PDB-3zm0: Catalytic domain of human SHP2

ID or keywords:

Entry

Database: PDB / ID: 3zm0

Title

Catalytic domain of human SHP2

Components

TYROSINE-PROTEIN PHOSPHATASE NON-RECEPTOR TYPE 11

Keywords

HYDROLASE / PTP1B

Function / homology

Function and homology information

negative regulation of cortisol secretion / intestinal epithelial cell migration / microvillus organization / negative regulation of growth hormone secretion / genitalia development / atrioventricular canal development / negative regulation of cell adhesion mediated by integrin / STAT5 Activation / Netrin mediated repulsion signals / cerebellar cortex formation ...negative regulation of cortisol secretion / intestinal epithelial cell migration / microvillus organization / negative regulation of growth hormone secretion / genitalia development / atrioventricular canal development / negative regulation of cell adhesion mediated by integrin / STAT5 Activation / Netrin mediated repulsion signals / cerebellar cortex formation / negative regulation of neutrophil activation / positive regulation of hormone secretion / regulation of protein export from nucleus / positive regulation of ossification / positive regulation of lipopolysaccharide-mediated signaling pathway / Interleukin-37 signaling / hormone metabolic process / Signaling by Leptin / MET activates PTPN11 / negative regulation of chondrocyte differentiation / Regulation of RUNX1 Expression and Activity / Regulation of T cell activation by CD28 family / face morphogenesis / Signal regulatory protein family interactions / ERBB signaling pathway / platelet formation / megakaryocyte development / organ growth / triglyceride metabolic process / peptide hormone receptor binding / negative regulation of type I interferon production / Interleukin-20 family signaling / Co-inhibition by CTLA4 / PI-3K cascade:FGFR3 / Interleukin-6 signaling / Platelet sensitization by LDL / STAT5 activation downstream of FLT3 ITD mutants / PI-3K cascade:FGFR2 / PI-3K cascade:FGFR4 / MAPK3 (ERK1) activation / PI-3K cascade:FGFR1 / Prolactin receptor signaling / regulation of cell adhesion mediated by integrin / regulation of type I interferon-mediated signaling pathway / MAPK1 (ERK2) activation / PECAM1 interactions / neurotrophin TRK receptor signaling pathway / inner ear development / Bergmann glial cell differentiation / platelet-derived growth factor receptor signaling pathway / peptidyl-tyrosine dephosphorylation / phosphoprotein phosphatase activity / RET signaling / Interleukin-3, Interleukin-5 and GM-CSF signaling / Regulation of IFNA/IFNB signaling / PI3K Cascade / ephrin receptor signaling pathway / Co-inhibition by PD-1 / fibroblast growth factor receptor signaling pathway / GAB1 signalosome / Activated NTRK2 signals through FRS2 and FRS3 / regulation of protein-containing complex assembly / negative regulation of insulin secretion / Regulation of IFNG signaling / positive regulation of insulin receptor signaling pathway / FRS-mediated FGFR3 signaling / Signaling by CSF3 (G-CSF) / Signaling by FLT3 ITD and TKD mutants / cell adhesion molecule binding / GPVI-mediated activation cascade / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / homeostasis of number of cells within a tissue / Tie2 Signaling / FRS-mediated FGFR1 signaling / hormone-mediated signaling pathway / T cell costimulation / FLT3 Signaling / phosphotyrosine residue binding / protein tyrosine phosphatase activity / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity, metal-dependent / histone H2AXY142 phosphatase activity / non-membrane spanning protein tyrosine phosphatase activity / cellular response to epidermal growth factor stimulus / positive regulation of mitotic cell cycle / Downstream signal transduction / axonogenesis / positive regulation of interferon-beta production / protein tyrosine kinase binding / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / DNA damage checkpoint signaling / integrin-mediated signaling pathway / positive regulation of D-glucose import / Negative regulation of FGFR3 signaling / Negative regulation of FGFR2 signaling / Negative regulation of FGFR4 signaling / insulin receptor binding / Negative regulation of FGFR1 signaling / Spry regulation of FGF signaling
Similarity search - Function

Biological species

HOMO SAPIENS (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.5 Å

Authors

Bohm, K. / Schuetz, A. / Roske, Y. / Heinemann, U.

Citation

Journal: Chemmedchem / Year: 2015
Title: Selective Inhibitors of the Protein Tyrosine Phosphatase Shp2 Block Cellular Motility and Growth of Cancer Cells in Vitro and in Vivo.
Authors: Grosskopf, S. / Eckert, C. / Arkona, C. / Radetzki, S. / Bohm, K. / Heinemann, U. / Wolber, G. / Von Kries, J. / Birchmeier, W. / Rademann, J.

History

Deposition	Feb 4, 2013	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Apr 23, 2014	Provider: repository / Type: Initial release
Revision 1.1	Apr 29, 2015	Group: Database references
Revision 1.2	May 13, 2015	Group: Database references
Revision 1.3	Dec 20, 2023	Group: Data collection / Database references ...Data collection / Database references / 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 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	3zm0.cif.gz	124.5 KB	Display	PDBx/mmCIF format
PDB format	pdb3zm0.ent.gz	98 KB	Display	PDB format
PDBx/mmJSON format	3zm0.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	3zm0_validation.pdf.gz	425.4 KB	Display	wwPDB validaton report
Full document	3zm0_full_validation.pdf.gz	431.5 KB	Display
Data in XML	3zm0_validation.xml.gz	14.3 KB	Display
Data in CIF	3zm0_validation.cif.gz	20.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/zm/3zm0 ftp://data.pdbj.org/pub/pdb/validation_reports/zm/3zm0	HTTPS FTP

-
Related structure data

Related structure data	3zm1C 3zm2C 3zm3C 3b7oS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	2oc9-d 6s4u-2 6li5-2 6b8x-d 1jop-2 1t79-d 1p93-4 6bab-3 1rtc-d 6f9p-2 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	#148 - Apr 2012 Ras Protein similarity (11) #60 - Dec 2004 Ubiquitin similarity (10) #126 - Jun 2010 Epidermal Growth Factor similarity (15) #43 - Jul 2003 Src Tyrosine Kinase similarity (9) #236 - Aug 2019 Cyclin and Cyclin-dependent Kinase similarity (2) #52 - Apr 2004 Growth Hormone similarity (1) #122 - Feb 2010 Enhanceosome similarity (7) #134 - Feb 2011 Integrin similarity (1) #195 - Mar 2016 RAF Protein Kinases similarity (10) #149 - May 2012 Leptin similarity (1) #128 - Aug 2010 Interferons similarity (2) #145 - Jan 2012 Messenger RNA Capping similarity (5) #225 - Sep 2018 Phytase similarity (5) #224 - Aug 2018 Legumain similarity (1) #56 - Aug 2004 Caspases similarity (1) #98 - Feb 2008 Small Interfering RNA similarity (1) #204 - Dec 2016 PD-1 similarity (1) #63 - Mar 2005 T-Cell Receptor similarity (1) #239 - Nov 2019 Phospholipase A2 similarity (1) #28 - Apr 2002 Anthrax Toxin similarity (1) #214 - Oct 2017 Chimeric Antigen Receptors similarity (1) #247 - Jul 2020 Myelin-associated Glycoprotein similarity (1) #245 - May 2020 Spliceosomes similarity (1) #222 - Jun 2018 Proteins and Nanoparticles similarity (1) #169 - Jan 2014 HIV Envelope Glycoprotein similarity (1) #209 - May 2017 Tissue Transglutaminase and Celiac Disease similarity (1) #62 - Feb 2005 Major Histocompatibility Complex similarity (1) #68 - Aug 2005 Neurotrophins similarity (1) #267 - Mar 2022 Vascular Endothelial Growth Factor (VegF similarity (1) #143 - Nov 2011 Toll-like Receptors similarity (1) #234 - Jun 2019 MDM2 and Cancer similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#148 - Apr 2012
Ras Protein
similarity (11)
#60 - Dec 2004
Ubiquitin
similarity (10)
#126 - Jun 2010
Epidermal Growth Factor
similarity (15)
#43 - Jul 2003
Src Tyrosine Kinase
similarity (9)
#236 - Aug 2019
Cyclin and Cyclin-dependent Kinase
similarity (2)
#52 - Apr 2004
Growth Hormone
similarity (1)
#122 - Feb 2010
Enhanceosome
similarity (7)
#134 - Feb 2011
Integrin
similarity (1)
#195 - Mar 2016
RAF Protein Kinases
similarity (10)
#149 - May 2012
Leptin
similarity (1)
#128 - Aug 2010
Interferons
similarity (2)
#145 - Jan 2012
Messenger RNA Capping
similarity (5)
#225 - Sep 2018
Phytase
similarity (5)
#224 - Aug 2018
Legumain
similarity (1)
#56 - Aug 2004
Caspases
similarity (1)
#98 - Feb 2008
Small Interfering RNA
similarity (1)
#204 - Dec 2016
PD-1
similarity (1)
#63 - Mar 2005
T-Cell Receptor
similarity (1)
#239 - Nov 2019
Phospholipase A2
similarity (1)
#28 - Apr 2002
Anthrax Toxin
similarity (1)
#214 - Oct 2017
Chimeric Antigen Receptors
similarity (1)
#247 - Jul 2020
Myelin-associated Glycoprotein
similarity (1)
#245 - May 2020
Spliceosomes
similarity (1)
#222 - Jun 2018
Proteins and Nanoparticles
similarity (1)
#169 - Jan 2014
HIV Envelope Glycoprotein
similarity (1)
#209 - May 2017
Tissue Transglutaminase and Celiac Disease
similarity (1)
#62 - Feb 2005
Major Histocompatibility Complex
similarity (1)
#68 - Aug 2005
Neurotrophins
similarity (1)
#267 - Mar 2022
Vascular Endothelial Growth Factor (VegF
similarity (1)
#143 - Nov 2011
Toll-like Receptors
similarity (1)
#234 - Jun 2019
MDM2 and Cancer
similarity (1)

Deposited unit

A: TYROSINE-PROTEIN PHOSPHATASE NON-RECEPTOR TYPE 11

33.1 kDa, 1 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)	40.216, 42.257, 49.197
Angle α, β, γ (deg.)	72.52, 81.63, 74.73
Int Tables number	1
Space group name H-M	P1

#1: Protein	TYROSINE-PROTEIN PHOSPHATASE NON-RECEPTOR TYPE 11 / PROTEIN-TYROSINE PHOSPHATASE 1D / PTP-1D / PROTEIN-TYROSINE PHOSPHATASE 2C / PTP-2C / SH-PTP2 / SHP- ...PROTEIN-TYROSINE PHOSPHATASE 1D / PTP-1D / PROTEIN-TYROSINE PHOSPHATASE 2C / PTP-2C / SH-PTP2 / SHP-2 / SHP2 / SH-PTP3 Mass: 33109.609 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN, RESIDUES 248-527 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PT7HT (MODIFIED PET) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): SCS1 ROSETTA T1R / References: UniProt: Q06124, protein-tyrosine-phosphatase
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 206 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

TYROSINE-PROTEIN PHOSPHATASE NON-RECEPTOR TYPE 11 / PROTEIN-TYROSINE PHOSPHATASE 1D / PTP-1D / PROTEIN-TYROSINE PHOSPHATASE 2C / PTP-2C / SH-PTP2 / SHP- ...

Mass: 33109.609 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN, RESIDUES 248-527
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

HOMO SAPIENS (human) / Plasmid: PT7HT (MODIFIED PET) / Production host:

ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): SCS1 ROSETTA T1R / References: UniProt: Q06124, protein-tyrosine-phosphatase

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 206 / 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: 2.32 Å³/Da / Density % sol: 46.92 % / Description: NONE
Crystal grow	Details: 16-22 % (W/V) PEG3350, 0.1-0.2 M SODIUM CITRATE

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184
Detector	Type: MARRESEARCH / Detector: CCD / Date: Feb 26, 2009
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9184 Å / Relative weight: 1
Reflection	Resolution: 1.5→20 Å / Num. obs: 40770 / % possible obs: 86 % / Observed criterion σ(I): 0 / Redundancy: 3.2 % / R_merge(I) obs: 0.05 / Net I/σ(I): 17.4
Reflection shell	Resolution: 1.5→1.59 Å / R_merge(I) obs: 0.02 / Mean I/σ(I) obs: 5.5 / % possible all: 51.6

-
Processing

Software

Name	Version	Classification
REFMAC	5.2.0019	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3B7O

3b7o

Resolution: 1.5→19.6 Å / Cor.coef. F_o:F_c: 0.958 / Cor.coef. F_o:F_c free: 0.945 / SU B: 2.178 / SU ML: 0.042 / Cross valid method: THROUGHOUT / ESU R: 0.078 / ESU R Free: 0.079 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 256-262, 314-323 AND 407-410 ARE DISORDERED.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.21342	2107	5 %	RANDOM
R_work	0.18413	-	-	-
obs	0.18559	40031	85.8 %	-

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: 20.499 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.27 Å²	-0.19 Å²	0.01 Å²
2-	-	0.34 Å²	0.33 Å²
3-	-	-	-0.71 Å²

Refinement step

Cycle: LAST / Resolution: 1.5→19.6 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2139	0	0	206	2345

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.022	0.022	2207
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.862	1.934	2984
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.512	5	263
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.885	23.86	114
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.112	15	399
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	20.591	15	17
X-RAY DIFFRACTION	r_chiral_restr	0.13	0.2	321
X-RAY DIFFRACTION	r_gen_planes_refined	0.01	0.02	1678
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.239	0.2	1007
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.311	0.2	1508
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.128	0.2	144
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	0.195	0.2	36
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.116	0.2	8
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	1.524	2	1342
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	2.344	3	2129
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	3.723	5	993
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	5.37	7	852
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

LS refinement shell

Resolution: 1.5→1.539 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.242	88	-
R_work	0.201	1675	-
obs	-	-	100 %

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	5.7605	-3.74	-5.6997	4.9542	3.5247	8.7888	0.1787	-0.1381	-0.0516	-0.1481	-0.0082	-0.1019	-0.1197	0.1104	-0.1705	0.1091	-0.0246	-0.0164	0.0184	0.0273	0.0048	20.7885	24.0961	48.8671
2	2.2011	0.1652	-0.3395	2.303	-0.5218	3.9191	0.1106	0.0639	-0.0999	-0.0829	-0.0805	-0.1997	0.7113	0.4018	-0.0301	0.1405	0.0758	-0.0334	-0.0049	-0.0215	0.0115	26.6324	18.0338	20.7183
3	0.1512	0.1035	-0.8683	0.1	-0.2159	9.9091	0.004	-0.002	-0.012	0.0644	-0.0042	-0.021	0.2614	0.2699	0.0002	0.1099	-0.0049	-0.0299	0.044	-0.0147	0.0252	18.7759	22.9387	8.0009
4	1.3246	-0.3748	-0.7177	1.9311	0.5968	5.7238	0.1086	0.1189	-0.0589	-0.0124	-0.0581	0.0891	0.3074	-0.1978	-0.0505	0.0995	-0.0095	-0.025	0.0058	-0.005	0.0415	19.1325	22.8123	18.5619
5	5.6141	0.002	-2.5065	2.085	-0.4828	5.8381	0.0143	-0.039	-0.0406	-0.0104	0.0111	0.1127	0.16	-0.0734	-0.0254	0.1035	0.0003	-0.0172	0.0438	-0.0057	0.0796	19.6615	29.6623	22.4517
6	1.6921	-0.2299	-0.7376	1.3066	0.8332	2.5418	-0.0236	0.1098	-0.0462	-0.1069	-0.0197	0.0602	0.1009	-0.0704	0.0434	0.0622	-0.0025	-0.0079	0.0383	0.0036	0.0388	16.4522	33.355	14.953
7	11.5164	-0.3607	-1.5486	0.7728	0.4594	1.8803	-0.0209	-0.3412	-0.0284	0.0453	0.0265	-0.1508	-0.0375	0.3692	-0.0056	0.016	-0.0225	-0.0116	0.0763	0.009	0.0541	32.322	37.7649	26.33
8	1.1368	-1.9107	1.4571	4.3631	-2.9404	2.2909	-0.0036	0.1125	0.1355	0.0046	-0.0132	-0.1101	-0.3132	0.2667	0.0168	0.062	-0.0547	0.0101	0.0519	0.0273	0.0249	25.0762	45.151	14.7872
9	0.5637	-1.3646	-0.1506	6.2442	2.4082	2.8314	0.0728	0.1149	0.0556	-0.424	-0.1437	-0.0966	-0.2424	0.0054	0.0709	0.1051	-0.0254	0.0138	0.0189	0.0277	0.0104	19.8468	43.2297	9.1189
10	2.0316	1.2007	1.8094	3.846	-0.2195	5.8021	-0.0634	0.0002	0.1467	0.3705	-0.0895	-0.0208	-0.5437	0.0787	0.1529	0.1152	-0.0282	-0.0109	-0.0273	0.0083	0.0301	20.3462	48.7408	25.2778
11	2.518	-1.0655	0.7412	2.2094	-0.1334	6.3906	0.0411	0.3105	-0.0558	-0.4632	-0.0865	0.1282	-0.1279	-0.3512	0.0454	0.0781	-0.0024	-0.0206	0.055	0.0062	0.0484	13.0938	41.2402	12.6317
12	2.828	-0.399	2.9107	0.4972	-1.6732	6.6105	-0.0414	0.0865	0.1345	0.1035	-0.1133	-0.1126	-0.204	0.5364	0.1546	0.0637	-0.0381	-0.0132	0.0277	-0.0086	0.0368	27.2296	41.3308	34.5037
13	4.8162	-0.2617	4.6554	0.6336	0.6315	5.7838	-0.116	-0.2311	0.1672	0.0762	-0.0444	0.0786	-0.2209	-0.4162	0.1603	0.052	0.0012	0.0013	0.0376	0.0005	0.0329	12.4234	42.3465	32.7587
14	0.9081	-0.1154	0.4758	0.7879	-0.2376	1.9535	0.0083	-0.0584	0.0042	0.0873	0.0117	0.0779	0.0006	-0.1789	-0.02	0.0514	-0.0171	0.0024	0.0328	-0.0012	0.0478	15.3604	33.2057	31.232
15	0.1206	-0.4458	1.7114	6.5709	6.16	55.9768	0.176	-0.4354	-0.3929	-0.6028	0.664	0.0571	2.3662	-0.9001	-0.84	0.158	0.0228	-0.0322	0.1852	0.1365	0.1733	4.5653	30.9194	45.871
16	0.3322	-0.0942	0.5168	1.5713	0.7456	4.5103	0.0353	-0.0549	-0.0114	0.14	0.0679	0.0613	0.352	-0.2377	-0.1032	0.1063	-0.0336	-0.0225	0.0108	0.0115	0.0272	18.0027	22.1231	36.1322
17	3.8167	-1.5674	-0.0237	4.2411	1.0222	3.583	-0.0189	-0.1796	0.0076	0.2227	0.077	-0.031	0.1027	0.0241	-0.0581	0.095	-0.0222	-0.0047	0.0484	0.0074	0.0349	22.3909	32.3189	43.7345
18	17.2668	-8.3811	1.7055	11.0456	-7.43	9.7138	-0.3622	-0.8747	1.0768	0.8289	0.3034	0.0552	-0.6793	-0.699	0.0588	0.0535	0.1126	0.0496	0.0661	-0.0476	0.013	10.1921	41.081	46.1748

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	244 - 254
2	X-RAY DIFFRACTION	2	A	255 - 288
3	X-RAY DIFFRACTION	3	A	289 - 299
4	X-RAY DIFFRACTION	4	A	300 - 312
5	X-RAY DIFFRACTION	5	A	313 - 337
6	X-RAY DIFFRACTION	6	A	338 - 353
7	X-RAY DIFFRACTION	7	A	354 - 366
8	X-RAY DIFFRACTION	8	A	367 - 377
9	X-RAY DIFFRACTION	9	A	378 - 389
10	X-RAY DIFFRACTION	10	A	390 - 401
11	X-RAY DIFFRACTION	11	A	402 - 417
12	X-RAY DIFFRACTION	12	A	418 - 431
13	X-RAY DIFFRACTION	13	A	432 - 448
14	X-RAY DIFFRACTION	14	A	449 - 480
15	X-RAY DIFFRACTION	15	A	481 - 488
16	X-RAY DIFFRACTION	16	A	489 - 505
17	X-RAY DIFFRACTION	17	A	506 - 520
18	X-RAY DIFFRACTION	18	A	521 - 525

-
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