PDB-4a5a: Crystal structure of the C258S/C268S variant of Toxoplasma gondii...

ID or keywords:

Entry

Database: PDB / ID: 4a5a

Title

Crystal structure of the C258S/C268S variant of Toxoplasma gondii nucleoside triphosphate diphosphohydrolase 3 (NTPDase3) in complex with magnesium and AMPPNP

Components

NUCLEOSIDE-TRIPHOSPHATASE 1

Keywords

HYDROLASE / NTPDASE

Function / homology

Function and homology information

symbiont-containing vacuole / nucleoside diphosphate catabolic process / nucleoside diphosphate phosphatase activity / ribonucleoside triphosphate phosphatase activity / nucleoside-triphosphate phosphatase / membrane
Similarity search - Function

Biological species

TOXOPLASMA GONDII (eukaryote)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.85 Å

Authors

Krug, U. / Zebisch, M. / Straeter, N.

Citation

Journal: J.Biol.Chem. / Year: 2012
Title: Structural Insight Into the Activation Mechanism of Toxoplasma Gondii Nucleoside Triphosphate Diphosphohydrolases by Disulfide Reduction.
Authors: Krug, U. / Zebisch, M. / Krauss, M. / Straeter, N.

History

Deposition	Oct 24, 2011	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Nov 30, 2011	Provider: repository / Type: Initial release
Revision 1.1	Jan 11, 2012	Group: Other
Revision 1.2	Feb 15, 2012	Group: Other
Revision 1.3	Dec 25, 2013	Group: Structure summary
Revision 1.4	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 / 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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5	Nov 6, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4a5a.cif.gz	899.1 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	4a5a_validation.pdf.gz	1.4 MB	Display	wwPDB validaton report
Full document	4a5a_full_validation.pdf.gz	1.4 MB	Display
Data in XML	4a5a_validation.xml.gz	82.9 KB	Display
Data in CIF	4a5a_validation.cif.gz	109.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/a5/4a5a ftp://data.pdbj.org/pub/pdb/validation_reports/a5/4a5a	HTTPS FTP

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Related structure data

Related structure data	4a57SC 4a59C 4a5bC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4kh6-1 4kh4-1 4kh5-1 4f92-d 1ekm-d 4hny-d 5urm-1 4f93-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) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#108 - Dec 2008 Hsp90 similarity (1) #168 - Dec 2013 DNA Helicase similarity (1) #182 - Feb 2015 Insulin receptor similarity (1) #214 - Oct 2017 Chimeric Antigen Receptors similarity (1) #238 - Oct 2019 Ribonucleotide Reductase similarity (1) #43 - Jul 2003 Src Tyrosine Kinase similarity (1) #50 - Feb 2004 Glycolytic Enzymes similarity (1) #60 - Dec 2004 Ubiquitin similarity (1) #73 - Jan 2006 Topoisomerase similarity (1) #80 - Aug 2006 AAA+ Proteases similarity (1) #95 - Nov 2007 Multidrug Resistance Transporters similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#108 - Dec 2008
Hsp90
similarity (1)
#168 - Dec 2013
DNA Helicase
similarity (1)
#182 - Feb 2015
Insulin receptor
similarity (1)
#214 - Oct 2017
Chimeric Antigen Receptors
similarity (1)
#238 - Oct 2019
Ribonucleotide Reductase
similarity (1)
#43 - Jul 2003
Src Tyrosine Kinase
similarity (1)
#50 - Feb 2004
Glycolytic Enzymes
similarity (1)
#60 - Dec 2004
Ubiquitin
similarity (1)
#73 - Jan 2006
Topoisomerase
similarity (1)
#80 - Aug 2006
AAA+ Proteases
similarity (1)
#95 - Nov 2007
Multidrug Resistance Transporters
similarity (1)

Deposited unit

A: NUCLEOSIDE-TRIPHOSPHATASE 1

B: NUCLEOSIDE-TRIPHOSPHATASE 1

C: NUCLEOSIDE-TRIPHOSPHATASE 1

D: NUCLEOSIDE-TRIPHOSPHATASE 1

hetero molecules

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

1

A: NUCLEOSIDE-TRIPHOSPHATASE 1

B: NUCLEOSIDE-TRIPHOSPHATASE 1

hetero molecules

A: NUCLEOSIDE-TRIPHOSPHATASE 1

B: NUCLEOSIDE-TRIPHOSPHATASE 1

hetero molecules

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

2

C: NUCLEOSIDE-TRIPHOSPHATASE 1

D: NUCLEOSIDE-TRIPHOSPHATASE 1

hetero molecules

C: NUCLEOSIDE-TRIPHOSPHATASE 1

D: NUCLEOSIDE-TRIPHOSPHATASE 1

hetero molecules

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

Unit cell

Length a, b, c (Å)	71.953, 150.668, 486.988
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	20
Space group name H-M	C222₁

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
3	1	C
4	1	D

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Refine code	Auth asym-ID	Auth seq-ID
1	1	1	1	A	30 - 701
2	1	1	1	B	30 - 701
3	1	1	1	C	30 - 701
4	1	1	1	D	30 - 701

NCS oper:

ID	Code	Matrix	Vector
1	given	(1), (1), (1)
2	given	(-0.999816, -0.018739, 0.004117), (0.018674, -0.901226, 0.432946), (-0.004403, 0.432944, 0.90141)	115.22475, -1.49417, 0.16821
3	given	(0.900631, 0.019345, 0.434153), (0.116352, -0.973272, -0.198), (0.418719, 0.228839, -0.87881)	77.32625, 13.33689, -131.73936
4	given	(-0.89797, -0.020783, -0.439565), (0.082877, 0.973022, -0.215311), (0.432181, -0.229772, -0.872023)	37.39164, -70.59174, -111.82097

#1: Protein	NUCLEOSIDE-TRIPHOSPHATASE 1 / NTPASE-I / NUCLEOSIDE TRIPHOSPHATE HYDROLASE 1 / NUCLEOSIDE-TRIPHOSPHATASE I / NTPDASE3 Mass: 67625.789 Da / Num. of mol.: 4 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) TOXOPLASMA GONDII (eukaryote) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA PLYSS / References: UniProt: Q27893, apyrase
#2: Chemical	ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER Mass: 506.196 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₀H₁₇N₆O₁₂P₃ / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
Compound details	ENGINEERED RESIDUE IN CHAIN A, CYS 258 TO SER ENGINEERED RESIDUE IN CHAIN A, CYS 268 TO SER ...ENGINEERED RESIDUE IN CHAIN A, CYS 258 TO SER ENGINEERED RESIDUE IN CHAIN A, CYS 268 TO SER ENGINEERED RESIDUE IN CHAIN B, CYS 258 TO SER ENGINEERED RESIDUE IN CHAIN B, CYS 268 TO SER ENGINEERED RESIDUE IN CHAIN C, CYS 258 TO SER ENGINEERED RESIDUE IN CHAIN C, CYS 268 TO SER ENGINEERED RESIDUE IN CHAIN D, CYS 258 TO SER ENGINEERED RESIDUE IN CHAIN D, CYS 268 TO SER
Has protein modification	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.48 Å³/Da / Density % sol: 50.5 % / Description: NONE
Crystal grow	pH: 8.5 Details: 100 MM KCL, 10 MM MGCL2, 50 MM TRIS PH 8.5, 30% PEG 400, 2 MM AMPPNP AND 10 MM MAGNESIUM ACETATE.

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841
Detector	Type: MARRESEARCH / Detector: CCD
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.91841 Å / Relative weight: 1
Reflection	Resolution: 2.85→39 Å / Num. obs: 61587 / % possible obs: 98.3 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / R_merge(I) obs: 0.17 / Net I/σ(I): 5
Reflection shell	Resolution: 2.85→3 Å / Redundancy: 3.4 % / R_merge(I) obs: 0.45 / Mean I/σ(I) obs: 5 / % possible all: 94.3

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Processing

Software

Name	Version	Classification
REFMAC	5.6.0116	refinement
XDS		data reduction
SCALA		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4A57

4a57

Resolution: 2.85→40 Å / Cor.coef. F_o:F_c: 0.878 / Cor.coef. F_o:F_c free: 0.82 / SU B: 42.838 / SU ML: 0.37 / Cross valid method: THROUGHOUT / ESU R Free: 0.467 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.28411	3124	5.1 %	RANDOM
R_work	0.23369	-	-	-
obs	0.23627	58171	97.75 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 36.962 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	2.33 Å²	0 Å²	0 Å²
2-	-	-0.57 Å²	0 Å²
3-	-	-	-1.76 Å²

Refinement step

Cycle: LAST / Resolution: 2.85→40 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	18292	0	128	0	18420

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.019	18803
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.45	1.972	25494
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.587	5	2355
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	38.777	24.184	846
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.759	15	3243
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	22.279	15	138
X-RAY DIFFRACTION	r_chiral_restr	0.098	0.2	2843
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.021	14170
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
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it
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

Refine LS restraints NCS

Ens-ID: 1 / Number: 4539 / Refine-ID: X-RAY DIFFRACTION

Dom-ID	Auth asym-ID	Type	Rms dev position (Å)	Weight position
1	A	tight positional	0.06	0.05
2	B	tight positional	0.07	0.05
3	C	tight positional	0.08	0.05
4	D	tight positional	0.07	0.05
1	A	tight thermal	7.88	0.5
2	B	tight thermal	8.63	0.5
3	C	tight thermal	10.24	0.5
4	D	tight thermal	5.38	0.5

LS refinement shell

Resolution: 2.848→2.922 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.403	162	-
R_work	0.334	3780	-
obs	-	-	92.17 %

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	14.1526	-8.6895	-13.1038	7.6943	11.4478	17.0667	-0.8329	-0.9128	-0.3943	0.1052	0.0211	0.6245	0.241	0.0929	0.8117	0.5827	0.1356	-0.0265	0.5848	-0.0272	0.3806	38.8363	26.263	18.3872
2	1.1629	0.042	-0.1008	0.8269	0.0871	0.7397	0.0772	-0.0349	0.1061	0.044	-0.0106	-0.0026	-0.1423	-0.0698	-0.0666	0.2501	0.0816	0.0171	0.1114	-0.0183	0.0194	52.9073	16.0866	-23.213
3	6.0529	-16.0747	-2.9179	42.804	8.255	3.8826	-0.2361	-0.1653	-0.6726	0.8534	0.2652	1.7415	0.6725	-0.9604	-0.029	0.423	-0.0911	0.0506	0.5919	0.0952	0.3522	36.8125	-9.2162	-7.2653
4	1.3824	-0.1015	0.1849	0.9751	-0.2557	1.4757	0.0843	0.1726	0.0044	-0.0866	0.0247	0.1282	-0.1745	-0.4439	-0.109	0.222	0.1024	0.003	0.2866	-0.0126	0.0388	37.6646	3.038	-42.8611
5	12.2067	3.9325	18.3478	6.2166	-2.818	43.0164	-0.5521	0.1107	0.2506	-1.1748	-0.1302	-0.0947	1.03	0.5521	0.6822	0.531	0.2099	0.0391	0.2089	-0.0275	0.0332	74.143	-14.4723	24.0942
6	1.0982	0.2642	0.6513	0.5364	0.6966	1.6239	0.0522	-0.0716	-0.1399	0.1553	-0.0022	-0.0473	0.106	-0.1332	-0.05	0.276	0.0323	-0.0139	0.0586	-0.0075	0.024	62.7256	-24.8086	-13.7103
7	11.0903	-16.0483	6.6211	32.3099	-10.8811	9.1662	-0.2049	-0.184	0.3984	-0.9786	0.243	-0.9239	-0.9992	0.5044	-0.0382	0.42	-0.1303	0.0787	0.5157	-0.0375	0.1149	78.3007	5.1878	-10.3897
8	0.708	-0.2845	-0.1106	1.355	0.5254	1.2068	0.0235	0.1279	0.0531	-0.0299	0.0868	-0.1493	0.0398	0.1523	-0.1102	0.1538	0.0256	0.0006	0.0944	-0.0238	0.0241	77.8275	-21.2533	-37.1542
9	1.8537	0.2362	6.0464	4.9425	10.3566	38.493	-0.1233	-0.0146	0.0583	0.0155	-0.7302	0.2863	-0.318	-1.6414	0.8534	0.0753	-0.1612	0.0857	0.5821	-0.0857	0.4618	28.7708	21.4304	-153.7731
10	0.8267	-0.1804	-0.1566	0.5297	0.1208	2.3781	-0.0227	-0.0202	-0.077	-0.0779	-0.0073	-0.0284	0.2089	0.096	0.0299	0.0539	-0.0046	0.0582	0.0489	0.0003	0.1675	23.7392	21.6766	-106.4928
11	6.3949	10.8018	5.2337	35.595	18.2489	9.6939	0.0029	0.4152	0.1415	-0.9981	-0.5211	1.9999	-0.8941	-0.4378	0.5182	0.4736	0.2202	0.4112	0.3287	0.1157	0.8878	13.0346	49.6579	-122.5264
12	0.6161	0.5639	-0.2295	1.4986	-0.456	1.1551	0.0335	-0.0251	0.1833	0.1349	0.0621	0.2761	0.0067	-0.0816	-0.0957	0.0448	0.0035	0.0817	0.0642	-0.0134	0.1906	0.5937	29.6923	-93.2393
13	16.9007	0.0049	-5.8066	1.0782	-0.8994	2.7557	0.2984	-0.9702	-0.0577	-0.0898	-0.4415	-0.0399	-0.005	0.8024	0.1431	0.3095	-0.1707	0.1119	0.6811	-0.027	0.2727	64.128	63.449	-134.894
14	1.1652	-0.1575	-0.5542	0.3982	-0.054	1.2909	0.0646	0.086	0.0882	-0.0052	-0.0455	-0.0443	-0.1169	-0.0704	-0.0191	0.0438	-0.0047	0.067	0.016	-0.0157	0.1322	31.5338	63.661	-102.7255
15	10.4011	6.9733	-3.99	4.7095	-2.6973	1.5454	-0.1045	-0.2633	-0.9283	0.0813	-0.1466	-0.5294	-0.0576	0.0636	0.2511	0.5539	0.17	0.272	0.331	0.134	0.5777	50.7434	35.714	-104.1347
16	0.5657	-0.3534	-0.3338	0.9744	0.2606	2.2549	0.0633	-0.1605	0.0315	0.1774	-0.0036	-0.1004	-0.0713	0.1716	-0.0597	0.0978	-0.0584	0.0296	0.0662	-0.0142	0.0963	35.6661	55.7963	-76.1163
17	2.3083	0.843	-2.3843	7.5658	3.0419	4.5926	0.0195	0.12	-0.0387	-0.5264	-0.2699	0.2971	-0.1903	-0.283	0.2504	0.4266	0.0903	0.0584	0.2096	0.0112	0.0319	60.7036	-0.2465	-50.54
18	2.1379	1.3715	0.0166	7.3	2.7364	5.3464	-0.0483	0.1914	0.0415	-0.0824	-0.0734	0.2578	0.0271	-0.005	0.1217	0.1255	0.0767	0.0002	0.1075	-0.0118	0.0127	54.7646	-22.0692	-45.385
19	5.8438	0.3695	-2.3047	8.7927	-2.44	4.1697	-0.0478	-0.0902	-0.0271	0.8473	-0.0874	0.0141	-0.3567	-0.171	0.1351	0.1405	-0.0537	0.0593	0.1185	-0.083	0.0947	17.4272	31.499	-75.8227
20	0.9077	-1.6743	2.2386	7.9573	-1.0529	7.4644	-0.023	-0.1295	0.0111	0.5458	-0.037	0	0.1837	-0.5079	0.06	0.1052	-0.0528	0.1036	0.2149	-0.0256	0.1837	11.3598	53.8791	-78.7767

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	28 - 58
2	X-RAY DIFFRACTION	2	A	59 - 256
3	X-RAY DIFFRACTION	2	A	586 - 629
4	X-RAY DIFFRACTION	3	A	257 - 268
5	X-RAY DIFFRACTION	4	A	269 - 394
6	X-RAY DIFFRACTION	4	A	425 - 585
7	X-RAY DIFFRACTION	5	B	28 - 58
8	X-RAY DIFFRACTION	6	B	59 - 256
9	X-RAY DIFFRACTION	6	B	586 - 629
10	X-RAY DIFFRACTION	7	B	257 - 268
11	X-RAY DIFFRACTION	8	B	269 - 394
12	X-RAY DIFFRACTION	8	B	425 - 585
13	X-RAY DIFFRACTION	9	C	28 - 58
14	X-RAY DIFFRACTION	10	C	59 - 256
15	X-RAY DIFFRACTION	10	C	586 - 629
16	X-RAY DIFFRACTION	11	C	257 - 268
17	X-RAY DIFFRACTION	12	C	269 - 394
18	X-RAY DIFFRACTION	12	C	425 - 585
19	X-RAY DIFFRACTION	13	D	28 - 58
20	X-RAY DIFFRACTION	14	D	59 - 256
21	X-RAY DIFFRACTION	14	D	586 - 629
22	X-RAY DIFFRACTION	15	D	257 - 268
23	X-RAY DIFFRACTION	16	D	269 - 394
24	X-RAY DIFFRACTION	16	D	425 - 585
25	X-RAY DIFFRACTION	17	A	395 - 424
26	X-RAY DIFFRACTION	18	B	395 - 424
27	X-RAY DIFFRACTION	19	C	395 - 424
28	X-RAY DIFFRACTION	20	D	395 - 424

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