PDB-1ng9: E.coli MutS R697A: an ATPase-asymmetry mutant

ID or keywords:

Entry

Database: PDB / ID: 1ng9

Title

E.coli MutS R697A: an ATPase-asymmetry mutant

Components

5'-D(*AP*GP*CP*TP*GP*CP*CP*AP*GP*GP*CP*AP*CP*CP*AP*GP*TP*GP*TP*CP*AP*GP*CP*GP*TP*CP*CP*TP*AP*T)-3'
5'-D(*AP*TP*AP*GP*GP*AP*CP*GP*CP*TP*GP*AP*CP*AP*CP*TP*GP*GP*TP*GP*CP*TP*TP*GP*GP*CP*AP*GP*CP*T)-3'
DNA mismatch repair protein MutS

Keywords

DNA BINDING PROTEIN / ABC ATPase / alternating ATPase /

asymmetry /

DNA repair /

DNA binding

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: 2.6 Å

Authors

Lamers, M.H. / Winterwerp, H.H.K. / Sixma, T.K.

Citation

Journal: Embo J. / Year: 2003
Title: The alternating ATPase domains of MutS control DNA mismatch repair
Authors: Lamers, M.H. / Winterwerp, H.H.K. / Sixma, T.K.

History

Deposition	Dec 17, 2002	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 11, 2003	Provider: repository / Type: Initial release
Revision 1.1	Apr 29, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.3	Oct 27, 2021	Group: Database references / Derived calculations Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _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.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.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4	Aug 16, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	1ng9.cif.gz	337.1 KB	Display	PDBx/mmCIF format
PDB format	pdb1ng9.ent.gz	267.9 KB	Display	PDB format
PDBx/mmJSON format	1ng9.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ng/1ng9 ftp://data.pdbj.org/pub/pdb/validation_reports/ng/1ng9	HTTPS FTP

-
Related structure data

Related structure data	1e3mS 1ewq 1ewr 1fw6 S: Starting model for refinement
Similar structure data	1wb9-d 1w7a-d 1oh7-d 1wbb-d 1oh8-d 2wtu-d 1wbd-d 1e3m-d 3zlj-1 2o8e-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) #91 - Jul 2007 Thymine Dimers similarity (1) #255 - Mar 2021 Cisplatin and DNA similarity (1) #168 - Dec 2013 DNA Helicase similarity (1) #253 - Jan 2021 Expressome similarity (1) #172 - Apr 2014 RecA and Rad51 similarity (1) #122 - Feb 2010 Enhanceosome similarity (1) #181 - Jan 2015 Cascade and CRISPR similarity (1) #84 - Dec 2006 Transposase similarity (1) #48 - Dec 2003 Catabolite Activator Protein similarity (1) #227 - Nov 2018 Telomerase similarity (1) #112 - Apr 2009 Oct and Sox Transcription Factors similarity (1) #150 - Jun 2012 Sliding Clamps similarity (1) #180 - Dec 2014 TAL Effectors similarity (1) #135 - Mar 2011 Integrase similarity (1) #40 - Apr 2003 RNA Polymerase similarity (1) #155 - Nov 2012 Vitamin D Receptor similarity (1) #87 - Mar 2007 Zinc Fingers similarity (1) #73 - Jan 2006 Topoisomerase similarity (1) #3 - Mar 2000 DNA Polymerase similarity (1) #139 - Jul 2011 DNA Methyltransferase similarity (1) #125 - May 2010 Parvoviruses similarity (1) #131 - Nov 2010 Inteins similarity (1) #8 - Aug 2000 Restriction Enzymes similarity (1) #7 - Jul 2000 Nucleosome similarity (1) #55 - Jul 2004 DNA Ligase similarity (1) #45 - Sep 2003 Estrogen Receptor similarity (1) #33 - Sep 2002 HIV Reverse Transcriptase similarity (1) #39 - Mar 2003 lac Repressor similarity (1) #160 - Apr 2013 Actinomycin 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) #119 - Nov 2009 Designed DNA Crystal similarity (1) #240 - Dec 2019 Hypoxia-Inducible Factors similarity (1) #23 - Nov 2001 DNA similarity (1) #190 - Oct 2015 Two-component Systems 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)
#91 - Jul 2007
Thymine Dimers
similarity (1)
#255 - Mar 2021
Cisplatin and DNA
similarity (1)
#168 - Dec 2013
DNA Helicase
similarity (1)
#253 - Jan 2021
Expressome
similarity (1)
#172 - Apr 2014
RecA and Rad51
similarity (1)
#122 - Feb 2010
Enhanceosome
similarity (1)
#181 - Jan 2015
Cascade and CRISPR
similarity (1)
#84 - Dec 2006
Transposase
similarity (1)
#48 - Dec 2003
Catabolite Activator Protein
similarity (1)
#227 - Nov 2018
Telomerase
similarity (1)
#112 - Apr 2009
Oct and Sox Transcription Factors
similarity (1)
#150 - Jun 2012
Sliding Clamps
similarity (1)
#180 - Dec 2014
TAL Effectors
similarity (1)
#135 - Mar 2011
Integrase
similarity (1)
#40 - Apr 2003
RNA Polymerase
similarity (1)
#155 - Nov 2012
Vitamin D Receptor
similarity (1)
#87 - Mar 2007
Zinc Fingers
similarity (1)
#73 - Jan 2006
Topoisomerase
similarity (1)
#3 - Mar 2000
DNA Polymerase
similarity (1)
#139 - Jul 2011
DNA Methyltransferase
similarity (1)
#125 - May 2010
Parvoviruses
similarity (1)
#131 - Nov 2010
Inteins
similarity (1)
#8 - Aug 2000
Restriction Enzymes
similarity (1)
#7 - Jul 2000
Nucleosome
similarity (1)
#55 - Jul 2004
DNA Ligase
similarity (1)
#45 - Sep 2003
Estrogen Receptor
similarity (1)
#33 - Sep 2002
HIV Reverse Transcriptase
similarity (1)
#39 - Mar 2003
lac Repressor
similarity (1)
#160 - Apr 2013
Actinomycin
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)
#119 - Nov 2009
Designed DNA Crystal
similarity (1)
#240 - Dec 2019
Hypoxia-Inducible Factors
similarity (1)
#23 - Nov 2001
DNA
similarity (1)
#190 - Oct 2015
Two-component Systems
similarity (1)
#92 - Aug 2007
Anabolic Steroids
similarity (1)
#241 - Jan 2020
Twenty Years of Molecules
similarity (1)

Deposited unit

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

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

A: DNA mismatch repair protein MutS

B: DNA mismatch repair protein MutS

hetero molecules

198 kDa, 4 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)	89.902, 92.404, 261.593
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Details

One MutS homodimer binds to one DNA oligo

-
DNA chain , 2 types, 2 molecules EF

#1: DNA chain	5'-D(APGPCPTPGPCPCPAPGPGPCPAPCPCPAPGPTPGPTPCPAPGPCPGPTPCPCPTPAPT)-3' Mass: 9184.905 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain	5'-D(APTPAPGPGPAPCPGPCPTPGPAPCPAPCPTPGPGPTPGPCPTPTPGPGPCPAPGPCPT)-3' Mass: 9279.964 Da / Num. of mol.: 1 / Source method: obtained synthetically

-
Protein , 1 types, 2 molecules AB

#3: Protein	DNA mismatch repair protein MutS / Mass: 89518.242 Da / Num. of mol.: 2 / Fragment: residues 1-800 / Mutation: R697A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: MutS / Plasmid: pET3D / Production host: Escherichia coli (E. coli) / Strain (production host): E.coli B834 (DE3) pLysS / References: UniProt: P23909

#3: Protein

DNA mismatch repair protein MutS /

Mass: 89518.242 Da / Num. of mol.: 2 / Fragment: residues 1-800 / Mutation: R697A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Escherichia coli (E. coli) / Gene: MutS / Plasmid: pET3D / Production host:

Escherichia coli (E. coli) / Strain (production host): E.coli B834 (DE3) pLysS / References: UniProt: P23909

-
Non-polymers , 3 types, 368 molecules

#4: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical	ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₀H₁₅N₅O₁₀P₂ / Comment: ADP, energy-carrying molecule*YM
#6: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 364 / 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: 2.89 Å³/Da / Density % sol: 57.13 %

Crystal grow

Temperature: 297 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 6000, NaCl, MgCl2, HEPES, ADP, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 297K

Components of the solutions

ID	Name	Crystal-ID	Sol-ID
1	PEG 6000	1	1
2	NaClSodium chloride	1	1
3	MgCl2	1	1
4	HEPES	1	1
5	ADPAdenosine diphosphate	1	1
6	water	1	1
7	NaClSodium chloride	1	2
8	MgCl2	1	2
9	PEG 6000	1	2

Crystal grow

*PLUS

Details: Lamers, M.H., (2000) Nature, 407, 711., used microseeding

Components of the solutions

*PLUS

ID	Conc.	Common name	Crystal-ID	Sol-ID	Chemical formula
1	14 mg/ml	protein	1	drop
2	25 mM	HEPES	1	drop
3	250 mM		1	drop	NaCl
4	10-20 mM	beta-mercaptoethanol	1	drop
5	12-14 %	PEG6000	1	reservoir
6	150-300 mM		1	reservoir	NaCl
7	100 mM	HEPES	1	reservoir
8	10 mM		1	reservoir	MgCl2
9	0.100-0.150 mM	ADP	1	reservoir

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
Detector	Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 3, 2002 / Details: mirrors
Radiation	Monochromator: Diamond (111), Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.933 Å / Relative weight: 1
Reflection	Resolution: 2.6→30 Å / Num. all: 66737 / Num. obs: 66708 / % possible obs: 98.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1.1 / Redundancy: 3.5 % / B_iso Wilson estimate: 57.1 Å² / R_merge(I) obs: 0.124 / R_sym value: 0.124 / Net I/σ(I): 4.6
Reflection shell	Resolution: 2.6→2.74 Å / Redundancy: 3.5 % / R_merge(I) obs: 0.657 / Mean I/σ(I) obs: 1.1 / Num. unique all: 9717 / R_sym value: 0.657 / % possible all: 98.7
Reflection	PLUS Lowest resolution*: 30 Å
Reflection shell	PLUS Highest resolution: 2.6 Å / % possible obs*: 99.1 %

-
Processing

Software

Name	Version	Classification
MOSFLM		data reduction
SCALA		data scaling
MOLREP		phasing
REFMAC	5.1.19	refinement
CCP4	(SCALA)	data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1E3M

1e3m

Resolution: 2.6→20 Å / Cor.coef. F_o:F_c: 0.932 / Cor.coef. F_o:F_c free: 0.908 / SU B: 12.627 / SU ML: 0.254 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: TLS / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.61 / ESU R Free: 0.297 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.24892	1283	1.9 %	RANDOM
R_work	0.21497	-	-	-
all	0.21565	67769	-	-
obs	0.21565	65273	98.21 %	-

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: 10.362 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-4.67 Å²	0 Å²	0 Å²
2-	-	9.14 Å²	0 Å²
3-	-	-	-4.47 Å²

Refinement step

Cycle: LAST / Resolution: 2.6→20 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	12286	714	56	364	13420

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.021	13363
X-RAY DIFFRACTION	r_bond_other_d	0.003	0.02	12072
X-RAY DIFFRACTION	r_angle_refined_deg	1.133	2.046	18243
X-RAY DIFFRACTION	r_angle_other_deg	0.792	3	28017
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.82	5	1554
X-RAY DIFFRACTION	r_dihedral_angle_2_deg
X-RAY DIFFRACTION	r_chiral_restr	0.06	0.2	2037
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	14294
X-RAY DIFFRACTION	r_gen_planes_other	0.008	0.02	2529
X-RAY DIFFRACTION	r_nbd_refined	0.182	0.2	2802
X-RAY DIFFRACTION	r_nbd_other	0.21	0.2	14240
X-RAY DIFFRACTION	r_nbtor_other	0.082	0.2	7937
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.193	0.2	378
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.126	0.2	36
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.236	0.2	140
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.146	0.2	6
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_mcbond_it	0.273	1.5	7765
X-RAY DIFFRACTION	r_mcangle_it	0.523	2	12473
X-RAY DIFFRACTION	r_scbond_it	0.995	3	5598
X-RAY DIFFRACTION	r_scangle_it	1.381	4.5	5770
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.6→2.666 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.42	86	-
R_work	0.338	4770	-
obs	-	-	98.94 %

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	4.5068	-0.4609	-0.84	3.6135	-0.3079	4.8952	0.0273	0.113	-0.2176	-0.1641	-0.0334	-0.2997	0.2328	0.0295	0.0062	0.7555	-0.0187	-0.0134	0.3072	-0.0359	0.6341	38.834	10.122	33.883
2	4.365	0.7958	0.066	2.5598	0.1162	1.577	0.0752	0.1753	0.0388	-0.1825	0.076	-0.0896	-0.0071	-0.108	-0.1511	0.7138	-0.0057	0.006	0.1528	0.0027	0.6249	13.124	8.967	18.857
3	1.4442	-0.4989	1.4827	0.8448	-0.6273	2.6537	0.1088	-0.4626	0.1889	0.051	0.0411	0.1166	-0.0762	-0.1707	-0.1499	0.7459	-0.0548	0.0366	0.3902	-0.0539	0.6997	-0.468	21.288	32.869
4	3.3949	-1.3868	2.2928	-0.0278	-1.5151	5.2238	-0.3818	-0.5456	0.0362	0.1601	0.3831	0.2647	-0.528	-0.3398	-0.0012	0.7835	-0.0095	0.0503	0.395	-0.0221	0.6555	-8.078	28.47	32.118
5	2.9822	2.9021	1.0204	7.2658	-0.835	12.8583	0.027	0.1591	0.2775	0.0497	0.2491	0.172	0.1039	-0.7245	-0.2761	0.7321	0.0966	-0.019	0.4164	0.0316	0.5764	41.961	16.869	77.085
6	6.855	-2.2581	3.4896	2.7136	-2.411	4.4749	-0.2149	-1.0274	-0.2094	0.4995	0.2127	-0.0483	-0.0228	-0.316	0.0022	0.9459	-0.0448	0.0684	0.6605	0.0435	0.6021	8.281	9.187	54.154
7	3.7946	-0.0499	3.4583	0.0445	0.2958	2.372	0.6627	-0.3598	-0.3159	0.1346	-0.2644	-0.1531	0.795	-0.1844	-0.3983	0.9156	-0.156	-0.0446	0.7409	0.1057	0.7655	18.266	4.73	54.89
8	1.0587	0.259	-1.1165	1.6458	-0.7318	4.4305	0.0853	-0.0576	0.0819	-0.0419	-0.0338	0.0363	-0.07	0.1725	-0.0515	0.6848	-0.0196	-0.0753	0.1099	-0.014	0.7755	-5.302	34.162	5.209
9	7.5534	5.8844	7.2883	5.1417	4.907	11.9826	-0.1297	-0.402	1.1198	0.1379	-0.1147	0.7438	-1.138	0.0102	0.2443	0.8014	0.0392	0.0724	0.2763	-0.0249	0.9847	-9.138	51.444	6.06
10	10.7977	3.4742	2.4257	4.6828	0.3826	4.2219	-0.4245	-0.7589	0.5191	-0.4449	0.1483	0.6913	0.0023	0.0289	0.2762	0.7827	0.1059	0.0024	0.1939	-0.0114	0.8083	1.025	60.19	-4.9
11	6.8026	2.8552	2.1146	5.3068	1.4566	7.557	0.6965	-1.2388	-0.5674	1.2502	-0.6031	0.36	1.5359	-1.2568	-0.0934	1.3635	-0.3478	-0.0074	0.736	0.0375	0.8278	27.669	44.262	45.059
12	2.8218	0.573	0.419	3.3901	-0.8953	3.5486	0.0899	-0.1612	0.2657	-0.105	0.0048	0.3086	-0.1962	-0.4045	-0.0947	0.7359	0.0189	-0.0053	0.2187	-0.044	0.6226	32.903	65.146	25.88
13	1.6011	-0.0828	1.7535	0.8549	-0.4565	3.1746	0.1185	-0.0191	-0.0928	0.0181	-0.0753	-0.0683	0.2286	0.01	-0.0432	0.7524	0.0161	-0.0092	0.1393	-0.0428	0.6526	47.222	51.54	13.712
14	2.959	0.5245	5.1326	-0.3081	3.6999	18.389	0.2739	0.4493	-0.31	0.0861	0.2886	-0.3701	0.9251	1.2412	-0.5625	0.7597	0.0624	-0.0046	0.1543	-0.0679	0.6082	48.909	48.548	3.889
15	5.1591	3.9653	1.4191	11.9413	-2.7918	3.2739	0.0125	0.0123	-0.1272	-0.0715	-0.3402	-0.3863	-0.0213	0.5811	0.3277	0.8034	0.025	0.059	0.6818	0.0829	0.5899	62.025	18.795	61.936
16	1.9113	-1.2686	1.2787	2.6366	-5.2268	11.0903	0.1732	-0.1431	0.1198	0.1212	-0.3223	-0.0436	-0.0151	0.9087	0.1491	0.8049	-0.0244	-0.0683	0.2888	-0.0711	0.7595	63.858	48.178	33.729
17	1.286	-1.175	1.3657	2.3651	-0.5488	0.143	-0.0516	-0.4569	-0.0267	0.7011	0.0474	-0.1514	-0.561	0.2319	0.0042	0.8506	-0.0721	-0.038	0.5366	0.0275	0.7232	60.842	47.765	43.97
18	6.5175	-0.9028	1.1723	0.9529	0.0649	1.2485	-0.0136	-0.0957	-0.0091	-0.0354	0.0325	0.2112	0.009	-0.0915	-0.0188	0.7152	-0.0093	-0.028	0.0712	-0.021	0.673	24.375	54.576	-6.7
19	1.6039	0.9039	1.3412	30.6755	-1.7951	-0.327	-0.0946	0.2121	-0.6107	0.3201	0.2426	-0.5162	0.2707	-0.0182	-0.1479	0.8161	0.0451	0.0349	0.238	-0.044	0.7978	22.702	39.854	-16.51
20	5.3383	3.2901	-0.7286	9.7739	-5.0119	5.4458	-0.3977	0.1216	-0.2298	-0.6251	0.3666	0.1961	0.3791	-0.162	0.0311	0.828	0.0353	-0.069	0.1477	-0.1128	0.6748	5.489	34.694	-16.182
21	3.0853	2.3331	2.278	-0.476	0.7873	8.6733	-0.1178	-0.1387	-0.4047	0.2378	0.2303	-0.3888	-0.1157	0.6806	-0.1125	0.8703	-0.0736	-0.0322	0.475	-0.0085	0.7175	49.09	14.687	51.254

Refinement TLS group

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

Refinement

*PLUS

Highest resolution: 2.6 Å / Lowest resolution: 30 Å / Num. reflection R_free: 1240 / R_factor R_free: 0.249 / R_factor R_work: 0.215

Solvent computation

*PLUS

Displacement parameters

*PLUS

Refine LS restraints

*PLUS

Refine-ID	Type	Dev ideal
X-RAY DIFFRACTION	r_bond_d	0.01
X-RAY DIFFRACTION	r_angle_d
X-RAY DIFFRACTION	r_angle_deg	1.133

LS refinement shell

*PLUS

Highest resolution: 2.6 Å / Lowest resolution: 2.74 Å

-
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

-
DNA chain , 2 types, 2 molecules EF

-
Protein , 1 types, 2 molecules AB

-
Non-polymers , 3 types, 368 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

-DNA chain , 2 types, 2 molecules EF

-Protein , 1 types, 2 molecules AB

-Non-polymers , 3 types, 368 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

-
DNA chain , 2 types, 2 molecules EF

-
Protein , 1 types, 2 molecules AB

-
Non-polymers , 3 types, 368 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