PDB-3ve2: The 2.1 angstrom crystal structure of Transferrin binding protein...

ID or keywords:

Entry

Database: PDB / ID: 3ve2

Title

The 2.1 angstrom crystal structure of Transferrin binding protein B (TbpB) from serogroup B M982 Neisseria meningitidis

Components

Transferrin-binding protein 2

Keywords

Transferrin-binding protein / Lipoprotein / transferrin receptor / iron acquisition / vaccine candidate / host pathogen interaction / Beta barrel / Receptor / Transferrin / Outermembrane

Function / homology

Function and homology information

cell outer membrane / cell surface
Similarity search - Function

Biological species

Neisseria meningitidis serogroup B (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.14 Å

Authors

Calmettes, C. / Moraes, T.F.

Citation

Journal: Nat.Struct.Mol.Biol. / Year: 2012
Title: The structural basis of transferrin sequestration by transferrin-binding protein B.
Authors: Calmettes, C. / Alcantara, J. / Yu, R.H. / Schryvers, A.B. / Moraes, T.F.

History

Deposition	Jan 6, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 22, 2012	Provider: repository / Type: Initial release
Revision 1.1	Sep 5, 2012	Group: Database references

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3ve2.cif.gz	438.9 KB	Display	PDBx/mmCIF format
PDB format	pdb3ve2.ent.gz	371 KB	Display	PDB format
PDBx/mmJSON format	3ve2.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3ve2_validation.pdf.gz	494 KB	Display	wwPDB validaton report
Full document	3ve2_full_validation.pdf.gz	532.2 KB	Display
Data in XML	3ve2_validation.xml.gz	48.5 KB	Display
Data in CIF	3ve2_validation.cif.gz	69.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ve/3ve2 ftp://data.pdbj.org/pub/pdb/validation_reports/ve/3ve2	HTTPS FTP

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Related structure data

Related structure data	3ve1C C: citing same article (ref.)
Similar structure data	3gbm-d 2odf-d 22856 5ux5-d 5v1x-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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

3ve1C

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#35 - Nov 2002 Ferritin and Transferrin similarity (1) #244 - Apr 2020 Photosynthetic Supercomplexes similarity (1) #59 - Nov 2004 Photosystem II similarity (1)

Deposited unit

A: Transferrin-binding protein 2

B: Transferrin-binding protein 2

hetero molecules

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

1

B: Transferrin-binding protein 2

hetero molecules

B: Transferrin-binding protein 2

hetero molecules

A: Transferrin-binding protein 2

hetero molecules

A: Transferrin-binding protein 2

hetero molecules

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

2

B: Transferrin-binding protein 2

hetero molecules

B: Transferrin-binding protein 2

hetero molecules

A: Transferrin-binding protein 2

hetero molecules

A: Transferrin-binding protein 2

hetero molecules

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

3

B: Transferrin-binding protein 2

hetero molecules

A: Transferrin-binding protein 2

hetero molecules

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

4

A: Transferrin-binding protein 2

hetero molecules

defined by software
72.1 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

5

B: Transferrin-binding protein 2

hetero molecules

defined by software
72.5 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	46.604, 149.336, 199.600
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	17
Space group name H-M	P222₁

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Selection details	Auth asym-ID	Auth seq-ID
1	1	1	chain A and (resseq 38:107 or resseq 121:149 or resseq...	A	38 - 107
1	2	1	chain A and (resseq 38:107 or resseq 121:149 or resseq...	A	121 - 149
1	3	1	chain A and (resseq 38:107 or resseq 121:149 or resseq...	A	153 - 263
1	4	1	chain A and (resseq 38:107 or resseq 121:149 or resseq...	A	272 - 287
1	5	1	chain A and (resseq 38:107 or resseq 121:149 or resseq...	A	289 - 296
1	6	1	chain A and (resseq 38:107 or resseq 121:149 or resseq...	A	303 - 348
1	7	1	chain A and (resseq 38:107 or resseq 121:149 or resseq...	A	377 - 417
1	8	1	chain A and (resseq 38:107 or resseq 121:149 or resseq...	A	436 - 446
1	9	1	chain A and (resseq 38:107 or resseq 121:149 or resseq...	A	475 - 498
1	10	1	chain A and (resseq 38:107 or resseq 121:149 or resseq...	A	520 - 554
1	11	1	chain A and (resseq 38:107 or resseq 121:149 or resseq...	A	556 - 569
1	12	1	chain A and (resseq 38:107 or resseq 121:149 or resseq...	A	571 - 588
1	13	1	chain A and (resseq 38:107 or resseq 121:149 or resseq...	A	675 - 687
2	1	1	chain B and (resseq 38:107 or resseq 121:149 or resseq...	B	38 - 107
2	2	1	chain B and (resseq 38:107 or resseq 121:149 or resseq...	B	121 - 149
2	3	1	chain B and (resseq 38:107 or resseq 121:149 or resseq...	B	153 - 263
2	4	1	chain B and (resseq 38:107 or resseq 121:149 or resseq...	B	272 - 287
2	5	1	chain B and (resseq 38:107 or resseq 121:149 or resseq...	B	289 - 296
2	6	1	chain B and (resseq 38:107 or resseq 121:149 or resseq...	B	303 - 348
2	7	1	chain B and (resseq 38:107 or resseq 121:149 or resseq...	B	377 - 417
2	8	1	chain B and (resseq 38:107 or resseq 121:149 or resseq...	B	436 - 446
2	9	1	chain B and (resseq 38:107 or resseq 121:149 or resseq...	B	475 - 498
2	10	1	chain B and (resseq 38:107 or resseq 121:149 or resseq...	B	520 - 554
2	11	1	chain B and (resseq 38:107 or resseq 121:149 or resseq...	B	556 - 569
2	12	1	chain B and (resseq 38:107 or resseq 121:149 or resseq...	B	571 - 588
2	13	1	chain B and (resseq 38:107 or resseq 121:149 or resseq...	B	675 - 687

NCS oper: (Code: given
Matrix: (-0.946295, -0.012595, -0.32306), (0.041559, -0.99569, -0.082913), (-0.320623, -0.091886, 0.942739)
Vector: 60.854, -34.257301, 8.6033)

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Protein , 1 types, 2 molecules AB

#1: Protein	Transferrin-binding protein 2 / TBP-2 Mass: 71406.695 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Neisseria meningitidis serogroup B (bacteria) Strain: M982 / Gene: tbpB, tbp2 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q09057

#1: Protein

Transferrin-binding protein 2 / TBP-2

Mass: 71406.695 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Neisseria meningitidis serogroup B (bacteria)
Strain: M982 / Gene: tbpB, tbp2 / Plasmid: pET / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q09057

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Non-polymers , 5 types, 638 molecules

#2: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO₄
#4: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₃O₂
#5: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 618 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.43 Å³/Da / Density % sol: 49.42 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 0.1M sodium citrate pH 4.5, 1.85M Ammonium sulfate, vapor diffusion, hanging drop, temperature 20K, temperature 293K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 24-ID-E / Wavelength: 0.9795 Å

Detector

Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 26, 2011

Radiation

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

Radiation wavelength

Wavelength: 0.9795 Å / Relative weight: 1

Reflection

Resolution: 2.1→50 Å / Num. obs: 76520 / % possible obs: 93.4 % / Redundancy: 2.9 % / R_merge(I) obs: 0.073 / Χ²: 0.981 / Net I/σ(I): 8.5

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	Χ²	Diffraction-ID	% possible all
2.1-2.18	2.7	0.646	7611	0.799	1	95
2.18-2.26	2.7	0.507	7688	0.798	1	95.1
2.26-2.37	2.7	0.394	7713	0.76	1	95.4
2.37-2.49	2.8	0.299	7686	0.754	1	95.1
2.49-2.65	2.8	0.208	7713	0.786	1	95.1
2.65-2.85	2.9	0.146	7687	0.87	1	94.4
2.85-3.14	2.9	0.082	7709	0.926	1	94.1
3.14-3.59	3	0.057	7652	1.261	1	93.1
3.59-4.52	3	0.047	7543	1.905	1	91.2
4.52-50	3.1	0.024	7518	0.823	1	86.6

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
PHENIX	1.7.1_743	refinement
PDB_EXTRACT	3.1	data extraction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.14→45.383 Å / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8782 / SU ML: 0.68 / σ(F): 1.34 / Phase error: 19.29 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2091	1919	2.63 %
R_work	0.1713	-	-
obs	0.1723	72950	93.36 %

Solvent computation

Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 73.755 Å² / k_sol: 0.376 e/Å³

Displacement parameters

B_iso max: 207.75 Å² / B_iso mean: 60.5452 Å² / B_iso min: 9.96 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	2.5036 Å²	-0 Å²	0 Å²
2-	-	-7.4843 Å²	-0 Å²
3-	-	-	4.9807 Å²

Refinement step

Cycle: LAST / Resolution: 2.14→45.383 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8122	0	106	618	8846

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	8403
X-RAY DIFFRACTION	f_angle_d	1.105	11280
X-RAY DIFFRACTION	f_chiral_restr	0.083	1158
X-RAY DIFFRACTION	f_plane_restr	0.004	1463
X-RAY DIFFRACTION	f_dihedral_angle_d	14.373	3098

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Number	Refine-ID	Type	Rms dev position (Å)
1	1	A	3420	X-RAY DIFFRACTION	POSITIONAL	0.066
1	2	B	3420	X-RAY DIFFRACTION	POSITIONAL	0.066

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / 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 (%)
2.14-2.1935	0.2762	101	0.2523	5086	5187	95
2.1935-2.2528	0.2714	202	0.2279	5034	5236	95
2.2528-2.3191	0.2535	101	0.2231	5178	5279	95
2.3191-2.394	0.2702	101	0.2148	5116	5217	95
2.394-2.4795	0.2792	202	0.2057	5059	5261	95
2.4795-2.5788	0.2193	101	0.186	5159	5260	95
2.5788-2.6961	0.2165	190	0.172	5049	5239	95
2.6961-2.8383	0.2043	113	0.1646	5107	5220	94
2.8383-3.0161	0.2205	101	0.1527	5139	5240	94
3.0161-3.2489	0.2155	202	0.168	5017	5219	94
3.2489-3.5757	0.1708	101	0.1561	5116	5217	93
3.5757-4.0928	0.1952	101	0.147	5043	5144	92
4.0928-5.1554	0.1673	202	0.1405	4942	5144	90
5.1554-45.3935	0.2187	101	0.1849	4986	5087	85

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	1.3022	-0.1506	0.2938	1.6404	1.3464	2.7474	-0.0341	0.0053	-0.3477	0.0971	0.0335	0.0889	0.2605	0.1107	-0.0046	0.1118	-0.0131	0.0393	0.2534	-0.0238	0.1632	30.2619	-34.8429	35.6523
2	3.0332	1.3306	0.3567	3.497	-4.4939	8.3679	0.28	-0.1811	0.3072	0.6966	-0.2137	0.5193	-0.5839	-0.854	-0.0713	0.2746	0.0163	0.0304	0.4045	-0.1535	0.2428	27.4146	-27.8816	18.6977
3	0.9416	-0.1502	-0.2132	0.7827	0.1661	1.2912	-0.0072	0.1992	-0.2515	-0.2699	0.0389	-0.0763	0.0496	0.0709	0.0715	0.1178	-0.0362	0.0566	0.357	-0.1152	0.1417	37.7794	-32.1828	24.0262
4	1.2001	0.1312	1.5198	2.8817	-3.8423	7.528	0.0572	0.9347	1.4334	-1.3266	-0.2183	-2.1349	-0.8797	1.903	0.134	0.5001	-0.2151	0.1833	0.6606	-0.0039	0.7949	48.0363	-19.4507	14.1804
5	0.8982	-0.8198	-0.6738	1.1935	0.1192	2.1531	-0.0708	0.047	-0.135	-0.0795	0.0793	-0.1785	0.132	0.3564	-0.1771	0.1469	0.0488	0.0859	0.2873	-0.1838	0.2493	45.2522	-40.1202	23.2039
6	1.3388	1.7708	-0.7856	3.5681	-1.8966	4.2225	0.1058	0.0674	-0.4091	0.2968	-0.0694	0.4078	0.4954	-0.2587	-0.014	0.4276	-0.0813	0.0423	0.251	-0.2489	0.8062	26.2555	-61.2006	21.3834
7	0.0445	0.0214	-0.0313	0.7826	0.3768	0.4012	-0.0095	0.0686	-0.4399	0.3674	0.0767	0.437	0.2182	-0.0909	0.33	0.5417	0.0045	0.2542	0.287	-0.1906	1.3025	26.232	-75.4718	18.5336
8	0.275	1.0461	0.8697	6.0632	1.1767	4.9352	0.2251	0.1495	-0.1736	-0.0674	-0.3906	0.2801	0.4798	0.0354	0.1298	0.4677	0.0006	0.2331	0.3181	-0.1695	1.182	25.825	-76.2663	15.8984
9	0.9597	0.0917	-0.9323	1.8716	-1.0581	2.525	0.0259	0.0598	0.1294	0.1819	-0.0324	-0.0946	-0.2805	-0.0295	-0.0237	0.1332	-0.0254	-0.0093	0.2161	0.003	0.0739	20.9203	-1.7785	34.5397
10	3.9771	-0.4219	-3.6094	2.9931	-3.3508	8.0037	-0.2101	0.4977	-0.7585	-0.2261	0.1884	0.0662	0.8293	-0.3982	-0.0015	0.2774	-0.0645	-0.0853	0.7428	0.0213	0.5762	32.1353	-11.5759	24.8574
11	0.5442	-0.0916	-0.0327	0.6267	-0.2727	1.2773	0.0099	0.0913	0.1158	-0.1813	0.0054	-0.04	-0.0637	-0.0253	-0.0035	0.1392	-0.0139	0.0026	0.2554	0.0352	0.0622	17.0954	-3.3297	21.7125
12	0.5903	-0.7172	-0.729	2	3.9766	1.9377	0.3937	0.6416	-0.1716	-1.8186	-0.4327	2.226	-0.4473	-1.5743	0.055	0.4729	0.1305	-0.1249	0.6331	0.073	0.5158	10.1117	-15.2092	5.3474
13	0.8099	-0.3576	0.054	1.8435	-0.2685	2.8912	-0.0567	0.0941	0.102	-0.0874	0.0593	0.1745	-0.1656	-0.3295	-0.126	0.176	0.0617	-0.0085	0.2565	0.0914	0.0329	10.6429	5.1545	18.8557
14	4.4513	1.0715	1.4789	5.114	1.595	6.2731	0.1599	-0.1119	0.6746	0.4914	-0.0602	-0.5419	-0.4281	0.5038	-0.1435	0.4789	-0.1267	0.017	0.2025	0.0301	0.4832	28.6326	26.5026	25.7891
15	0.3279	0.1657	0.1321	0.6443	0.2383	0.7285	0.0382	0.0581	0.5156	0.0279	0.0469	-0.1739	-0.4915	0.14	0.2253	0.8306	-0.0965	-0.0207	0.1892	0.0178	0.8638	26.7485	39.8875	25.1956
16	1.4641	1.9975	0.1614	5.6208	0.6284	2.062	0.1254	-0.0177	-0.0229	0.0583	0.0569	-0.6254	-0.4069	0.2786	-0.0171	0.5697	-0.0881	0.0833	0.2266	0.1158	0.927	31.2781	42.6218	21.4133

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 38:101)	A	38 - 101
2	X-RAY DIFFRACTION	2	(chain A and resid 102:123)	A	102 - 123
3	X-RAY DIFFRACTION	3	(chain A and resid 124:260)	A	124 - 260
4	X-RAY DIFFRACTION	4	(chain A and resid 261:272)	A	261 - 272
5	X-RAY DIFFRACTION	5	(chain A and resid 273:346)	A	273 - 346
6	X-RAY DIFFRACTION	6	(chain A and resid 347:438)	A	347 - 438
7	X-RAY DIFFRACTION	7	(chain A and resid 439:649)	A	439 - 649
8	X-RAY DIFFRACTION	8	(chain A and resid 650:689)	A	650 - 689
9	X-RAY DIFFRACTION	9	(chain B and resid 38:106)	B	38 - 106
10	X-RAY DIFFRACTION	10	(chain B and resid 107:121)	B	107 - 121
11	X-RAY DIFFRACTION	11	(chain B and resid 122:262)	B	122 - 262
12	X-RAY DIFFRACTION	12	(chain B and resid 263:273)	B	263 - 273
13	X-RAY DIFFRACTION	13	(chain B and resid 274:376)	B	274 - 376
14	X-RAY DIFFRACTION	14	(chain B and resid 377:417)	B	377 - 417
15	X-RAY DIFFRACTION	15	(chain B and resid 436:615)	B	436 - 615
16	X-RAY DIFFRACTION	16	(chain B and resid 616:687)	B	616 - 687

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Protein , 1 types, 2 molecules AB

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Non-polymers , 5 types, 638 molecules

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Experimental details

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Experiment

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Sample preparation

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-Yorodumi

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Movie

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Structure viewers

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Viewer log

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This page

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Open data

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Download

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Validation report

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Assembly

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Protein , 1 types, 2 molecules AB

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Non-polymers , 5 types, 638 molecules

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Experimental details

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Experiment

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Sample preparation

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Data collection

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Processing

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About Yorodumi

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Feb 9, 2022. New format data for meta-information of EMDB entries

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Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

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Yorodumi