PDB-2po4: X-ray crystal structure of polymerase domain of the bacteriophage...

ID or keywords:

Entry

Database: PDB / ID: 2po4

Title

X-ray crystal structure of polymerase domain of the bacteriophage N4 virion RNA polymerase

Components

Virion RNA polymerase

Keywords

TRANSFERASE / right hand shape

Function / homology

Function and homology information

DNA-directed RNA polymerase complex / virion component / : / : / : / : / : / : / DNA-directed RNA polymerase / GTP binding ...
Similarity search - Function

Biological species

Enterobacteria phage N4 (virus)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 2 Å

Authors

Murakami, K.S. / Davydova, E.K. / Rothman-Denes, L.B.

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 2008
Title: X-ray crystal structure of polymerase domain of the bacteriophage N4 virion RNA polymerase
Authors: Murakami, K.S. / Davydova, E.K. / Rothman-Denes, L.B.

History

Deposition	Apr 25, 2007	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 1, 2008	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Oct 18, 2017	Group: Refinement description / Category: software
Revision 1.3	Feb 21, 2024	Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	2po4.cif.gz	233.3 KB	Display	PDBx/mmCIF format
PDB format	pdb2po4.ent.gz	181.6 KB	Display	PDB format
PDBx/mmJSON format	2po4.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	2po4_validation.pdf.gz	426.1 KB	Display	wwPDB validaton report
Full document	2po4_full_validation.pdf.gz	446.6 KB	Display
Data in XML	2po4_validation.xml.gz	43.3 KB	Display
Data in CIF	2po4_validation.cif.gz	62.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/po/2po4 ftp://data.pdbj.org/pub/pdb/validation_reports/po/2po4	HTTPS FTP

-
Related structure data

Similar structure data	5hmq-2 3c46-2 4ff1-1 5hmq-1 6qnu-d 3c3l-1 3c3l-2 4ff3-2 3c2p-1 4r1i-d 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

Deposited unit

A: Virion RNA polymerase

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

1

Idetical with deposited unit
defined by author

Unit cell

Length a, b, c (Å)	83.047, 103.258, 159.430
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Virion RNA polymerase Mass: 121559.703 Da / Num. of mol.: 1 / Fragment: RNA polymerase Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacteria phage N4 (virus) / Genus: N4-like viruses / Gene: gp50 / Plasmid: pEKD27 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q859P9, DNA-directed RNA polymerase
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 475 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

Virion RNA polymerase

Mass: 121559.703 Da / Num. of mol.: 1 / Fragment: RNA polymerase
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Enterobacteria phage N4 (virus) / Genus: N4-like viruses / Gene: gp50 / Plasmid: pEKD27 / Species (production host): Escherichia coli / Production host:

Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q859P9, DNA-directed RNA polymerase

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 475 / 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: 2.84 Å³/Da / Density % sol: 56.65 %
Crystal grow	Temperature: 300 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 10mM Tris-HCl (pH 8), 100mM NaCl and 0.1mM EDTA , pH 5, VAPOR DIFFUSION, HANGING DROP, temperature 300K

-
Data collection

Diffraction

ID	Mean temperature (K)	Crystal-ID
1	100	1
2		1
3		1

Diffraction source

Source:

SYNCHROTRON / Site:

NSLS

/ Beamline: X25 / Wavelength: 1.1, 0.9790, 0.9793, 0.9649

Detector

Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 30, 2005

Radiation

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

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	1.1	1
2	0.979	1
3	0.9793	1
4	0.9649	1

Reflection

D res high: 2.3 Å / D res low: 40 Å / Redundancy: 3.9 %

ID	Av σ(I) over netI	Number	R_merge(I) obs	Χ²	Num. obs	% possible obs
1	15.3	243292	0.085	1.13	59907	98.4
2	13.7	241343	0.074	0.96	59975	98.4
3	13.1	245229	0.073	0.96	60687	99.1

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	% possible obs (%)	ID	R_merge(I) obs	Chi squared	Redundancy
4.95	40	99.8	1	0.071	1.139	3.9
3.93	4.95	99.9	1	0.062	1.113	4
3.44	3.93	99.7	1	0.056	0.995	4
3.12	3.44	99.5	1	0.077	1.139	4
2.9	3.12	99.4	1	0.11	1.126	4
2.73	2.9	99.5	1	0.152	1.161	4
2.59	2.73	99.2	1	0.195	1.17	3.9
2.48	2.59	99.1	1	0.261	1.163	3.9
2.38	2.48	99.1	1	0.346	1.133	4
2.3	2.38	89	1	0.445	1.145	3.8
4.95	40	99.8	2	0.05	0.974	3.9
3.93	4.95	99.9	2	0.045	0.808	4
3.44	3.93	99.8	2	0.05	0.916	4
3.12	3.44	99.7	2	0.07	0.974	4
2.9	3.12	99.4	2	0.105	0.931	4
2.73	2.9	99.4	2	0.16	0.945	4
2.59	2.73	99.2	2	0.215	0.961	3.9
2.48	2.59	99.1	2	0.312	1.028	3.9
2.38	2.48	99.1	2	0.438	1.072	4
2.3	2.38	88.9	2	0.565	1.063	3.8
4.95	40	99.8	3	0.047	1.042	3.9
3.93	4.95	99.9	3	0.042	0.923	4
3.44	3.93	99.8	3	0.047	1.047	4
3.12	3.44	99.7	3	0.069	0.847	4
2.9	3.12	99.4	3	0.109	0.874	4
2.73	2.9	99.4	3	0.171	0.913	4
2.59	2.73	99.2	3	0.243	0.954	3.9
2.48	2.59	99.1	3	0.357	1.009	3.9
2.38	2.48	99.1	3	0.489	1.032	4
2.3	2.38	95.6	3	0.652	1.027	3.8

Reflection

Resolution: 2→50 Å / Num. obs: 91553 / % possible obs: 98.3 % / Redundancy: 3.9 % / R_merge(I) obs: 0.071 / Χ²: 0.92 / Net I/σ(I): 10.1

Reflection shell

Resolution: 2→2.07 Å / Redundancy: 3.8 % / R_merge(I) obs: 0.596 / Num. unique all: 9120 / Χ²: 0.855 / % possible all: 98.9

-
Phasing

Phasing

Method:

MAD

Phasing MAD

D res high: 2 Å / D res low: 30 Å / FOM : 0.447 / FOM acentric: 0.456 / FOM centric: 0.354 / Reflection: 59570 / Reflection acentric: 54360 / Reflection centric: 5210

Phasing MAD set

Lowest resolution: 30 Å

ID	R cullis acentric	R cullis centric	Highest resolution (Å)	Loc acentric	Loc centric	Power acentric	Power centric	Reflection acentric	Reflection centric
1	1.67	1	2.3	0.5	0.4	0	0	54360	5210
2	1	1	2.3	15	20.6	0	0	53820	5136
3	1	1	2.4	21.3	31.2	0	0	48756	4943
4	0.91	0.84	2.3	29.9	41.5	0.75	0.58	53977	4989

Phasing MAD set shell

ID	Resolution (Å)	R cullis acentric	R cullis centric	Loc acentric	Loc centric	Power acentric	Power centric	Reflection acentric	Reflection centric
1	10.92-30	1.14	1	0.8	0.6	0	0	419	206
1	6.67-10.92	1.18	1	0.7	0.5	0	0	1635	408
1	4.81-6.67	1.45	1	0.7	0.4	0	0	3721	617
1	3.76-4.81	1.09	1	0.6	0.5	0	0	6629	803
1	3.08-3.76	1.41	1	0.6	0.4	0	0	10393	999
1	2.61-3.08	2.13	1	0.5	0.2	0	0	14949	1187
1	2.27-2.61	2.5	1	0.4	0.2	0	0	16614	990
1	2-2.27	0	0	0	0	0	0	0	0
2	10.92-30	1	1	17.6	19.7	0	0	418	205
2	6.67-10.92	1	1	16.2	18.6	0	0	1635	408
2	4.81-6.67	1.01	1	15.9	20.5	0	0	3721	616
2	3.76-4.81	1	1	16	20.7	0	0	6629	802
2	3.08-3.76	1	1	14.1	20.1	0	0	10392	999
2	2.61-3.08	1	1	13.8	19.7	0	0	14948	1187
2	2.27-2.61	1	1	16	23.4	0	0	16077	919
2	2-2.27	0	0	0	0	0	0	0	0
3	10.92-30	1	1	36.6	51.1	0	0	418	205
3	6.67-10.92	1	1	29.6	38.4	0	0	1635	407
3	4.81-6.67	1	1	26	33.7	0	0	3721	615
3	3.76-4.81	1	1	26.3	33.5	0	0	6629	802
3	3.08-3.76	1	1	21.8	30.8	0	0	10393	999
3	2.61-3.08	1	1	18.1	25.8	0	0	14947	1187
3	2.27-2.61	1	1	18.6	26.1	0	0	11013	728
3	2-2.27	0	0	0	0	0	0	0	0
4	10.92-30	0.79	0.7	39.1	44.8	1.28	1.09	367	172
4	6.67-10.92	0.8	0.73	38.3	44.3	1.15	0.84	1599	386
4	4.81-6.67	0.84	0.78	36.7	45.5	1.01	0.74	3717	593
4	3.76-4.81	0.91	0.85	43.6	58.2	0.73	0.5	6611	773
4	3.08-3.76	0.92	0.87	35.2	47.2	0.72	0.49	10350	965
4	2.61-3.08	0.91	0.85	24.3	32	0.77	0.54	14860	1147
4	2.27-2.61	0.95	0.93	23.7	29.2	0.59	0.44	16473	953
4	2-2.27	0	0	0	0	0	0	0	0

Phasing MAD set site

ID	Atom type symbol	B iso	Fract x	Fract y	Fract z	Occupancy
1	Se	25	0.497	0.299	0.599	0
2	Se	25	0.503	0.306	0.621	0
3	Se	25	0.149	0.372	0.614	0
4	Se	25	0.235	0.175	0.772	0
5	Se	25	0.056	0.11	0.581	0
6	Se	25	0.091	0.25	0.689	0
7	Se	25	0.234	0.463	0.713	0
8	Se	25	0.066	0.056	0.831	0
9	Se	25	0.197	0.289	0.512	0
10	Se	25	0.124	0.266	0.518	0
11	Se	25	0.305	0.459	0.604	0
12	Se	25	0.286	0.48	0.671	0
13	Se	25	0.3	0.859	0.379	0
14	Se	25	0.862	0.895	0.87	0
15	Se	25	0.434	0.655	0.129	0
16	Se	25	0.612	0.141	0.353	0
17	Se	25	0.342	0.571	0.773	0
18	Se	25	0.217	0.392	0.553	0
19	Se	25	0.027	0.418	0.632	0
20	Se	25	0.108	0.451	0.682	0
21	Se	25	0.815	0.357	0.17	0
22	Se	25	0.489	0.62	0.894	0
23	Se	25	0.479	0.633	0.921	0
24	Se	25	0.562	0.207	0.614	0
25	Se	25	0.839	0.551	0.935	0
26	Se	25	0.286	0.493	0.111	0
27	Se	25	0.07	0.175	0.597	0
28	Se	25	0.677	0.05	0.22	0
29	Se	25	0.77	0.642	0.888	0
30	Se	25	0.889	0.59	0.927	0
31	Se	25	0.802	0.194	0.131	0
32	Se	25	0.785	0.094	0.979	0
33	Se	25	0.403	0.866	0.104	0
34	Se	25	0.341	0.507	0.84	0
35	Se	25	0.567	0.742	0.769	0
36	Se	25	0.891	0.873	0.787	0
37	Se	25	0.423	0.644	0.192	0
38	Se	25	0.506	0.853	0.242	0
39	Se	25	0.025	0.89	0.014	0
40	Se	25	0.498	0.299	0.599	0
41	Se	25	0.503	0.306	0.622	0
42	Se	25	0.149	0.372	0.614	0
43	Se	25	0.235	0.176	0.772	0
44	Se	25	0.056	0.11	0.581	0
45	Se	25	0.09	0.25	0.689	0
46	Se	25	0.234	0.463	0.713	0
47	Se	25	0.066	0.056	0.831	0
48	Se	25	0.198	0.289	0.512	0
49	Se	25	0.124	0.266	0.518	0
50	Se	25	0.305	0.459	0.604	0
51	Se	25	0.286	0.481	0.671	0
52	Se	25	0.3	0.859	0.379	0
53	Se	25	0.863	0.894	0.87	0
54	Se	25	0.434	0.655	0.129	0
55	Se	25	0.612	0.141	0.353	0
56	Se	25	0.342	0.571	0.773	0
57	Se	25	0.218	0.392	0.553	0
58	Se	25	0.027	0.419	0.632	0
59	Se	25	0.109	0.451	0.682	0
60	Se	25	0.815	0.357	0.17	0
61	Se	25	0.49	0.62	0.894	0
62	Se	25	0.479	0.633	0.921	0
63	Se	25	0.563	0.208	0.614	0
64	Se	25	0.839	0.551	0.935	0
65	Se	25	0.286	0.493	0.111	0
66	Se	25	0.07	0.175	0.597	0
67	Se	25	0.678	0.051	0.22	0
68	Se	25	0.77	0.641	0.888	0
69	Se	25	0.888	0.59	0.927	0
70	Se	25	0.802	0.194	0.131	0
71	Se	25	0.785	0.095	0.979	0
72	Se	25	0.403	0.867	0.105	0
73	Se	25	0.34	0.507	0.84	0
74	Se	25	0.567	0.742	0.769	0
75	Se	25	0.891	0.872	0.787	0
76	Se	25	0.423	0.644	0.191	0
77	Se	25	0.506	0.854	0.242	0
78	Se	25	0.025	0.89	0.014	0
79	Se	25	0.498	0.299	0.599	0
80	Se	25	0.503	0.306	0.621	0
81	Se	25	0.149	0.372	0.614	0
82	Se	25	0.235	0.176	0.772	0
83	Se	25	0.056	0.11	0.581	0
84	Se	25	0.09	0.25	0.689	0
85	Se	25	0.235	0.464	0.713	0
86	Se	25	0.066	0.056	0.831	0
87	Se	25	0.198	0.29	0.512	0
88	Se	25	0.123	0.267	0.518	0
89	Se	25	0.305	0.459	0.604	0
90	Se	25	0.286	0.481	0.671	0
91	Se	25	0.3	0.858	0.379	0
92	Se	25	0.863	0.895	0.87	0
93	Se	25	0.434	0.656	0.128	0
94	Se	25	0.611	0.141	0.353	0
95	Se	25	0.342	0.571	0.773	0
96	Se	25	0.217	0.393	0.553	0
97	Se	25	0.026	0.419	0.632	0
98	Se	25	0.108	0.451	0.683	0
99	Se	25	0.815	0.358	0.17	0
100	Se	25	0.489	0.62	0.894	0
101	Se	25	0.48	0.633	0.92	0
102	Se	25	0.562	0.208	0.615	0
103	Se	25	0.838	0.551	0.936	0
104	Se	25	0.287	0.493	0.111	0
105	Se	25	0.069	0.175	0.597	0
106	Se	25	0.677	0.05	0.22	0
107	Se	25	0.77	0.642	0.888	0
108	Se	25	0.89	0.591	0.927	0
109	Se	25	0.8	0.195	0.132	0
110	Se	25	0.785	0.094	0.979	0
111	Se	25	0.403	0.867	0.104	0
112	Se	25	0.342	0.506	0.84	0
113	Se	25	0.568	0.741	0.769	0
114	Se	25	0.892	0.873	0.787	0
115	Se	25	0.424	0.645	0.191	0
116	Se	25	0.506	0.854	0.242	0
117	Se	25	0.024	0.89	0.014	0
118	Se	25	0.499	0.304	0.599	-0.186
119	Se	25	0.504	0.307	0.62	-0.168
120	Se	25	0.153	0.371	0.614	-0.127
121	Se	25	0.232	0.176	0.771	-0.17
122	Se	25	0.052	0.107	0.579	-0.148
123	Se	25	0.091	0.248	0.688	-0.16
124	Se	25	0.231	0.461	0.714	-0.146
125	Se	25	0.063	0.056	0.832	-0.14
126	Se	25	0.197	0.289	0.511	-0.116
127	Se	25	0.122	0.266	0.517	-0.072
128	Se	25	0.305	0.457	0.602	-0.11
129	Se	25	0.288	0.477	0.669	-0.149
130	Se	25	0.299	0.859	0.379	-0.124
131	Se	25	0.862	0.896	0.87	-0.133
132	Se	25	0.433	0.654	0.129	-0.178
133	Se	25	0.608	0.141	0.353	-0.187
134	Se	25	0.341	0.572	0.771	-0.115
135	Se	25	0.219	0.392	0.555	-0.131
136	Se	25	0.028	0.419	0.632	-0.127
137	Se	25	0.103	0.452	0.682	-0.17
138	Se	25	0.814	0.358	0.171	-0.155
139	Se	25	0.485	0.618	0.895	-0.129
140	Se	25	0.474	0.634	0.919	-0.15
141	Se	25	0.564	0.211	0.618	-0.141
142	Se	25	0.838	0.553	0.933	-0.133
143	Se	25	0.289	0.486	0.113	-0.174
144	Se	25	0.065	0.173	0.597	-0.156
145	Se	25	0.669	0.048	0.22	-0.134
146	Se	25	0.769	0.643	0.888	-0.13
147	Se	25	0.89	0.593	0.925	-0.107
148	Se	25	0.801	0.192	0.132	-0.062
149	Se	25	0.783	0.099	0.98	-0.078
150	Se	25	0.402	0.87	0.103	-0.153
151	Se	25	0.338	0.511	0.84	-0.132
152	Se	25	0.57	0.74	0.769	-0.1
153	Se	25	0.894	0.871	0.788	-0.128
154	Se	25	0.427	0.647	0.192	-0.183
155	Se	25	0.505	0.85	0.243	-0.098
156	Se	25	0.041	0.877	0.013	-0.019

Phasing MAD shell

Resolution (Å)	FOM	FOM acentric	FOM centric	Reflection	Reflection acentric	Reflection centric
10.92-30	0.585	0.647	0.459	625	419	206
6.67-10.92	0.618	0.661	0.449	2043	1635	408
4.81-6.67	0.628	0.659	0.443	4338	3721	617
3.76-4.81	0.574	0.599	0.367	7432	6629	803
3.08-3.76	0.537	0.554	0.354	11392	10393	999
2.61-3.08	0.439	0.447	0.347	16136	14949	1187
2.27-2.61	0.271	0.274	0.233	17604	16614	990
2-2.27	0	0	0		0	0

Phasing dm

FOM : 0.46 / FOM acentric: 0.46 / FOM centric: 0.51 / Reflection: 90172 / Reflection acentric: 83431 / Reflection centric: 6741

Phasing dm shell

Resolution (Å)	FOM	FOM acentric	FOM centric	Reflection	Reflection acentric	Reflection centric
5.7-29.794	0.93	0.94	0.86	4044	3255	789
3.6-5.7	0.91	0.92	0.83	12389	11045	1344
2.9-3.6	0.78	0.78	0.69	15335	14103	1232
2.5-2.9	0.55	0.56	0.48	15286	14264	1022
2.1-2.5	0.21	0.21	0.19	26960	25394	1566
2-2.1	0.05	0.05	0.04	16158	15370	788

-
Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
MLPHARE		phasing
RESOLVE	2.03	phasing
CNS		refinement
PDB_EXTRACT	2	data extraction
CBASS		data collection
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MAD / Resolution: 2→50 Å / FOM work R set: 0.828 / σ(F): 0

	R_factor	Num. reflection	% reflection
R_free	0.248	8657	9.3 %
R_work	0.219	-	-
obs	-	86736	93.1 %

Solvent computation

B_sol: 43.593 Å²

Displacement parameters

B_iso mean: 32.448 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.503 Å²	0 Å²	0 Å²
2-	-	-2.263 Å²	0 Å²
3-	-	-	0.76 Å²

Refinement step

Cycle: LAST / Resolution: 2→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8441	0	0	475	8916

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target
X-RAY DIFFRACTION	c_mcbond_it	1.262	1.5
X-RAY DIFFRACTION	c_scbond_it	2.188	2
X-RAY DIFFRACTION	c_mcangle_it	2.011	2
X-RAY DIFFRACTION	c_scangle_it	3.19	2.5

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 50

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection obs
2-2.01	0.333	127	0.276	1265	1392
2.01-2.03	0.328	185	0.311	1378	1563
2.03-2.04	0.359	163	0.284	1428	1591
2.04-2.06	0.323	152	0.282	1414	1566
2.06-2.07	0.31	166	0.28	1499	1665
2.07-2.09	0.304	139	0.278	1453	1592
2.09-2.1	0.299	182	0.279	1494	1676
2.1-2.12	0.294	170	0.269	1460	1630
2.12-2.14	0.293	191	0.271	1478	1669
2.14-2.15	0.316	142	0.272	1471	1613
2.15-2.17	0.312	182	0.267	1495	1677
2.17-2.19	0.272	190	0.244	1487	1677
2.19-2.21	0.298	160	0.25	1502	1662
2.21-2.23	0.281	170	0.247	1515	1685
2.23-2.25	0.302	184	0.247	1544	1728
2.25-2.27	0.273	185	0.234	1529	1714
2.27-2.3	0.289	155	0.248	1553	1708
2.3-2.32	0.271	160	0.234	1499	1659
2.32-2.35	0.283	165	0.234	1549	1714
2.35-2.37	0.286	155	0.225	1581	1736
2.37-2.4	0.26	183	0.222	1536	1719
2.4-2.43	0.312	176	0.245	1570	1746
2.43-2.46	0.268	190	0.234	1584	1774
2.46-2.49	0.292	178	0.236	1569	1747
2.49-2.52	0.252	180	0.24	1570	1750
2.52-2.55	0.278	173	0.227	1567	1740
2.55-2.59	0.242	156	0.227	1646	1802
2.59-2.63	0.25	150	0.231	1615	1765
2.63-2.67	0.271	159	0.227	1607	1766
2.67-2.71	0.251	166	0.222	1629	1795
2.71-2.76	0.277	176	0.22	1584	1760
2.76-2.81	0.284	187	0.223	1587	1774
2.81-2.87	0.247	146	0.236	1648	1794
2.87-2.92	0.251	168	0.228	1635	1803
2.92-2.99	0.254	184	0.234	1593	1777
2.99-3.06	0.257	203	0.221	1602	1805
3.06-3.13	0.244	167	0.238	1644	1811
3.13-3.22	0.252	180	0.236	1663	1843
3.22-3.31	0.243	184	0.227	1611	1795
3.31-3.42	0.225	148	0.222	1665	1813
3.42-3.54	0.24	198	0.214	1646	1844
3.54-3.68	0.218	197	0.213	1620	1817
3.68-3.85	0.237	184	0.2	1634	1818
3.85-4.05	0.21	167	0.178	1659	1826
4.05-4.31	0.205	199	0.173	1633	1832
4.31-4.64	0.197	193	0.172	1614	1807
4.64-5.11	0.192	189	0.179	1632	1821
5.11-5.85	0.221	161	0.196	1657	1818
5.85-7.37	0.233	198	0.222	1645	1843
7.37-500.01	0.213	194	0.175	1620	1814

Xplor file

Refine-ID	Serial no	Param file
X-RAY DIFFRACTION	1	CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION	2	CNS_TOPPAR:water.param

-
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