PDB-2pmu: Crystal structure of the DNA-binding domain of PhoP

ID or keywords:

Entry

Database: PDB / ID: 2pmu

Title

Crystal structure of the DNA-binding domain of PhoP

Components

response regulator PHOP

Keywords

TRANSCRIPTION REGULATION / winged helix-tun-helx

Function / homology

Function and homology information

protein secretion by the type VII secretion system / glycolipid biosynthetic process / phosphorelay response regulator activity / phosphorelay signal transduction system / positive regulation of lipid biosynthetic process / protein-DNA complex / response to oxidative stress / transcription cis-regulatory region binding / negative regulation of DNA-templated transcription / positive regulation of gene expression ...
Similarity search - Function

Biological species

Mycobacterium tuberculosis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.779 Å

Authors

Wang, S.

Citation

Journal: Biochemistry / Year: 2007
Title: Structure of the DNA-binding domain of the response regulator PhoP from Mycobacterium tuberculosis
Authors: Wang, S. / Engohang-Ndong, J. / Smith, I.

History

Deposition	Apr 23, 2007	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 26, 2008	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2	Oct 18, 2017	Group: Refinement description / Category: software
Revision 1.3	Aug 30, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	2pmu.cif.gz	145.9 KB	Display	PDBx/mmCIF format
PDB format	pdb2pmu.ent.gz	113.2 KB	Display	PDB format
PDBx/mmJSON format	2pmu.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	2pmu_validation.pdf.gz	468.4 KB	Display	wwPDB validaton report
Full document	2pmu_full_validation.pdf.gz	474.8 KB	Display
Data in XML	2pmu_validation.xml.gz	13.7 KB	Display
Data in CIF	2pmu_validation.cif.gz	23.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/pm/2pmu ftp://data.pdbj.org/pub/pdb/validation_reports/pm/2pmu	HTTPS FTP

-
Related structure data

Related structure data	1kgsS S: Starting model for refinement
Similar structure data	2hik-2 2nti-2 2hik-3 1zke-4 2ix2-d 2hii-2 6t7x-1 5eev-2 6hrs-2 2hii-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	#190 - Oct 2015 Two-component Systems similarity (10) #235 - Jul 2019 AMPA Receptor similarity (1) #97 - Jan 2008 Circadian Clock Proteins similarity (1) #142 - Oct 2011 PDB Pioneers similarity (1)

Deposited unit

A: response regulator PHOP

B: response regulator PHOP

C: response regulator PHOP

D: response regulator PHOP

E: response regulator PHOP

F: response regulator PHOP

hetero molecules

77.6 kDa, 6 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)	103.884, 101.129, 86.930
Angle α, β, γ (deg.)	90.00, 126.72, 90.00
Int Tables number	5
Space group name H-M	C121

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Refine code	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	1	LEU	LEU	GLU	GLU	1	A	A	151 - 178	12 - 39
2	1	1	LEU	LEU	GLU	GLU	1	D	D	151 - 178	12 - 39
3	2	1	VAL	VAL	LYS	LYS	1	A	A	213 - 230	74 - 91
4	2	1	VAL	VAL	LYS	LYS	1	D	D	213 - 230	74 - 91
5	3	1	VAL	VAL	ARG	ARG	1	A	A	239 - 244	100 - 105
6	3	1	VAL	VAL	ARG	ARG	1	D	D	239 - 244	100 - 105
7	4	1	PHE	PHE	PHE	PHE	3	A	A	179	40
8	4	1	PHE	PHE	PHE	PHE	3	D	D	179	40
9	5	1	ARG	ARG	ARG	ARG	3	A	A	204	65
10	5	1	ARG	ARG	ARG	ARG	3	D	D	204	65
11	6	1	ARG	ARG	ARG	ARG	3	A	A	231	92
12	6	1	ARG	ARG	ARG	ARG	3	D	D	231	92
13	7	1	LEU	LEU	LEU	LEU	3	A	A	233	94
14	7	1	LEU	LEU	LEU	LEU	3	D	D	233	94
15	8	1	THR	THR	TRP	TRP	1	A	A	180 - 203	41 - 64
16	8	1	THR	THR	TRP	TRP	1	D	D	180 - 203	41 - 64
17	9	1	TYR	TYR	TYR	TYR	1	A	A	205	66
18	9	1	TYR	TYR	TYR	TYR	1	D	D	205	66
19	10	1	LEU	LEU	LEU	LEU	1	A	A	232	93
20	10	1	LEU	LEU	LEU	LEU	1	D	D	232	93
21	11	1	HIS	HIS	LEU	LEU	1	A	A	234 - 236	95 - 97
22	11	1	HIS	HIS	LEU	LEU	1	D	D	234 - 236	95 - 97
1	1	2	PRO	PRO	VAL	VAL	1	B	B	146 - 149	7 - 10
2	1	2	PRO	PRO	VAL	VAL	1	E	E	146 - 149	7 - 10
3	2	2	HIS	HIS	ASP	ASP	1	B	B	201 - 206	62 - 67
4	2	2	HIS	HIS	ASP	ASP	1	E	E	201 - 206	62 - 67
5	3	2	ASN	ASN	ASN	ASN	1	B	B	212	73
6	3	2	ASN	ASN	ASN	ASN	1	E	E	212	73
7	4	2	LEU	LEU	LEU	LEU	1	B	B	232 - 236	93 - 97
8	4	2	LEU	LEU	LEU	LEU	1	E	E	232 - 236	93 - 97
9	5	2	GLY	GLY	GLY	GLY	1	B	B	240	101
10	5	2	GLY	GLY	GLY	GLY	1	E	E	240	101
11	6	2	ARG	ARG	ARG	ARG	3	B	B	150	11
12	6	2	ARG	ARG	ARG	ARG	3	E	E	150	11
13	7	2	GLU	GLU	GLU	GLU	3	B	B	160	21
14	7	2	GLU	GLU	GLU	GLU	3	E	E	160	21
15	8	2	PHE	PHE	PHE	PHE	3	B	B	179	40
16	8	2	PHE	PHE	PHE	PHE	3	E	E	179	40
17	9	2	VAL	VAL	VAL	VAL	3	B	B	213	74
18	9	2	VAL	VAL	VAL	VAL	3	E	E	213	74
19	10	2	TYR	TYR	TYR	TYR	3	B	B	241	102
20	10	2	TYR	TYR	TYR	TYR	3	E	E	241	102
21	11	2	LEU	LEU	LEU	LEU	3	B	B	243	104
22	11	2	LEU	LEU	LEU	LEU	3	E	E	243	104
23	12	2	LEU	LEU	ASP	ASP	1	B	B	151 - 159	12 - 20
24	12	2	LEU	LEU	ASP	ASP	1	E	E	151 - 159	12 - 20
25	13	2	GLU	GLU	GLU	GLU	1	B	B	161 - 178	22 - 39
26	13	2	GLU	GLU	GLU	GLU	1	E	E	161 - 178	22 - 39
27	14	2	THR	THR	LEU	LEU	1	B	B	180 - 199	41 - 60
28	14	2	THR	THR	LEU	LEU	1	E	E	180 - 199	41 - 60
29	15	2	VAL	VAL	ASP	ASP	1	B	B	214 - 226	75 - 87
30	15	2	VAL	VAL	ASP	ASP	1	E	E	214 - 226	75 - 87
31	16	2	VAL	VAL	VAL	VAL	1	B	B	242	103
32	16	2	VAL	VAL	VAL	VAL	1	E	E	242	103
33	17	2	ARG	ARG	ARG	ARG	1	B	B	244	105
34	17	2	ARG	ARG	ARG	ARG	1	E	E	244	105
1	1	3	LEU	LEU	ASP	ASP	1	C	C	151 - 159	12 - 20
2	1	3	LEU	LEU	ASP	ASP	1	F	F	151 - 159	12 - 20
3	2	3	THR	THR	TRP	TRP	1	C	C	162 - 203	23 - 64
4	2	3	THR	THR	TRP	TRP	1	F	F	162 - 203	23 - 64
5	3	3	VAL	VAL	GLY	GLY	1	C	C	213 - 228	74 - 89
6	3	3	VAL	VAL	GLY	GLY	1	F	F	213 - 228	74 - 89
7	4	3	GLY	GLY	LEU	LEU	1	C	C	240 - 243	101 - 104
8	4	3	GLY	GLY	LEU	LEU	1	F	F	240 - 243	101 - 104
9	5	3	ARG	ARG	HIS	HIS	1	C	C	231 - 234	92 - 95
10	5	3	ARG	ARG	HIS	HIS	1	F	F	231 - 234	92 - 95

NCS ensembles :

ID
1
2
3

-
Protein , 1 types, 6 molecules ABCDEF

#1: Protein	response regulator PHOP / POSSIBLE TWO COMPONENT SYSTEM RESPONSE TRANSCRIPTIONAL POSITIVE REGULATOR PHOP Mass: 12790.662 Da / Num. of mol.: 6 / Fragment: DNA-binding domain, residues 144-247 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: PhoP / Plasmid: pET28 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P71814, UniProt: Q7D9B8*PLUS

#1: Protein

response regulator PHOP / POSSIBLE TWO COMPONENT SYSTEM RESPONSE TRANSCRIPTIONAL POSITIVE REGULATOR PHOP

Mass: 12790.662 Da / Num. of mol.: 6 / Fragment: DNA-binding domain, residues 144-247
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: PhoP / Plasmid: pET28 / Species (production host): Escherichia coli / Production host:

Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P71814, UniProt: Q7D9B8*PLUS

-
Non-polymers , 6 types, 507 molecules

#2: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO₄
#3: Chemical	ChemComp-K / POTASSIUM ION Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#4: Chemical	ChemComp-UNX / UNKNOWN ATOM OR ION Num. of mol.: 4 / Source method: obtained synthetically
#5: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#6: Chemical	ChemComp-GLY / GLYCINE Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₂H₅NO₂
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 489 / 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: 2.38 Å³/Da / Density % sol: 48.4 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion / pH: 5.6 Details: 1.4 M Na/K phosphate, pH 5.6, 100 mM glycine, VAPOR DIFFUSION, temperature 298K

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.9795 Å
Detector	Type: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 8, 2006
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9795 Å / Relative weight: 1
Reflection	Resolution: 1.779→20 Å / Num. obs: 65220 / % possible obs: 94.8 % / Redundancy: 2.9 % / R_merge(I) obs: 0.036 / Χ²: 1.033 / Net I/σ(I): 18.6
Reflection shell	Resolution: 1.779→1.84 Å / Redundancy: 2.7 % / R_merge(I) obs: 0.582 / Mean I/σ(I) obs: 2.03 / Num. unique all: 6629 / Χ²: 1.05 / % possible all: 96.7

-
Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
REFMAC	5.2.0019	refinement
PDB_EXTRACT	2	data extraction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 1KGS C-terminal domain

1kgs

Resolution: 1.779→20 Å / Cor.coef. F_o:F_c: 0.956 / Cor.coef. F_o:F_c free: 0.935 / SU B: 5.454 / SU ML: 0.09 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotopic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.131 / ESU R Free: 0.129 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.238	3310	5.1 %	RANDOM
R_work	0.196	-	-	-
obs	0.198	65210	94.63 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 41.509 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.35 Å²	0 Å²	0.43 Å²
2-	-	-0.48 Å²	0 Å²
3-	-	-	0.64 Å²

Refinement step

Cycle: LAST / Resolution: 1.779→20 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4796	0	46	489	5331

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.016	0.022	4966
X-RAY DIFFRACTION	r_angle_refined_deg	1.554	1.97	6748
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.719	5	588
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.006	22.361	233
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.73	15	856
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.734	15	49
X-RAY DIFFRACTION	r_chiral_restr	0.117	0.2	764
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	3711
X-RAY DIFFRACTION	r_nbd_refined	0.236	0.2	2286
X-RAY DIFFRACTION	r_nbtor_refined	0.316	0.2	3303
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.13	0.2	467
X-RAY DIFFRACTION	r_metal_ion_refined	0.378	0.2	9
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.266	0.2	117
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.186	0.2	28
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined	0.115	0.2	4
X-RAY DIFFRACTION	r_mcbond_it	2.594	2	2935
X-RAY DIFFRACTION	r_mcangle_it	3.729	3	4788
X-RAY DIFFRACTION	r_scbond_it	3.185	2	2059
X-RAY DIFFRACTION	r_scangle_it	4.449	3	1954

Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	A	672	TIGHT POSITIONAL	0.02	0.05
1	A	25	LOOSE POSITIONAL	0.67	5
1	A	672	TIGHT THERMAL	0.37	1
1	A	25	LOOSE THERMAL	1.13	20
2	B	677	TIGHT POSITIONAL	0.03	0.05
2	B	34	LOOSE POSITIONAL	0.73	5
2	B	677	TIGHT THERMAL	0.33	1
2	B	34	LOOSE THERMAL	1	20
3	C	608	TIGHT POSITIONAL	0.02	0.05
3	C	608	TIGHT THERMAL	0.32	1

LS refinement shell

Resolution: 1.779→1.825 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.324	227	-
R_work	0.274	4508	-
obs	-	4735	94 %

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	2.8368	-1.5187	0.0298	4.1451	0.3198	3.4911	-0.1114	-0.0357	0.0298	-0.099	-0.016	0.0346	-0.0301	-0.057	0.1274	-0.2471	0.0501	-0.0379	-0.1961	-0.0729	-0.2313	14.665	-18.057	-21.123
2	3.077	-0.8261	-1.0188	4.6283	-0.436	5.4606	-0.1201	-0.1714	-0.4755	0.313	-0.0389	0.2644	0.4399	-0.0597	0.159	-0.191	0.025	0.004	-0.1711	-0.0424	-0.1291	14.586	-27.132	4.801
3	3.4514	0.7415	0.9621	10.1411	2.7871	4.6037	0.0211	-0.3561	-0.1553	0.7085	0.4267	-0.635	0.3309	0.3694	-0.4478	-0.1412	0.0302	-0.0143	-0.1317	-0.0535	-0.1228	12.868	-10.611	25.539
4	2.5491	1.3695	0.2019	4.2236	0.3502	3.449	-0.1044	0.0176	-0.0532	0.1095	-0.0142	0.0194	0.0385	-0.0515	0.1186	-0.2463	-0.0466	0.0372	-0.1907	-0.0704	-0.2331	14.708	17.59	21.332
5	2.966	0.8097	1.1304	4.3397	-0.2981	5.8082	-0.15	0.1491	0.4751	-0.2958	-0.0121	0.2751	-0.4664	-0.0551	0.1621	-0.1888	-0.0226	-0.0111	-0.1796	-0.0427	-0.1258	14.501	26.972	-4.634
6	3.5038	-0.8589	-1.08	10.1619	2.6818	4.5004	0.0236	0.3504	0.1249	-0.7863	0.392	-0.5894	-0.3336	0.3574	-0.4156	-0.1282	-0.0324	0.0054	-0.1329	-0.0465	-0.1259	12.881	10.242	-25.637

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	A	A	149 - 246	10 - 107
2	2	B	B	144 - 246	5 - 107
3	3	C	C	148 - 246	9 - 107
4	4	D	D	149 - 246	10 - 107
5	5	E	E	144 - 246	5 - 107
6	6	F	F	148 - 246	9 - 107

-
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

-
Protein , 1 types, 6 molecules ABCDEF

-
Non-polymers , 6 types, 507 molecules

-
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

-Protein , 1 types, 6 molecules ABCDEF

-Non-polymers , 6 types, 507 molecules

-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

-
Protein , 1 types, 6 molecules ABCDEF

-
Non-polymers , 6 types, 507 molecules

-
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