PDB-3nic: DNA binding and cleavage by the GIY-YIG endonuclease R.Eco29kI in...

ID or keywords:

Entry

Database: PDB / ID: 3nic

Title

DNA binding and cleavage by the GIY-YIG endonuclease R.Eco29kI inactive variant Y49F

Components

DNA (5'-D(P*CP*GP*GP*GP*AP*GP*GP*CP*CP*CP*GP*CP*GP*GP*GP*CP*CP*GP*CP*CP*GP*C)-3')
DNA (5'-D(P*GP*CP*GP*GP*CP*GP*GP*CP*CP*CP*GP*CP*GP*GP*GP*CP*CP*TP*CP*CP*CP*G)-3')
Eco29kIR

Keywords

HYDROLASE/DNA / type II restriction endonuclease / GIY-YIG endonuclease / DNA-bound / HYDROLASE-DNA complex

Function / homology

Restriction endonuclease, type II, Eco29kI / Eco29kI restriction endonuclease / identical protein binding / PHOSPHATE ION / DNA / DNA (> 10) / Eco29kIR

Function and homology information

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.8 Å

Authors

Mak, A.N.S. / Lambert, A.R. / Stoddard, B.L.

Citation

Journal: Structure / Year: 2010
Title: Folding, DNA Recognition, and Function of GIY-YIG Endonucleases: Crystal Structures of R.Eco29kI.
Authors: Mak, A.N. / Lambert, A.R. / Stoddard, B.L.

History

Deposition	Jun 15, 2010	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 8, 2010	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Feb 21, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3	Apr 3, 2024	Group: Refinement description / Category: pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	3nic.cif.gz	871.4 KB	Display	PDBx/mmCIF format
PDB format	pdb3nic.ent.gz	711.6 KB	Display	PDB format
PDBx/mmJSON format	3nic.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	3nic_validation.pdf.gz	586.2 KB	Display	wwPDB validaton report
Full document	3nic_full_validation.pdf.gz	675.8 KB	Display
Data in XML	3nic_validation.xml.gz	78 KB	Display
Data in CIF	3nic_validation.cif.gz	107.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ni/3nic ftp://data.pdbj.org/pub/pdb/validation_reports/ni/3nic	HTTPS FTP

-
Related structure data

Related structure data	3mx1C 3mx4C C: citing same article (ref.)
Similar structure data	3mx4-4 3mx4-3 3zs1-2 4rm2-1 7bjv-1 2qrb-d 4ljj-d 6hli-2 4eb4-2 6q9c-2 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

3mx1C

3mx4C

C: citing same article (ref.)

Similar structure data

-
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: Eco29kIR

B: Eco29kIR

C: Eco29kIR

D: Eco29kIR

E: Eco29kIR

F: Eco29kIR

G: Eco29kIR

H: Eco29kIR

M: DNA (5'-D(P*CP*GP*GP*GP*AP*GP*GP*CP*CP*CP*GP*CP*GP*GP*GP*CP*CP*GP*CP*CP*GP*C)-3')

N: DNA (5'-D(P*GP*CP*GP*GP*CP*GP*GP*CP*CP*CP*GP*CP*GP*GP*GP*CP*CP*TP*CP*CP*CP*G)-3')

I: DNA (5'-D(P*CP*GP*GP*GP*AP*GP*GP*CP*CP*CP*GP*CP*GP*GP*GP*CP*CP*GP*CP*CP*GP*C)-3')

J: DNA (5'-D(P*GP*CP*GP*GP*CP*GP*GP*CP*CP*CP*GP*CP*GP*GP*GP*CP*CP*TP*CP*CP*CP*G)-3')

K: DNA (5'-D(P*CP*GP*GP*GP*AP*GP*GP*CP*CP*CP*GP*CP*GP*GP*GP*CP*CP*GP*CP*CP*GP*C)-3')

L: DNA (5'-D(P*GP*CP*GP*GP*CP*GP*GP*CP*CP*CP*GP*CP*GP*GP*GP*CP*CP*TP*CP*CP*CP*G)-3')

O: DNA (5'-D(P*CP*GP*GP*GP*AP*GP*GP*CP*CP*CP*GP*CP*GP*GP*GP*CP*CP*GP*CP*CP*GP*C)-3')

P: DNA (5'-D(P*GP*CP*GP*GP*CP*GP*GP*CP*CP*CP*GP*CP*GP*GP*GP*CP*CP*TP*CP*CP*CP*G)-3')

hetero molecules

269 kDa, 16 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Eco29kIR

H: Eco29kIR

M: DNA (5'-D(P*CP*GP*GP*GP*AP*GP*GP*CP*CP*CP*GP*CP*GP*GP*GP*CP*CP*GP*CP*CP*GP*C)-3')

N: DNA (5'-D(P*GP*CP*GP*GP*CP*GP*GP*CP*CP*CP*GP*CP*GP*GP*GP*CP*CP*TP*CP*CP*CP*G)-3')

hetero molecules

defined by author&software
67.4 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Eco29kIR

D: Eco29kIR

K: DNA (5'-D(P*CP*GP*GP*GP*AP*GP*GP*CP*CP*CP*GP*CP*GP*GP*GP*CP*CP*GP*CP*CP*GP*C)-3')

L: DNA (5'-D(P*GP*CP*GP*GP*CP*GP*GP*CP*CP*CP*GP*CP*GP*GP*GP*CP*CP*TP*CP*CP*CP*G)-3')

hetero molecules

defined by author&software
67.5 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: Eco29kIR

G: Eco29kIR

I: DNA (5'-D(P*CP*GP*GP*GP*AP*GP*GP*CP*CP*CP*GP*CP*GP*GP*GP*CP*CP*GP*CP*CP*GP*C)-3')

J: DNA (5'-D(P*GP*CP*GP*GP*CP*GP*GP*CP*CP*CP*GP*CP*GP*GP*GP*CP*CP*TP*CP*CP*CP*G)-3')

hetero molecules

defined by author&software
67.2 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

E: Eco29kIR

F: Eco29kIR

O: DNA (5'-D(P*CP*GP*GP*GP*AP*GP*GP*CP*CP*CP*GP*CP*GP*GP*GP*CP*CP*GP*CP*CP*GP*C)-3')

P: DNA (5'-D(P*GP*CP*GP*GP*CP*GP*GP*CP*CP*CP*GP*CP*GP*GP*GP*CP*CP*TP*CP*CP*CP*G)-3')

hetero molecules

defined by author&software
67.4 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	99.870, 101.346, 142.346
Angle α, β, γ (deg.)	90.00, 109.59, 90.00
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS ensembles :

#1: Protein	Eco29kIR / Restriction endonuclease Mass: 26793.996 Da / Num. of mol.: 8 / Mutation: Y49F, L69K Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: 29k / Gene: eco29kIR / Plasmid: pET-15HE / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)/pLysS References: UniProt: Q46944, type II site-specific deoxyribonuclease
#2: DNA chain	DNA (5'-D(PCPGPGPGPAPGPGPCPCPCPGPCPGPGPGPCPCPGPCPCPGPC)-3') Mass: 6781.331 Da / Num. of mol.: 4 / Source method: obtained synthetically
#3: DNA chain	DNA (5'-D(PGPCPGPGPCPGPGPCPCPCPGPCPGPGPGPCPCPTPCPCPCPG)-3') Mass: 6732.292 Da / Num. of mol.: 4 / Source method: obtained synthetically
#4: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: PO₄
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 466 / 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: 2.53 Å³/Da / Density % sol: 51.35 %

Crystal grow

Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.1 M sodium acetate trihydrate, 2M ammonium sulphate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Components of the solutions

ID	Name	Crystal-ID	Sol-ID
1	sodium acetate trihydrate	1	1
2	ammonium sulphate	1	1
3	sodium acetate trihydrate	1	2
4	ammonium sulphate	1	2

-
Data collection

Diffraction	Mean temperature: 110 K
Diffraction source	Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: May 27, 2010
Radiation	Monochromator: single crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.8→50 Å / Num. all: 65980 / Num. obs: 62596 / % possible obs: 99.5 % / Redundancy: 7.4 % / B_iso Wilson estimate: 13.44 Å² / R_merge(I) obs: 0.106 / Net I/σ(I): 18.69
Reflection shell	Resolution: 2.8→2.87 Å / Redundancy: 6.9 % / R_merge(I) obs: 0.345 / Mean I/σ(I) obs: 4.36 / Num. unique all: 6405 / % possible all: 97.7

-
Processing

Software

Name	Version	Classification
ADSC	Quantum	data collection
PHASER		phasing
REFMAC	5.5.0088	refinement
HKL-2000		data reduction
SCALEPACK		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: DNA-bound-L69K-E142Q-R.Eco29kI

Resolution: 2.8→50 Å / Cor.coef. F_o:F_c: 0.951 / Cor.coef. F_o:F_c free: 0.908 / SU B: 34.794 / SU ML: 0.31 / Cross valid method: THROUGHOUT / ESU R Free: 0.417 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.27856	3347	5.1 %	RANDOM
R_work	0.20641	-	-	-
obs	0.20996	62596	99.5 %	-
all	-	65980	-	-

Solvent computation

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

Displacement parameters

B_iso mean: 46.075 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-3.1 Å²	-0 Å²	0.61 Å²
2-	-	-3.51 Å²	-0 Å²
3-	-	-	7.02 Å²

Refinement step

Cycle: LAST / Resolution: 2.8→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	13150	3608	55	466	17279

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.016	0.021	17621
X-RAY DIFFRACTION	r_angle_refined_deg	1.971	2.201	24637
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.224	5	1666
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.971	22.602	665
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	19.836	15	2019
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.813	15	103
X-RAY DIFFRACTION	r_chiral_restr	0.112	0.2	2578
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.021	12563
X-RAY DIFFRACTION	r_mcbond_it	0.64	1.5	8293
X-RAY DIFFRACTION	r_mcangle_it	1.223	2	13227
X-RAY DIFFRACTION	r_scbond_it	1.547	3	9328
X-RAY DIFFRACTION	r_scangle_it	2.486	4.5	11410

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-ID	Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	1	A	797	medium positional	0.32	0.5
1	2	B	797	medium positional	0.32	0.5
1	3	C	797	medium positional	0.29	0.5
1	4	D	797	medium positional	0.33	0.5
1	5	E	797	medium positional	0.33	0.5
1	6	F	797	medium positional	0.35	0.5
1	7	G	797	medium positional	0.33	0.5
1	8	H	797	medium positional	0.31	0.5
2	1	B	797	medium positional	0.32	0.5
2	2	A	797	medium positional	0.32	0.5
2	3	C	797	medium positional	0.29	0.5
2	4	D	797	medium positional	0.33	0.5
2	5	E	797	medium positional	0.33	0.5
2	6	F	797	medium positional	0.35	0.5
2	7	G	797	medium positional	0.33	0.5
2	8	H	797	medium positional	0.31	0.5
3	1	C	797	medium positional	0.29	0.5
3	2	A	797	medium positional	0.32	0.5
3	3	B	797	medium positional	0.32	0.5
3	4	D	797	medium positional	0.33	0.5
3	5	E	797	medium positional	0.33	0.5
3	6	F	797	medium positional	0.35	0.5
3	7	G	797	medium positional	0.33	0.5
3	8	H	797	medium positional	0.31	0.5
4	1	D	797	medium positional	0.33	0.5
4	2	A	797	medium positional	0.32	0.5
4	3	B	797	medium positional	0.32	0.5
4	4	C	797	medium positional	0.29	0.5
4	5	E	797	medium positional	0.33	0.5
4	6	F	797	medium positional	0.35	0.5
4	7	G	797	medium positional	0.33	0.5
4	8	H	797	medium positional	0.31	0.5
5	1	E	797	medium positional	0.33	0.5
5	2	A	797	medium positional	0.32	0.5
5	3	B	797	medium positional	0.32	0.5
5	4	C	797	medium positional	0.29	0.5
5	5	D	797	medium positional	0.33	0.5
5	6	F	797	medium positional	0.35	0.5
5	7	G	797	medium positional	0.33	0.5
5	8	H	797	medium positional	0.31	0.5
6	1	F	797	medium positional	0.35	0.5
6	2	A	797	medium positional	0.32	0.5
6	3	B	797	medium positional	0.32	0.5
6	4	C	797	medium positional	0.29	0.5
6	5	D	797	medium positional	0.33	0.5
6	6	E	797	medium positional	0.33	0.5
6	7	G	797	medium positional	0.33	0.5
6	8	H	797	medium positional	0.31	0.5
7	1	G	797	medium positional	0.33	0.5
7	2	A	797	medium positional	0.32	0.5
7	3	B	797	medium positional	0.32	0.5
7	4	C	797	medium positional	0.29	0.5
7	5	D	797	medium positional	0.33	0.5
7	6	E	797	medium positional	0.33	0.5
7	7	F	797	medium positional	0.35	0.5
7	8	H	797	medium positional	0.31	0.5
8	1	H	797	medium positional	0.31	0.5
8	2	A	797	medium positional	0.32	0.5
8	3	B	797	medium positional	0.32	0.5
8	4	C	797	medium positional	0.29	0.5
8	5	D	797	medium positional	0.33	0.5
8	6	E	797	medium positional	0.33	0.5
8	7	F	797	medium positional	0.35	0.5
8	8	G	797	medium positional	0.33	0.5
9	1	I	453	medium positional	0.49	0.5
9	2	K	453	medium positional	0.55	0.5
9	3	M	453	medium positional	0.45	0.5
9	4	O	453	medium positional	0.53	0.5
10	1	K	453	medium positional	0.55	0.5
10	2	I	453	medium positional	0.49	0.5
10	3	M	453	medium positional	0.45	0.5
10	4	O	453	medium positional	0.53	0.5
11	1	M	453	medium positional	0.45	0.5
11	2	I	453	medium positional	0.49	0.5
11	3	K	453	medium positional	0.55	0.5
11	4	O	453	medium positional	0.53	0.5
12	1	O	453	medium positional	0.53	0.5
12	2	I	453	medium positional	0.49	0.5
12	3	K	453	medium positional	0.55	0.5
12	4	M	453	medium positional	0.45	0.5
13	1	J	449	medium positional	0.59	0.5
13	2	L	449	medium positional	0.62	0.5
13	3	N	449	medium positional	0.59	0.5
13	4	P	449	medium positional	0.58	0.5
14	1	L	449	medium positional	0.62	0.5
14	2	J	449	medium positional	0.59	0.5
14	3	N	449	medium positional	0.59	0.5
14	4	P	449	medium positional	0.58	0.5
15	1	N	449	medium positional	0.59	0.5
15	2	J	449	medium positional	0.59	0.5
15	3	L	449	medium positional	0.62	0.5
15	4	P	449	medium positional	0.58	0.5
16	1	P	449	medium positional	0.58	0.5
16	2	J	449	medium positional	0.59	0.5
16	3	L	449	medium positional	0.62	0.5
16	4	N	449	medium positional	0.59	0.5
1	1	A	797	medium thermal	0.17	2
1	2	B	797	medium thermal	0.2	2
1	3	C	797	medium thermal	0.19	2
1	4	D	797	medium thermal	0.17	2
1	5	E	797	medium thermal	0.17	2
1	6	F	797	medium thermal	0.2	2
1	7	G	797	medium thermal	0.17	2
1	8	H	797	medium thermal	0.17	2
2	1	B	797	medium thermal	0.2	2
2	2	A	797	medium thermal	0.17	2
2	3	C	797	medium thermal	0.19	2
2	4	D	797	medium thermal	0.17	2
2	5	E	797	medium thermal	0.17	2
2	6	F	797	medium thermal	0.2	2
2	7	G	797	medium thermal	0.17	2
2	8	H	797	medium thermal	0.17	2
3	1	C	797	medium thermal	0.19	2
3	2	A	797	medium thermal	0.17	2
3	3	B	797	medium thermal	0.2	2
3	4	D	797	medium thermal	0.17	2
3	5	E	797	medium thermal	0.17	2
3	6	F	797	medium thermal	0.2	2
3	7	G	797	medium thermal	0.17	2
3	8	H	797	medium thermal	0.17	2
4	1	D	797	medium thermal	0.17	2
4	2	A	797	medium thermal	0.17	2
4	3	B	797	medium thermal	0.2	2
4	4	C	797	medium thermal	0.19	2
4	5	E	797	medium thermal	0.17	2
4	6	F	797	medium thermal	0.2	2
4	7	G	797	medium thermal	0.17	2
4	8	H	797	medium thermal	0.17	2
5	1	E	797	medium thermal	0.17	2
5	2	A	797	medium thermal	0.17	2
5	3	B	797	medium thermal	0.2	2
5	4	C	797	medium thermal	0.19	2
5	5	D	797	medium thermal	0.17	2
5	6	F	797	medium thermal	0.2	2
5	7	G	797	medium thermal	0.17	2
5	8	H	797	medium thermal	0.17	2
6	1	F	797	medium thermal	0.2	2
6	2	A	797	medium thermal	0.17	2
6	3	B	797	medium thermal	0.2	2
6	4	C	797	medium thermal	0.19	2
6	5	D	797	medium thermal	0.17	2
6	6	E	797	medium thermal	0.17	2
6	7	G	797	medium thermal	0.17	2
6	8	H	797	medium thermal	0.17	2
7	1	G	797	medium thermal	0.17	2
7	2	A	797	medium thermal	0.17	2
7	3	B	797	medium thermal	0.2	2
7	4	C	797	medium thermal	0.19	2
7	5	D	797	medium thermal	0.17	2
7	6	E	797	medium thermal	0.17	2
7	7	F	797	medium thermal	0.2	2
7	8	H	797	medium thermal	0.17	2
8	1	H	797	medium thermal	0.17	2
8	2	A	797	medium thermal	0.17	2
8	3	B	797	medium thermal	0.2	2
8	4	C	797	medium thermal	0.19	2
8	5	D	797	medium thermal	0.17	2
8	6	E	797	medium thermal	0.17	2
8	7	F	797	medium thermal	0.2	2
8	8	G	797	medium thermal	0.17	2
9	1	I	453	medium thermal	0.35	2
9	2	K	453	medium thermal	0.36	2
9	3	M	453	medium thermal	0.32	2
9	4	O	453	medium thermal	0.37	2
10	1	K	453	medium thermal	0.36	2
10	2	I	453	medium thermal	0.35	2
10	3	M	453	medium thermal	0.32	2
10	4	O	453	medium thermal	0.37	2
11	1	M	453	medium thermal	0.32	2
11	2	I	453	medium thermal	0.35	2
11	3	K	453	medium thermal	0.36	2
11	4	O	453	medium thermal	0.37	2
12	1	O	453	medium thermal	0.37	2
12	2	I	453	medium thermal	0.35	2
12	3	K	453	medium thermal	0.36	2
12	4	M	453	medium thermal	0.32	2
13	1	J	449	medium thermal	0.36	2
13	2	L	449	medium thermal	0.37	2
13	3	N	449	medium thermal	0.35	2
13	4	P	449	medium thermal	0.36	2
14	1	L	449	medium thermal	0.37	2
14	2	J	449	medium thermal	0.36	2
14	3	N	449	medium thermal	0.35	2
14	4	P	449	medium thermal	0.36	2
15	1	N	449	medium thermal	0.35	2
15	2	J	449	medium thermal	0.36	2
15	3	L	449	medium thermal	0.37	2
15	4	P	449	medium thermal	0.36	2
16	1	P	449	medium thermal	0.36	2
16	2	J	449	medium thermal	0.36	2
16	3	L	449	medium thermal	0.37	2
16	4	N	449	medium thermal	0.35	2

LS refinement shell

Resolution: 2.8→2.87 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.344	238	-
R_work	0.271	4343	-
obs	-	6405	94.41 %

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	3.2166	0.2325	-0.3983	1.5453	0.266	0.8383	-0.0119	0.2886	-0.1001	-0.1267	0.0347	0.109	0.118	-0.1412	-0.0227	0.1375	-0.014	-0.0462	0.1722	0.0203	0.2191	63.2135	-71.9238	-4.752
2	3.543	0.5277	-0.2355	2.2216	0.3709	0.7663	0.0021	0.1911	-0.0287	-0.0261	0.0054	0.1261	0.1359	-0.1132	-0.0075	0.1476	-0.0235	-0.022	0.1499	0.0174	0.1296	39.4669	-46.4848	62.5222
3	2.5373	0.4299	-0.609	2.0635	0.3418	1.0243	0.0001	0.245	-0.0427	-0.1942	0.0801	-0.131	-0.0278	0.0052	-0.0802	0.1101	0.0203	-0.0491	0.1375	-0.0161	0.1452	6.7699	-50.2794	-7.4515
4	3.2829	0.3218	-0.4497	2.936	0.329	1.9408	0.0675	-0.3201	-0.0991	0.3381	-0.1439	0.5919	0.1689	-0.3378	0.0764	0.2077	-0.0753	0.0161	0.2724	-0.086	0.2025	16.9716	-48.4766	71.7927
5	1.9226	-0.8733	-0.1433	2.5644	-0.1924	1.8879	0.0918	0.1875	0.0557	-0.5662	0.0454	-0.0856	0.0584	0.085	-0.1372	0.2008	-0.0101	-0.0255	0.188	0.0211	0.1531	-14.6928	-73.146	56.6723
6	2.2464	-0.3107	-0.3958	2.06	-0.1937	1.2394	-0.0022	-0.2751	0.004	0.1423	0.0759	0.1812	0.0322	-0.0271	-0.0737	0.1005	-0.0176	-0.0481	0.1021	0.0229	0.1952	-30.9927	-75.5906	74.5127
7	2.5234	0.7688	-0.078	2.7224	0.1281	1.5573	0.0999	-0.2501	0.0605	0.4868	-0.0507	0.1159	0.0035	-0.0938	-0.0492	0.1847	0.0149	-0.0124	0.1977	-0.0211	0.0945	-9.5474	-47.7421	10.4339
8	3.3413	0.0507	-0.2594	2.1884	0.3133	1.6709	-0.0125	-0.317	-0.1327	0.4182	-0.0506	0.4506	0.1891	-0.3109	0.063	0.1998	-0.0507	0.0174	0.2506	-0.0662	0.348	40.9866	-73.7882	4.5922
9	4.8815	-0.3697	-1.0926	3.2187	-2.8068	3.3371	-0.1242	0.1621	0.1058	-0.0484	-0.086	0.1181	-0.2419	0.0004	0.2101	0.3026	-0.0236	-0.1343	0.1921	-0.0831	0.3934	49.9396	-63.0221	-0.5563
10	4.9747	0.9301	1.5394	5.1199	2.9619	4.4699	0.0626	-0.1965	0.145	0.3522	0.0608	-0.2136	0.0437	-0.2681	-0.1234	0.1969	0.0027	-0.0103	0.2104	0.0553	0.2202	50.871	-62.9215	0.5003
11	8.4598	-1.9626	4.1476	5.0469	-3.5664	7.8961	0.1232	0.2483	-0.0467	-0.0584	-0.1295	-0.1502	0.2572	0.3891	0.0062	0.197	0.029	0.02	0.1952	-0.0206	0.272	-0.8284	-39.1913	0.5864
12	6.8974	1.1687	2.5398	5.2809	2.215	7.9012	0.0426	-0.1059	-0.3861	0.1239	0.0271	0.2407	-0.0487	-0.276	-0.0697	0.1996	-0.0226	0.0634	0.1601	-0.0066	0.2335	0.7983	-39.2451	1.5898
13	4.7635	0.0338	-1.1452	3.2784	-3.1383	3.2794	-0.1458	0.0126	0.2272	-0.0589	0.0572	-0.1082	0.0362	-0.0951	0.0885	0.3092	0.0255	-0.098	0.144	-0.0873	0.2893	26.1789	-37.6466	67.4078
14	3.7738	0.6023	0.6649	4.6108	1.6837	4.7947	-0.0573	-0.2581	0.2233	0.2937	0.1221	0.1004	-0.0403	-0.2407	-0.0647	0.1374	0.0214	-0.0236	0.2186	-0.0191	0.2554	27.0337	-37.5413	68.2447
15	8.8866	1.0997	3.7764	5.4474	3.5104	8.4886	0.2293	-0.3964	-0.8637	-0.0396	0.2209	-0.2066	0.0427	-0.2738	-0.4502	0.2113	-0.074	0.0193	0.1376	0.0625	0.3517	-22.7607	-64.4829	67.2998
16	4.5293	-1.8088	-0.304	4.7004	-2.7785	5.6679	-0.0439	0.0341	-0.4648	0.0292	0.2546	-0.0992	-0.5187	0.3528	-0.2106	0.2205	-0.033	-0.0196	0.2116	-0.0408	0.3025	-24.3845	-64.583	66.4209

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	-10 - 9999
2	X-RAY DIFFRACTION	2	B	-10 - 9999
3	X-RAY DIFFRACTION	3	C	-10 - 9999
4	X-RAY DIFFRACTION	4	D	-10 - 9999
5	X-RAY DIFFRACTION	5	E	-10 - 9999
6	X-RAY DIFFRACTION	6	F	-10 - 9999
7	X-RAY DIFFRACTION	7	G	-10 - 9999
8	X-RAY DIFFRACTION	8	H	-10 - 9999
9	X-RAY DIFFRACTION	9	M	-10 - 9999
10	X-RAY DIFFRACTION	10	N	-10 - 9999
11	X-RAY DIFFRACTION	11	I	-10 - 9999
12	X-RAY DIFFRACTION	12	J	-10 - 9999
13	X-RAY DIFFRACTION	13	K	-10 - 9999
14	X-RAY DIFFRACTION	14	L	-10 - 9999
15	X-RAY DIFFRACTION	15	O	-10 - 9999
16	X-RAY DIFFRACTION	16	P	-10 - 9999

-
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