PDB-3jxb: Crystal structure of the P22 c2 repressor protein in complex with...

ID or keywords:

Entry

Database: PDB / ID: 3jxb

Title

Crystal structure of the P22 c2 repressor protein in complex with synthetic operator 9C

Components

5'-D(*CP*AP*TP*TP*TP*AP*AP*GP*AP*CP*GP*TP*CP*TP*TP*AP*AP*AP*TP*A)-3'
5'-D(*TP*AP*TP*TP*TP*AP*AP*GP*AP*CP*GP*TP*CP*TP*TP*AP*AP*AP*TP*G)-3'
Repressor protein C2

Keywords

TRANSCRIPTION REGULATOR /

protein-DNA complex / DNA-binding /

Repressor /

Transcription /

Transcription regulation

Function / homology

Function and homology information

Biological species

Enterobacteria phage P22 (virus)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.67 Å

Authors

Watkins, D. / Koudelka, G.B. / Williams, L.D.

Citation

Journal: J.Mol.Biol. / Year: 2010
Title: Sequence Recognition of DNA by Protein-Induced Conformational Transitions
Authors: Watkins, D. / Mohan, S. / Koudelka, G.B. / Williams, L.D.

History

Deposition	Sep 18, 2009	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 19, 2010	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Sep 6, 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 / struct_ref_seq Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	3jxb.cif.gz	72 KB	Display	PDBx/mmCIF format
PDB format	pdb3jxb.ent.gz	51.3 KB	Display	PDB format
PDBx/mmJSON format	3jxb.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

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

-
Related structure data

Related structure data	3jxcC 3jxdC 2r1jS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	2r1j-d 3jxc-d 3od0-d 5azd-3 5azd-4 3jxd-d 7crx-d 6jy8-d 2z3r-7 3ogj-1 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#67 - Jul 2005 TATA-Binding Protein similarity (1) #168 - Dec 2013 DNA Helicase similarity (1) #255 - Mar 2021 Cisplatin and DNA similarity (1) #91 - Jul 2007 Thymine Dimers similarity (1) #181 - Jan 2015 Cascade and CRISPR similarity (1) #172 - Apr 2014 RecA and Rad51 similarity (1) #253 - Jan 2021 Expressome similarity (1) #122 - Feb 2010 Enhanceosome similarity (1) #112 - Apr 2009 Oct and Sox Transcription Factors similarity (2) #84 - Dec 2006 Transposase similarity (1) #135 - Mar 2011 Integrase similarity (1) #150 - Jun 2012 Sliding Clamps similarity (1) #180 - Dec 2014 TAL Effectors similarity (1) #227 - Nov 2018 Telomerase similarity (1) #48 - Dec 2003 Catabolite Activator Protein similarity (1) #139 - Jul 2011 DNA Methyltransferase similarity (1) #87 - Mar 2007 Zinc Fingers similarity (1) #3 - Mar 2000 DNA Polymerase similarity (1) #40 - Apr 2003 RNA Polymerase similarity (1) #73 - Jan 2006 Topoisomerase similarity (1) #155 - Nov 2012 Vitamin D Receptor similarity (1) #39 - Mar 2003 lac Repressor similarity (2) #92 - Aug 2007 Anabolic Steroids similarity (1) #55 - Jul 2004 DNA Ligase similarity (1) #7 - Jul 2000 Nucleosome similarity (1) #8 - Aug 2000 Restriction Enzymes similarity (1) #45 - Sep 2003 Estrogen Receptor similarity (1) #240 - Dec 2019 Hypoxia-Inducible Factors similarity (1) #33 - Sep 2002 HIV Reverse Transcriptase similarity (1) #31 - Jul 2002 p53 Tumor Suppressor similarity (1) #258 - Jun 2021 Glucocorticoid Receptor and Dexamethasone similarity (1) #257 - May 2021 Fetal Hemoglobin similarity (1) #23 - Nov 2001 DNA similarity (1) #190 - Oct 2015 Two-component Systems similarity (1) #160 - Apr 2013 Actinomycin similarity (1) #131 - Nov 2010 Inteins similarity (1) #125 - May 2010 Parvoviruses similarity (1) #119 - Nov 2009 Designed DNA Crystal similarity (1) #241 - Jan 2020 Twenty Years of Molecules similarity (6) #144 - Dec 2011 Complex I similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#67 - Jul 2005
TATA-Binding Protein
similarity (1)
#168 - Dec 2013
DNA Helicase
similarity (1)
#255 - Mar 2021
Cisplatin and DNA
similarity (1)
#91 - Jul 2007
Thymine Dimers
similarity (1)
#181 - Jan 2015
Cascade and CRISPR
similarity (1)
#172 - Apr 2014
RecA and Rad51
similarity (1)
#253 - Jan 2021
Expressome
similarity (1)
#122 - Feb 2010
Enhanceosome
similarity (1)
#112 - Apr 2009
Oct and Sox Transcription Factors
similarity (2)
#84 - Dec 2006
Transposase
similarity (1)
#135 - Mar 2011
Integrase
similarity (1)
#150 - Jun 2012
Sliding Clamps
similarity (1)
#180 - Dec 2014
TAL Effectors
similarity (1)
#227 - Nov 2018
Telomerase
similarity (1)
#48 - Dec 2003
Catabolite Activator Protein
similarity (1)
#139 - Jul 2011
DNA Methyltransferase
similarity (1)
#87 - Mar 2007
Zinc Fingers
similarity (1)
#3 - Mar 2000
DNA Polymerase
similarity (1)
#40 - Apr 2003
RNA Polymerase
similarity (1)
#73 - Jan 2006
Topoisomerase
similarity (1)
#155 - Nov 2012
Vitamin D Receptor
similarity (1)
#39 - Mar 2003
lac Repressor
similarity (2)
#92 - Aug 2007
Anabolic Steroids
similarity (1)
#55 - Jul 2004
DNA Ligase
similarity (1)
#7 - Jul 2000
Nucleosome
similarity (1)
#8 - Aug 2000
Restriction Enzymes
similarity (1)
#45 - Sep 2003
Estrogen Receptor
similarity (1)
#240 - Dec 2019
Hypoxia-Inducible Factors
similarity (1)
#33 - Sep 2002
HIV Reverse Transcriptase
similarity (1)
#31 - Jul 2002
p53 Tumor Suppressor
similarity (1)
#258 - Jun 2021
Glucocorticoid Receptor and Dexamethasone
similarity (1)
#257 - May 2021
Fetal Hemoglobin
similarity (1)
#23 - Nov 2001
DNA
similarity (1)
#190 - Oct 2015
Two-component Systems
similarity (1)
#160 - Apr 2013
Actinomycin
similarity (1)
#131 - Nov 2010
Inteins
similarity (1)
#125 - May 2010
Parvoviruses
similarity (1)
#119 - Nov 2009
Designed DNA Crystal
similarity (1)
#241 - Jan 2020
Twenty Years of Molecules
similarity (6)
#144 - Dec 2011
Complex I
similarity (1)

Deposited unit

A: 5'-D(*CP*AP*TP*TP*TP*AP*AP*GP*AP*CP*GP*TP*CP*TP*TP*AP*AP*AP*TP*A)-3'

B: 5'-D(*TP*AP*TP*TP*TP*AP*AP*GP*AP*CP*GP*TP*CP*TP*TP*AP*AP*AP*TP*G)-3'

C: Repressor protein C2

D: Repressor protein C2

27.3 kDa, 4 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)	40.602, 54.319, 114.112
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Details

Biological unit is the same as asymmetric unit.

#1: DNA chain	5'-D(CPAPTPTPTPAPAPGPAPCPGPTPCPTPTPAPAPAPTPA)-3' Mass: 6116.004 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic DNA Operator 9C
#2: DNA chain	5'-D(TPAPTPTPTPAPAPGPAPCPGPTPCPTPTPAPAPAPTPG)-3' Mass: 6147.014 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic DNA Operator 9C
#3: Protein	Repressor protein C2 / Mass: 7494.681 Da / Num. of mol.: 2 / Fragment: N-terminal domain: UNP residues 2-68 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacteria phage P22 (virus) / Gene: C2 / Plasmid: pUC18 / Production host: Escherichia coli (E. coli) / Strain (production host): XA90 / References: UniProt: P69202
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 300 / 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: 2.31 Å³/Da / Density % sol: 46.72 %

Crystal grow

Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: PEG 400, NaCl, Tris-HCl, MgCl2, LiCl, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Components of the solutions

ID	Name	Crystal-ID	Sol-ID
1	PEG 400	1	1
2	NaClSodium chloride	1	1
3	Tris-HClTris	1	1
4	MgCl2	1	1
5	LiCl	1	1
6	PEG 400	1	2
7	NaClSodium chloride	1	2
8	Tris-HClTris	1	2
9	MgCl2	1	2
10	LiCl	1	2

-
Data collection

Diffraction	Mean temperature: 110 K
Diffraction source	Source: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 1 Å
Detector	Type: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 13, 2007
Radiation	Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.67→19.9 Å / Num. all: 29254 / Num. obs: 29254 / % possible obs: 97.26 % / Observed criterion σ(I): 0 / Redundancy: 5.8 % / R_sym value: 0.069 / Net I/σ(I): 47.1
Reflection shell	Resolution: 1.67→1.71 Å / Redundancy: 4.7 % / R_merge(I) obs: 0.659 / Mean I/σ(I) obs: 2.12 / Num. unique all: 2003 / % possible all: 91.7

-
Processing

Software

Name	Version	Classification
REFMAC	5.2.0019	refinement
PDB_EXTRACT	3.005	data extraction
HKL-2000		data collection
DENZO		data reduction
SCALEPACK		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 2R1J

2r1j

Resolution: 1.67→19.9 Å / Cor.coef. F_o:F_c: 0.953 / Cor.coef. F_o:F_c free: 0.942 / Occupancy max: 1 / Occupancy min: 0.01 / SU B: 4.391 / SU ML: 0.076 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.114 / ESU R Free: 0.109 / Stereochemistry target values: MAXIMUM LIKELIHOOD

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.226	1501	5.1 %	RANDOM
R_work	0.196	-	-	-
obs	0.198	27753	97.26 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso max: 67.64 Å² / B_iso mean: 19.389 Å² / B_iso min: 7.51 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.02 Å²	0 Å²	0 Å²
2-	-	-0.04 Å²	0 Å²
3-	-	-	0.06 Å²

Refinement step

Cycle: LAST / Resolution: 1.67→19.9 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1031	814	0	300	2145

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.021	1993
X-RAY DIFFRACTION	r_angle_refined_deg	1.621	2.494	2862
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.318	5	144
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.738	23.478	46
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.655	15	226
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	7.156	15	13
X-RAY DIFFRACTION	r_chiral_restr	0.086	0.2	322
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	1217
X-RAY DIFFRACTION	r_nbd_refined	0.207	0.2	842
X-RAY DIFFRACTION	r_nbtor_refined	0.299	0.2	1315
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.134	0.2	230
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.234	0.2	41
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.109	0.2	28
X-RAY DIFFRACTION	r_mcbond_it	0.623	1.5	706
X-RAY DIFFRACTION	r_mcangle_it	0.882	2	1089
X-RAY DIFFRACTION	r_scbond_it	1.357	3	1731
X-RAY DIFFRACTION	r_scangle_it	1.979	4.5	1767

LS refinement shell

Resolution: 1.67→1.713 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.352	106	-
R_work	0.276	1897	-
all	-	2003	-
obs	-	-	91.67 %

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	3.1043	-3.3718	-1.8082	4.0237	0.276	8.9367	-0.0243	0.3897	-0.2267	-0.2439	-0.1106	0.3422	0.5432	-0.7128	0.1349	0.1225	0.0088	-0.0226	0.2323	0.0169	0.0761	2.217	-5.7382	-30.8765
2	6.4062	-3.8345	-0.9595	3.3919	-3.8956	18.3613	0.5242	-0.337	-0.1906	0.459	0.0569	0.3456	-0.7685	-0.9665	-0.581	0.0448	0.1342	0.0218	0.2204	0.0102	0.0755	-4.1011	0.8754	-15.0355
3	3.1413	-0.6858	0.0976	4.2652	2.268	6.3965	0.2608	0.091	0.3788	-0.283	-0.199	-0.1716	-0.7541	-0.5414	-0.0618	0.1373	0.082	0.0489	0.0425	0.0559	0.1165	8.6967	4.1224	-2.0141
4	3.2056	-1.4496	1.1956	1.7093	-1.6426	7.857	0.0087	-0.5506	0.5065	0.2117	0.1401	-0.0759	-1.2372	-0.3479	-0.1488	0.3554	0.0882	-0.0287	0.2138	-0.0707	0.1957	8.5749	9.3794	15.0455
5	1.8504	-0.2215	-4.287	0.0265	0.5131	9.9321	0.0205	-0.6885	0.2914	0.1323	0.1651	-0.3183	-0.8631	0.6466	-0.1857	0.1768	-0.0344	-0.096	0.1713	-0.0624	0.2075	15.953	3.995	14.2634
6	2.1623	-2.5335	1.0011	6.0891	-1.5129	13.4966	0.0739	-0.2412	0.2645	-0.3619	0.0464	0.2132	-1.1988	-1.1157	-0.1204	0.1717	0.1256	-0.0371	0.1577	-0.0064	0.1621	3.5429	7.9486	1.5955
7	4.9672	-0.6535	2.0521	0.7011	0.1761	4.5572	-0.0139	-0.1773	0.0149	0.1199	-0.0003	0.1167	-0.2171	-0.6935	0.0142	0.0286	0.0482	0.0293	0.1801	0.0508	0.0632	0.8557	-3.5462	-16.1261
8	23.5202	6.8712	-23.4313	10.3483	-11.6922	26.1594	0.0367	2.0746	0.3017	-0.6362	0.215	0.0792	-0.1886	-1.7625	-0.2517	0.1506	0.0173	-0.0638	0.5464	-0.0234	0.112	-4.1928	-2.153	-32.2896
9	3.4851	-0.1703	1.1386	29.1425	4.2294	6.1415	0.4213	-0.4369	-0.3059	-0.1038	-0.4115	0.6409	0.6891	-0.283	-0.0098	0.1019	-0.053	-0.0235	0.0403	0.0749	0.1032	13.0595	-14.7016	4.5652
10	5.8165	1.2052	-0.1896	7.3983	0.7798	8.4488	-0.019	-0.2924	0.0537	0.0744	0.0734	-0.3222	0.3365	0.4441	-0.0544	0.0236	0.0423	-0.0005	-0.006	0.0427	0.0978	20.6104	-9.838	6.3873
11	6.9563	0.3555	0.1424	17.321	-10.2523	19.2464	0.2336	0.0703	0.4372	0.5285	-0.7414	-0.7955	-0.1278	0.9247	0.5079	0.0534	0.0203	-0.0399	0.1984	0.0603	0.1823	26.5534	-6.8599	11.035
12	3.6914	3.0102	-3.5742	11.9754	1.362	12.0336	0.0828	-0.4366	0.1525	0.2639	0.1565	-1.0678	-0.3849	0.2613	-0.2393	-0.0108	-0.0382	-0.0137	0.0251	-0.0445	0.2125	21.9537	1.055	7.5766
13	41.8095	-6.3411	7.1692	15.1315	5.5901	12.828	-0.0548	-0.3596	0.5411	-0.0066	0.3325	-0.6527	-0.7898	0.6113	-0.2776	0.1131	-0.1236	0.0896	-0.0162	0.0153	0.1918	23.4155	2.7873	0.2209
14	3.8668	0.1296	-0.9791	4.5086	1.0808	6.0614	0.0771	-0.2622	0.3473	0.0808	0.0094	-0.269	-0.4702	-0.1238	-0.0866	0.0295	0.0115	0.0117	-0.0278	0.0089	0.0894	13.6096	-0.8021	4.4767
15	7.4188	1.035	-5.1393	1.1895	-2.6395	15.6552	0.0494	0.2081	0.1853	-0.1119	0.0415	-0.1279	-0.1091	-0.6179	-0.0909	0.0116	0.0257	0.0141	-0.0343	0.0429	0.0829	12.4418	-4.0908	-3.2114
16	2.4607	-0.2582	1.0044	4.0414	-2.0818	8.6876	0.2845	0.1553	0.0359	-0.0923	-0.0828	-0.1647	-0.0991	0.5704	-0.2017	-0.0161	0.0076	0.0187	0.0059	0.0335	0.0862	21.2354	-5.3647	-5.3476
17	5.8455	4.7323	-0.1798	7.9282	-0.6391	6.1727	0.0315	0.0328	-0.0769	0.1406	0.1163	-0.258	0.41	0.9661	-0.1478	0.0247	0.0832	-0.0035	0.1314	0.0246	0.135	24.3533	-11.134	-2.2157
18	21.5838	6.6663	13.1322	33.1208	5.348	23.3222	0.1183	0.5612	-0.7677	-0.7003	0.2487	0.2941	1.4213	0.3747	-0.3669	0.134	0.0159	0.0116	-0.0043	0.0304	0.0638	16.728	-16.5586	-3.3977
19	17.3251	1.7274	0.2941	7.0608	5.9242	6.3697	-0.0531	0.5917	0.6145	-0.5207	0.1595	-0.0616	-0.463	0.5552	-0.1065	0.0674	0.0034	0.0563	0.1772	0.0956	0.0947	19.9961	-0.944	-23.3104
20	4.5329	1.0445	3.8423	3.0881	-2.6581	7.6666	0.2148	0.4149	-0.1637	-0.3873	-0.1341	-0.3427	0.1133	0.3907	-0.0806	0.0734	0.0705	0.0698	0.1519	0.019	0.0855	16.8599	-8.4503	-26.7809
21	10.2357	-5.9295	0.5272	14.9131	2.4012	0.7572	-0.0781	0.6266	-0.4725	-0.0779	-0.0315	-0.3065	0.9592	0.8517	0.1096	0.2818	0.0896	0.1068	0.2662	-0.0424	0.1704	17.1633	-13.9354	-30.6602
22	3.1966	-0.2995	0.0704	4.8525	-1.6775	4.18	0.0757	0.2523	-0.1382	-0.2781	-0.0966	0.0946	0.344	-0.1685	0.0209	0.0382	0.0258	0.0089	0.0735	0.0251	0.0234	8.1739	-9.2128	-22.4968
23	3.6896	-6.3645	6.1654	12.3791	-9.0836	14.7973	0.0286	0.2059	0.0015	0.106	0.1022	0.0025	-0.0957	-0.3551	-0.1308	-0.0127	0.029	0.0428	0.0179	0.0487	0.0516	11.1139	-4.7932	-13.465
24	2.4205	1.0622	-3.3563	2.8202	1.1585	7.5949	0.1216	0.066	-0.1194	-0.2766	0.0538	-0.2625	0.2789	-0.0683	-0.1753	0.0362	0.0472	0.0071	0.0234	0.0353	0.0602	15.4594	-11.083	-13.6499
25	7.5363	5.715	2.1633	8.105	1.4743	5.4202	0.2134	0.3271	-0.4279	0.1994	0.0685	-0.4271	0.527	0.4826	-0.2819	0.0878	0.1013	0.0133	0.1416	-0.0115	0.1297	21.0975	-12.7958	-17.5942
26	12.567	-1.288	-4.9099	15.3988	-5.2404	18.1188	0.1675	-0.4164	0.1885	0.6184	-0.0279	-0.915	-0.0421	1.0054	-0.1396	-0.0385	0.0118	0.0151	0.2462	0.0297	0.102	24.827	-4.6235	-17.8656

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 5
2	X-RAY DIFFRACTION	2	A	6 - 10
3	X-RAY DIFFRACTION	3	A	11 - 15
4	X-RAY DIFFRACTION	4	A	16 - 20
5	X-RAY DIFFRACTION	5	B	21 - 24
6	X-RAY DIFFRACTION	6	B	25 - 30
7	X-RAY DIFFRACTION	7	B	31 - 36
8	X-RAY DIFFRACTION	8	B	37 - 40
9	X-RAY DIFFRACTION	9	C	3 - 8
10	X-RAY DIFFRACTION	10	C	9 - 14
11	X-RAY DIFFRACTION	11	C	15 - 19
12	X-RAY DIFFRACTION	12	C	20 - 25
13	X-RAY DIFFRACTION	13	C	26 - 30
14	X-RAY DIFFRACTION	14	C	31 - 40
15	X-RAY DIFFRACTION	15	C	41 - 48
16	X-RAY DIFFRACTION	16	C	49 - 54
17	X-RAY DIFFRACTION	17	C	55 - 63
18	X-RAY DIFFRACTION	18	C	64 - 68
19	X-RAY DIFFRACTION	19	D	4 - 9
20	X-RAY DIFFRACTION	20	D	10 - 14
21	X-RAY DIFFRACTION	21	D	15 - 19
22	X-RAY DIFFRACTION	22	D	20 - 41
23	X-RAY DIFFRACTION	23	D	42 - 48
24	X-RAY DIFFRACTION	24	D	49 - 53
25	X-RAY DIFFRACTION	25	D	54 - 62
26	X-RAY DIFFRACTION	26	D	63 - 68

-
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