.0187	-0.5071	-0.0567	-0.048	-0.0553	-0.1174	-0.0228	-0.0876	0.2885	0.0394	0.0243	0.2912	0.08	0.3949	-11.6536	24.9615	-6.1713
28	3.4583	0.1708	-1.0573	1.9205	1.4528	1.5495	-0.0379	0.551	-0.652	0.1053	-0.4727	-0.5516	1.0581	1.1936	0.2184	0.2007	0.1823	-0.0065	1.1237	0.3643	0.8384	40.1232	-3.8876	-14.4254
29	6.3506	0.6187	0.9058	4.0562	2.4401	6.8549	0.7599	0.0214	-0.7535	0.575	-0.7807	0.007	-0.1058	1.4103	0.128	0.7109	0.2209	0.1071	0.8255	0.1719	0.9563	36.2892	-10.5333	-13.8735
30	5.3636	0.7469	4.5812	7.5072	-0.4323	4.7397	0.4102	0.7106	-1.6539	0.1359	0.101	0.0378	1.1103	1.1006	-0.6695	0.5531	0.4783	0.0327	0.9888	0.3629	1.0489	42.7057	-11.126	-8.0134
31	5.1038	-2.5913	1.8995	1.4271	-0.9564	0.7888	0.043	0.7717	-0.4611	-0.1559	-0.3782	-0.575	-0.074	1.2015	0.1124	0.3606	-0.0209	-0.0001	1.018	0.2449	0.6205	38.9051	1.253	-7.2212
32	5.0513	0.5238	1.6713	2.6923	-0.6292	2.9715	-0.0799	0.0394	-0.6352	-0.1426	-0.2604	-0.4649	0.124	0.7846	0.1844	0.3332	0.0343	0.0536	0.3353	0.0699	0.3843	28.0171	2.0799	-21.9494
33	7.0446	2.7339	-3.0038	3.1136	-2.0504	4.0622	-0.34	0.4757	-0.467	-0.5561	0.0482	-0.0358	0.1031	0.2305	0.2425	0.4426	0.0014	0.0113	0.2802	-0.0222	0.3351	21.9133	7.5285	-27.8553
34	4.9109	0.59	1.1815	2.5587	-0.7448	4.6246	-0.2114	0.3634	-0.7677	-0.48	-0.0864	-0.3524	0.1159	0.9336	0.3018	0.4532	0.0322	0.083	0.416	0.0063	0.4603	24.8981	-1.4988	-24.1921
35	2.608	1.7953	-0.2416	1.6509	0.3528	1.832	0.2695	-0.2753	-0.5817	-0.0538	-0.9021	-0.1404	-0.8211	0.4141	0.361	0.7914	-0.164	-0.1941	0.7761	0.3066	0.491	33.8928	10.2531	-10.7176

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 0 through 20 )	A
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 21 through 34 )	A
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 35 through 50 )	A
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 51 through 86 )	A
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 87 through 131 )	A
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 132 through 148 )	A
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 149 through 159 )	A
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 160 through 200 )	A
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 201 through 216 )	A
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 1 through 86 )	B
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 87 through 131 )	B
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 132 through 160 )	B
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 161 through 216 )	B
14	X-RAY DIFFRACTION	14	chain 'C' and (resid -1 through 12 )	C
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 13 through 34 )	C
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 35 through 50 )	C
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 51 through 86 )	C
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 87 through 148 )	C
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 149 through 172 )	C
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 173 through 216 )	C
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 1 through 20 )	D
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 21 through 38 )	D
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 39 through 50 )	D
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 51 through 68 )	D
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 69 through 86 )	D
26	X-RAY DIFFRACTION	26	chain 'D' and (resid 87 through 172 )	D
27	X-RAY DIFFRACTION	27	chain 'D' and (resid 173 through 214 )	D
28	X-RAY DIFFRACTION	28	chain 'E' and (resid 1 through 20 )	E
29	X-RAY DIFFRACTION	29	chain 'E' and (resid 21 through 35 )	E
30	X-RAY DIFFRACTION	30	chain 'E' and (resid 36 through 50 )	E
31	X-RAY DIFFRACTION	31	chain 'E' and (resid 51 through 86 )	E
32	X-RAY DIFFRACTION	32	chain 'E' and (resid 87 through 131 )	E
33	X-RAY DIFFRACTION	33	chain 'E' and (resid 132 through 160 )	E
34	X-RAY DIFFRACTION	34	chain 'E' and (resid 161 through 200 )	E
35	X-RAY DIFFRACTION	35	chain 'E' and (resid 201 through 216 )	E

-
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://pdbjlvh1.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