PDB-1wbb: Crystal structure of E. coli DNA mismatch repair enzyme MutS, E38...

ID or keywords:

Entry

Database: PDB / ID: 1wbb

Title

Crystal structure of E. coli DNA mismatch repair enzyme MutS, E38A mutant, in complex with a G.T mismatch

Components

5'-D(*AP*CP*TP*GP*GP*TP*GP*CP*TP*TP *GP*GP*CP*AP*GP*CP*T)-3'
5'-D(*AP*GP*CP*TP*GP*CP*CP*AP*GP*GP *CP*AP*CP*CP*AP*GP*TP*G)-3'
DNA MISMATCH REPAIR PROTEIN MUTS

Keywords

DNA-BINDING / ATP-BINDING / DNA BINDING / DNA REPAIR / MISMATCH RECOGNITION

Function / homology

Function and homology information

adenine/cytosine mispair binding / MutS complex / mismatch repair complex / regulation of DNA recombination / mismatched DNA binding / DNA binding, bending / ATP-dependent DNA damage sensor activity / mismatch repair / ADP binding / damaged DNA binding ...
Similarity search - Function

Biological species

ESCHERICHIA COLI (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.5 Å

Authors

Natrajan, G. / Georgijevic, D. / Lebbink, J.H.G. / Winterwerp, H.H.K. / de Wind, N. / Sixma, T.K.

Citation

Journal: Embo J. / Year: 2006
Title: Dual Role of Muts Glutamate 38 in DNA Mismatch Discrimination and in the Authorization of Repair.
Authors: Lebbink, J.H.G. / Georgijevic, D. / Natrajan, G. / Fish, A. / Winterwerp, H.H.K. / Sixma, T.K. / De Wind, N.

History

Deposition	Oct 31, 2004	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jan 18, 2006	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Dec 13, 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 / pdbx_struct_conn_angle / struct_conn 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	1wbb.cif.gz	332.3 KB	Display	PDBx/mmCIF format
PDB format	pdb1wbb.ent.gz	265.3 KB	Display	PDB format
PDBx/mmJSON format	1wbb.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	1wbb_validation.pdf.gz	801.3 KB	Display	wwPDB validaton report
Full document	1wbb_full_validation.pdf.gz	823 KB	Display
Data in XML	1wbb_validation.xml.gz	55.7 KB	Display
Data in CIF	1wbb_validation.cif.gz	77.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/wb/1wbb ftp://data.pdbj.org/pub/pdb/validation_reports/wb/1wbb	HTTPS FTP

-
Related structure data

Related structure data	1wb9C 1wbdC 1e3mS 1ng9 1oh5 1oh6 1oh7 1oh8 1w7a S: Starting model for refinement C: citing same article (ref.)
Similar structure data	1wb9-d 1oh7-d 1e3m-d 2wtu-d 1w7a-d 3zlj-1 1wbd-d 1oh8-d 1oh6-d 1ng9-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
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) #122 - Feb 2010 Enhanceosome similarity (1) #172 - Apr 2014 RecA and Rad51 similarity (1) #181 - Jan 2015 Cascade and CRISPR similarity (1) #253 - Jan 2021 Expressome similarity (1) #112 - Apr 2009 Oct and Sox Transcription Factors 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) #84 - Dec 2006 Transposase similarity (1) #139 - Jul 2011 DNA Methyltransferase similarity (1) #155 - Nov 2012 Vitamin D Receptor similarity (1) #3 - Mar 2000 DNA Polymerase similarity (1) #40 - Apr 2003 RNA Polymerase similarity (1) #73 - Jan 2006 Topoisomerase similarity (1) #87 - Mar 2007 Zinc Fingers similarity (1) #119 - Nov 2009 Designed DNA Crystal similarity (1) #125 - May 2010 Parvoviruses similarity (1) #131 - Nov 2010 Inteins similarity (1) #160 - Apr 2013 Actinomycin similarity (1) #190 - Oct 2015 Two-component Systems similarity (1) #23 - Nov 2001 DNA similarity (1) #240 - Dec 2019 Hypoxia-Inducible Factors similarity (1) #257 - May 2021 Fetal Hemoglobin similarity (1) #258 - Jun 2021 Glucocorticoid Receptor and Dexamethasone similarity (1) #31 - Jul 2002 p53 Tumor Suppressor similarity (1) #33 - Sep 2002 HIV Reverse Transcriptase similarity (1) #39 - Mar 2003 lac Repressor similarity (1) #45 - Sep 2003 Estrogen Receptor similarity (1) #55 - Jul 2004 DNA Ligase similarity (1) #7 - Jul 2000 Nucleosome similarity (1) #8 - Aug 2000 Restriction Enzymes similarity (1) #92 - Aug 2007 Anabolic Steroids similarity (1) #241 - Jan 2020 Twenty Years of Molecules 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)
#122 - Feb 2010
Enhanceosome
similarity (1)
#172 - Apr 2014
RecA and Rad51
similarity (1)
#181 - Jan 2015
Cascade and CRISPR
similarity (1)
#253 - Jan 2021
Expressome
similarity (1)
#112 - Apr 2009
Oct and Sox Transcription Factors
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)
#84 - Dec 2006
Transposase
similarity (1)
#139 - Jul 2011
DNA Methyltransferase
similarity (1)
#155 - Nov 2012
Vitamin D Receptor
similarity (1)
#3 - Mar 2000
DNA Polymerase
similarity (1)
#40 - Apr 2003
RNA Polymerase
similarity (1)
#73 - Jan 2006
Topoisomerase
similarity (1)
#87 - Mar 2007
Zinc Fingers
similarity (1)
#119 - Nov 2009
Designed DNA Crystal
similarity (1)
#125 - May 2010
Parvoviruses
similarity (1)
#131 - Nov 2010
Inteins
similarity (1)
#160 - Apr 2013
Actinomycin
similarity (1)
#190 - Oct 2015
Two-component Systems
similarity (1)
#23 - Nov 2001
DNA
similarity (1)
#240 - Dec 2019
Hypoxia-Inducible Factors
similarity (1)
#257 - May 2021
Fetal Hemoglobin
similarity (1)
#258 - Jun 2021
Glucocorticoid Receptor and Dexamethasone
similarity (1)
#31 - Jul 2002
p53 Tumor Suppressor
similarity (1)
#33 - Sep 2002
HIV Reverse Transcriptase
similarity (1)
#39 - Mar 2003
lac Repressor
similarity (1)
#45 - Sep 2003
Estrogen Receptor
similarity (1)
#55 - Jul 2004
DNA Ligase
similarity (1)
#7 - Jul 2000
Nucleosome
similarity (1)
#8 - Aug 2000
Restriction Enzymes
similarity (1)
#92 - Aug 2007
Anabolic Steroids
similarity (1)
#241 - Jan 2020
Twenty Years of Molecules
similarity (1)

Deposited unit

A: DNA MISMATCH REPAIR PROTEIN MUTS

B: DNA MISMATCH REPAIR PROTEIN MUTS

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

F: 5'-D(*AP*CP*TP*GP*GP*TP*GP*CP*TP*TP *GP*GP*CP*AP*GP*CP*T)-3'

hetero molecules

190 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)	89.553, 92.494, 261.264
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

-
Protein , 1 types, 2 molecules AB

#1: Protein	DNA MISMATCH REPAIR PROTEIN MUTS Mass: 89546.320 Da / Num. of mol.: 2 / Fragment: RESIDUES 1-800 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Plasmid: PM800 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834 (BL21) / Variant (production host): PLYSS / References: UniProt: P23909

#1: Protein

DNA MISMATCH REPAIR PROTEIN MUTS

Mass: 89546.320 Da / Num. of mol.: 2 / Fragment: RESIDUES 1-800 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

ESCHERICHIA COLI (E. coli) / Plasmid: PM800 / Production host:

ESCHERICHIA COLI (E. coli) / Strain (production host): B834 (BL21) / Variant (production host): PLYSS / References: UniProt: P23909

-
DNA chain , 2 types, 2 molecules EF

#2: DNA chain	5'-D(APGPCPTPGPCPCPAPGPGP CPAPCPCPAPGPTPG)-3' Mass: 5526.581 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: G\:T MISMATCH DNA
#3: DNA chain	5'-D(APCPTPGPGPTPGPCPTPTP GPGPCPAPGPCPT)-3' Mass: 5234.382 Da / Num. of mol.: 1 / Source method*: obtained synthetically

-
Non-polymers , 3 types, 287 molecules

#4: Chemical	ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₀H₁₅N₅O₁₀P₂ / Comment: ADP, energy-carrying molecule*YM
#5: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 285 / Source method: isolated from a natural source / Formula: H₂O

-
Details

Compound details	ENGINEERED RESIDUES CHAINS A AND B, GLU 38 ALA

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.6 Å³/Da / Density % sol: 56.2 %
Crystal grow	pH: 7.5 Details: 25 MM HEPES(7.5), 300 MM NACL, 10 MM MGCL2, 14 % PEG 6000., pH 7.50

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.93
Detector	Type: ADSC CCD / Detector: CCD / Date: Nov 24, 2002 / Details: SAGITAL FOCUSSING GE (220) AND MULTILAYER.
Radiation	Monochromator: DIAMOND (111), GE (220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.93 Å / Relative weight: 1
Reflection	Resolution: 2.5→20 Å / Num. obs: 75289 / % possible obs: 99.3 % / Redundancy: 3.12 % / B_iso Wilson estimate: 53.02 Å² / R_merge(I) obs: 0.11 / Net I/σ(I): 9.81
Reflection shell	Resolution: 2.5→2.59 Å / Redundancy: 3.06 % / R_merge(I) obs: 0.72 / Mean I/σ(I) obs: 1.48 / % possible all: 98.3

-
Processing

Software

Name	Version	Classification
REFMAC	5.1.24	refinement
DENZO		data reduction
SCALEPACK		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1E3M

1e3m

Resolution: 2.5→20 Å / Cor.coef. F_o:F_c: 0.934 / Cor.coef. F_o:F_c free: 0.898 / SU B: 11.618 / SU ML: 0.246 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.439 / ESU R Free: 0.288 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.27	1452	1.9 %	SAME AS FOR ENTRY 1E3M
R_work	0.22	-	-	-
obs	0.221	73763	99.3 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 18.08 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-2.169 Å²	0 Å²	0 Å²
2-	-	4.915 Å²	0 Å²
3-	-	-	-2.746 Å²

Refinement step

Cycle: LAST / Resolution: 2.5→20 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	12163	714	28	285	13190

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.021	13200
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	11955
X-RAY DIFFRACTION	r_angle_refined_deg	1.225	2.044	18018
X-RAY DIFFRACTION	r_angle_other_deg	0.799	3	27736
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.067	5	1536
X-RAY DIFFRACTION	r_dihedral_angle_2_deg
X-RAY DIFFRACTION	r_dihedral_angle_3_deg
X-RAY DIFFRACTION	r_dihedral_angle_4_deg
X-RAY DIFFRACTION	r_chiral_restr	0.064	0.2	2012
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	14142
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	2512
X-RAY DIFFRACTION	r_nbd_refined	0.19	0.2	2700
X-RAY DIFFRACTION	r_nbd_other	0.216	0.2	13825
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other	0.084	0.2	8174
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.152	0.2	310
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	0.22	0.2	24
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.216	0.2	112
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.162	0.2	5
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	0.352	1.5	7676
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	0.673	2	12327
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	1.041	3	5524
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	1.763	4.5	5691
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: 2.5→2.56 Å / Total num. of bins used: 10 /

	R_factor	Num. reflection
R_free	0.367	99
R_work	0.309	5238

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	3.3665	-0.6675	0.9725	3.2067	-0.0381	3.4547	0.0773	-0.0629	-0.0237	-0.0397	0.0071	0.1484	-0.0091	-0.0304	-0.0844	0.2392	-0.018	0.0201	0.1741	0.0171	0.1879	95.744	82.316	33.858
2	2.9339	0.5863	-0.7067	1.8845	0.0304	1.4724	0.0642	0.1274	-0.0618	-0.1072	0.0274	0.0791	0.0026	0.1095	-0.0916	0.1475	0.0163	-0.0182	0.099	-0.0014	0.1986	121.35	83.495	18.899
3	1.2821	-0.2093	-1.0058	1.2183	0.9897	2.3782	0.0325	-0.2007	-0.1825	0.1607	0.0853	-0.1436	0.1139	0.0681	-0.1178	0.235	0.0109	-0.036	0.2211	0.0477	0.2827	135.084	71.163	32.805
4	4.5033	-2.9273	-3.4967	3.5696	4.3965	3.7476	-0.4245	-0.2327	-0.1123	0.0998	0.5612	-0.0357	0.4281	0.4678	-0.1367	0.253	0.0346	-0.0605	0.2316	0.0494	0.2101	142.748	64.009	32.087
5	3.728	1.3102	0.5419	4.9995	0.8123	10.2921	-0.1246	0.048	-0.1058	0.082	0.2811	-0.1068	-0.1984	0.4562	-0.1565	0.2824	0.0572	0.014	0.1689	-0.0424	0.1578	92.436	75.751	77.028
6	3.4105	-0.9384	-2.4731	1.8152	1.2425	3.2201	0.0247	-0.7152	0.389	0.4364	0.0976	0.0754	0.0926	0.2331	-0.1224	0.415	-0.0131	-0.0588	0.4838	-0.0196	0.2876	126.277	83.376	54.101
7	1.4752	-0.4072	-2.7779	0.2166	0.3605	1.711	0.2803	0.0107	0.3838	0.1807	-0.0167	0.0608	-0.2209	-0.0972	-0.2635	0.4025	-0.0634	0.0443	0.4969	-0.0762	0.3568	116.276	87.724	54.896
8	1.1173	0.3453	0.5659	1.0802	1.1075	2.5458	0.0464	-0.0947	0.0042	-0.0191	0.0244	-0.0745	0.0249	-0.1126	-0.0708	0.1822	-0.0033	0.0322	0.0742	-0.0016	0.3034	140.276	58.248	5.339
9	1.3922	-2.2606	1.8825	4.094	0.9477	5.4016	0.2159	-0.3257	-0.5915	0.6763	-0.2107	0.271	0.784	0.3804	-0.0052	0.335	0.0401	0.016	0.1279	-0.0263	0.5147	143.624	41.089	5.85
10	7.9112	2.278	-2.8345	6.4187	-2.0649	6.9707	-0.1669	-0.1465	-0.4632	-0.066	0.1634	-0.5399	0.3053	0.2365	0.0036	0.1505	0.1046	-0.0357	0.08	0.002	0.3033	133.577	32.477	-5.013
11	4.9885	1.6637	-0.0049	3.8561	1.4571	4.4839	0.3451	-0.5228	0.2494	0.6263	-0.2154	-0.4216	-0.7208	0.6432	-0.1297	0.5807	-0.1936	0.0114	0.4041	-0.0024	0.4278	106.183	48.144	43.639
12	2.2822	0.5958	-0.2087	2.991	0.8773	2.62	-0.0429	0.0232	-0.1743	-0.0519	0.1178	-0.3799	0.2838	0.3601	-0.0749	0.2538	0.023	0.011	0.1797	0.0183	0.218	101.618	27.416	25.963
13	1.482	-0.0832	-1.3644	0.7276	0.014	2.3719	0.0543	-0.0279	0.0386	-0.0362	-0.0163	-0.0033	-0.1037	0.0517	-0.038	0.2367	0.0035	-0.0021	0.0835	0.037	0.229	87.115	40.798	13.671
14	4.686	4.0139	-4.387	1.621	-2.7945	11.8593	0.1205	0.2076	0.1665	-0.0919	-0.0551	0.1284	-0.1509	-0.493	-0.0655	0.1573	0.107	0.0084	0.0915	0.0217	0.1821	85.406	43.716	3.818
15	4.7865	3.3224	-1.0751	8.6492	1.2379	3.4585	-0.0389	-0.134	0.0092	0.0822	-0.136	0.4018	-0.1515	-0.425	0.1749	0.3348	0.0607	-0.0359	0.4056	-0.0289	0.2188	72.28	73.903	61.731
16	2.3749	-1.4764	-1.9218	2.1664	4.0878	7.614	-0.0427	-0.1321	-0.1076	0.1077	-0.2586	0.2525	0.0614	-0.6561	0.3013	0.3073	-0.0328	0.032	0.1294	0.0922	0.288	70.361	44.295	33.65
17	1.1715	-0.749	-0.9158	2.2145	1.7078	1.8474	-0.1485	-0.1855	0.0663	0.6004	-0.0318	0.1732	0.4912	-0.1407	0.1803	0.362	-0.0235	0.0194	0.2595	0.0163	0.2686	73.356	44.822	43.879
18	5.6085	-0.2629	-0.7604	0.238	-0.2048	0.9526	0.0347	0.0153	-0.1503	-0.0308	0.0015	-0.071	-0.0168	0.0182	-0.0362	0.1981	0.0136	0.0109	0.008	0.0266	0.219	110.077	37.831	-6.809
19	2.0978	0.3599	-0.992	27.7252	1.2382	-1.4585	-0.1506	0.1711	0.599	0.2699	0.232	0.302	-0.0291	0.0243	-0.0814	0.2563	0.0304	-0.0133	0.2557	0.0167	0.296	111.971	52.542	-16.381
20	4.4128	2.735	1.1662	7.458	4.4597	4.759	-0.1367	-0.0106	0.295	-0.6158	0.1867	-0.1549	-0.2735	0.2684	-0.05	0.2262	0.0471	0.0335	0.1101	0.0842	0.1778	129.06	57.679	-16.31
21	1.7847	1.0517	-0.7246	2.2977	-1.8376	5.6939	-0.0117	0.0817	0.1088	0.2694	0.1417	0.5831	-0.131	-0.4068	-0.13	0.3759	-0.0675	0.0055	0.3386	0.0097	0.2849	85.296	77.925	51.13

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	2 - 115
2	X-RAY DIFFRACTION	2	A	116 - 265
3	X-RAY DIFFRACTION	3	A	266 - 387
4	X-RAY DIFFRACTION	4	A	550 - 567
5	X-RAY DIFFRACTION	5	A	444 - 503
6	X-RAY DIFFRACTION	6	A	388 - 443
7	X-RAY DIFFRACTION	7	A	504 - 549
8	X-RAY DIFFRACTION	8	A	568 - 741
9	X-RAY DIFFRACTION	8	A	1801
10	X-RAY DIFFRACTION	8	A	1802
11	X-RAY DIFFRACTION	9	A	742 - 765
12	X-RAY DIFFRACTION	10	A	766 - 800
13	X-RAY DIFFRACTION	11	B	14 - 115
14	X-RAY DIFFRACTION	12	B	116 - 265
15	X-RAY DIFFRACTION	13	B	266 - 387
16	X-RAY DIFFRACTION	14	B	550 - 567
17	X-RAY DIFFRACTION	15	B	444 - 503
18	X-RAY DIFFRACTION	16	B	388 - 443
19	X-RAY DIFFRACTION	17	B	504 - 549
20	X-RAY DIFFRACTION	18	B	568 - 741
21	X-RAY DIFFRACTION	19	B	742 - 765
22	X-RAY DIFFRACTION	20	B	766 - 800
23	X-RAY DIFFRACTION	21	E	1 - 18
24	X-RAY DIFFRACTION	21	F	14 - 30

-
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

-
Protein , 1 types, 2 molecules AB

-
DNA chain , 2 types, 2 molecules EF

-
Non-polymers , 3 types, 287 molecules

-
Details

-
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, 2 molecules AB

-DNA chain , 2 types, 2 molecules EF

-Non-polymers , 3 types, 287 molecules

-Details

-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, 2 molecules AB

-
DNA chain , 2 types, 2 molecules EF

-
Non-polymers , 3 types, 287 molecules

-
Details

-
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