PDB-5dlj: Crystal Structure of Cas-DNA-N1 complex

ID or keywords:

Entry

Database: PDB / ID: 5dlj

Title

Crystal Structure of Cas-DNA-N1 complex

Components

39-mer DNA N1-F
39-mer DNA N1-R
CRISPR-associated endonuclease Cas1
CRISPR-associated endoribonuclease Cas2

Keywords

HYDROLASE/DNA /

protein-DNA complex / HYDROLASE-DNA complex

Function / homology

Function and homology information

CRISPR-cas system / crossover junction DNA endonuclease activity / 5'-flap endonuclease activity / maintenance of CRISPR repeat elements / defense response to virus /

endonuclease activity /

Hydrolases; Acting on ester bonds /

DNA repair / DNA damage response / protein homodimerization activity ...
Similarity search - Function

Biological species

Escherichia coli K12 (bacteria)

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.6 Å

Authors

Wang, J. / Li, J. / Zhao, H. / Sheng, G. / Wang, M. / Yin, M. / Wang, Y.

Funding support

China, 1items

Citation

Journal: Cell / Year: 2015
Title: Structural and Mechanistic Basis of PAM-Dependent Spacer Acquisition in CRISPR-Cas Systems.
Authors: Wang, J. / Li, J. / Zhao, H. / Sheng, G. / Wang, M. / Yin, M. / Wang, Y.

History

Deposition	Sep 5, 2015	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Nov 11, 2015	Provider: repository / Type: Initial release
Revision 1.1	Nov 18, 2015	Group: Database references
Revision 1.2	Mar 20, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	5dlj.cif.gz	581.1 KB	Display	PDBx/mmCIF format
PDB format	pdb5dlj.ent.gz	477.6 KB	Display	PDB format
PDBx/mmJSON format	5dlj.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/dl/5dlj ftp://data.pdbj.org/pub/pdb/validation_reports/dl/5dlj	HTTPS FTP

-
Related structure data

Related structure data	5dqtC 5dquC 5dqzC C: citing same article (ref.)
Similar structure data	5dqt-1 3gwc-d 5dqu-d 5vvk-d 5awh-d 5dqt-2 5lg6-d 5ds4-d 5ds6-d 6rj1-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	#181 - Jan 2015 Cascade and CRISPR similarity (11) #67 - Jul 2005 TATA-Binding Protein similarity (1) #168 - Dec 2013 DNA Helicase similarity (1) #91 - Jul 2007 Thymine Dimers similarity (1) #255 - Mar 2021 Cisplatin and DNA similarity (1) #172 - Apr 2014 RecA and Rad51 similarity (1) #253 - Jan 2021 Expressome similarity (1) #122 - Feb 2010 Enhanceosome similarity (1) #112 - Apr 2009 Oct and Sox Transcription Factors similarity (1) #84 - Dec 2006 Transposase similarity (1) #135 - Mar 2011 Integrase similarity (1) #180 - Dec 2014 TAL Effectors similarity (1) #227 - Nov 2018 Telomerase similarity (1) #48 - Dec 2003 Catabolite Activator Protein similarity (1) #150 - Jun 2012 Sliding Clamps similarity (1) #139 - Jul 2011 DNA Methyltransferase similarity (1) #87 - Mar 2007 Zinc Fingers similarity (1) #73 - Jan 2006 Topoisomerase similarity (1) #40 - Apr 2003 RNA Polymerase similarity (1) #3 - Mar 2000 DNA Polymerase similarity (1) #155 - Nov 2012 Vitamin D Receptor similarity (1) #125 - May 2010 Parvoviruses similarity (1) #55 - Jul 2004 DNA Ligase similarity (1) #119 - Nov 2009 Designed DNA Crystal similarity (1) #160 - Apr 2013 Actinomycin similarity (1) #8 - Aug 2000 Restriction Enzymes similarity (1) #131 - Nov 2010 Inteins similarity (1) #7 - Jul 2000 Nucleosome similarity (1) #190 - Oct 2015 Two-component Systems similarity (1) #23 - Nov 2001 DNA similarity (1) #257 - May 2021 Fetal Hemoglobin similarity (1) #45 - Sep 2003 Estrogen Receptor similarity (1) #240 - Dec 2019 Hypoxia-Inducible Factors similarity (1) #39 - Mar 2003 lac Repressor similarity (1) #33 - Sep 2002 HIV Reverse Transcriptase similarity (1) #31 - Jul 2002 p53 Tumor Suppressor similarity (1) #258 - Jun 2021 Glucocorticoid Receptor and Dexamethasone 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

#181 - Jan 2015
Cascade and CRISPR
similarity (11)
#67 - Jul 2005
TATA-Binding Protein
similarity (1)
#168 - Dec 2013
DNA Helicase
similarity (1)
#91 - Jul 2007
Thymine Dimers
similarity (1)
#255 - Mar 2021
Cisplatin and DNA
similarity (1)
#172 - Apr 2014
RecA and Rad51
similarity (1)
#253 - Jan 2021
Expressome
similarity (1)
#122 - Feb 2010
Enhanceosome
similarity (1)
#112 - Apr 2009
Oct and Sox Transcription Factors
similarity (1)
#84 - Dec 2006
Transposase
similarity (1)
#135 - Mar 2011
Integrase
similarity (1)
#180 - Dec 2014
TAL Effectors
similarity (1)
#227 - Nov 2018
Telomerase
similarity (1)
#48 - Dec 2003
Catabolite Activator Protein
similarity (1)
#150 - Jun 2012
Sliding Clamps
similarity (1)
#139 - Jul 2011
DNA Methyltransferase
similarity (1)
#87 - Mar 2007
Zinc Fingers
similarity (1)
#73 - Jan 2006
Topoisomerase
similarity (1)
#40 - Apr 2003
RNA Polymerase
similarity (1)
#3 - Mar 2000
DNA Polymerase
similarity (1)
#155 - Nov 2012
Vitamin D Receptor
similarity (1)
#125 - May 2010
Parvoviruses
similarity (1)
#55 - Jul 2004
DNA Ligase
similarity (1)
#119 - Nov 2009
Designed DNA Crystal
similarity (1)
#160 - Apr 2013
Actinomycin
similarity (1)
#8 - Aug 2000
Restriction Enzymes
similarity (1)
#131 - Nov 2010
Inteins
similarity (1)
#7 - Jul 2000
Nucleosome
similarity (1)
#190 - Oct 2015
Two-component Systems
similarity (1)
#23 - Nov 2001
DNA
similarity (1)
#257 - May 2021
Fetal Hemoglobin
similarity (1)
#45 - Sep 2003
Estrogen Receptor
similarity (1)
#240 - Dec 2019
Hypoxia-Inducible Factors
similarity (1)
#39 - Mar 2003
lac Repressor
similarity (1)
#33 - Sep 2002
HIV Reverse Transcriptase
similarity (1)
#31 - Jul 2002
p53 Tumor Suppressor
similarity (1)
#258 - Jun 2021
Glucocorticoid Receptor and Dexamethasone
similarity (1)
#92 - Aug 2007
Anabolic Steroids
similarity (1)
#241 - Jan 2020
Twenty Years of Molecules
similarity (1)

Deposited unit

D: CRISPR-associated endonuclease Cas1

C: CRISPR-associated endonuclease Cas1

A: CRISPR-associated endonuclease Cas1

B: CRISPR-associated endonuclease Cas1

G: 39-mer DNA N1-F

H: 39-mer DNA N1-R

F: CRISPR-associated endoribonuclease Cas2

E: CRISPR-associated endoribonuclease Cas2

164 kDa, 8 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)	69.894, 193.652, 193.920
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	chain A and segid A
2	1	chain B and segid B
3	1	chain C and segid C
4	1	chain D and segid D
1	2	chain E and segid E
2	2	chain F and segid F

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Selection details	Auth asym-ID
1	1	1	chain A and segid A	A
2	1	1	chain B and segid B	B
3	1	1	chain C and segid C	C
4	1	1	chain D and segid D	D
1	1	2	chain E and segid E	E
2	1	2	chain F and segid F	F

NCS ensembles :

ID
1
2

#1: Protein	CRISPR-associated endonuclease Cas1 Mass: 30709.592 Da / Num. of mol.: 4 / Fragment: UNP residues 2-281 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K12 (bacteria) / Strain: K12 / Gene: ygbT, cas1, b2755, JW2725 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: Q46896, Hydrolases; Acting on ester bonds
#2: DNA chain	39-mer DNA N1-F Mass: 11949.645 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)
#3: DNA chain	39-mer DNA N1-R Mass: 11909.620 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)
#4: Protein	CRISPR-associated endoribonuclease Cas2 Mass: 8803.182 Da / Num. of mol.: 2 / Fragment: UNP residues 1-78 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K12 (bacteria) / Strain: K12 / Gene: ygbF, cas2, b2754, JW5438 / Production host: Escherichia coli (E. coli) References: UniProt: P45956, Hydrolases; Acting on ester bonds
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 205 / 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: 3.99 Å³/Da / Density % sol: 69.2 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 10% PEG400,50mM Na cacodylate,3mM spermine,15mM Magnesium chloride

-
Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

SSRF

/ Beamline: BL17U / Wavelength: 0.979 Å

Detector

Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 17, 2015 / Details: Mono-chromator and mirrors

Radiation

Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.979 Å / Relative weight: 1

Reflection

Resolution: 2.6→50 Å / Num. obs: 82019 / % possible obs: 99.9 % / Redundancy: 6.1 % / B_iso Wilson estimate: 38.23 Å² / R_merge(I) obs: 0.088 / Χ²: 0.919 / Net I/av σ(I): 19.042 / Net I/σ(I): 8.9 / Num. measured all: 499478

Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	Χ²	% possible all
2.6-2.69	5.6	0.807	8116	0.81	99.8
2.69-2.8	5.6	0.65	8059	0.836	99.8
2.8-2.93	5.5	0.504	8090	0.864	99.9
2.93-3.08	6.1	0.359	8103	0.909	99.9
3.08-3.28	6.2	0.231	8148	0.944	99.9
3.28-3.53	6	0.14	8158	1.021	99.9
3.53-3.88	6.4	0.096	8205	1.026	99.9
3.88-4.45	6.5	0.064	8187	1.022	99.9
4.45-5.6	6.5	0.052	8314	0.944	99.9
5.6-50	6.3	0.04	8639	0.783	99.7

-
Processing

Software

Name	Version	Classification
HKL-2000		data scaling
PHENIX		refinement
PDB_EXTRACT	3.15	data extraction
PHASER		phasing
HKL-2000		data processing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.6→39.835 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 20.25 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2075	3600	4.92 %
R_work	0.1794	69539	-
obs	0.1808	73139	89.13 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso max: 168.15 Å² / B_iso mean: 48.7784 Å² / B_iso min: 10.71 Å²

Refinement step

Cycle: final / Resolution: 2.6→39.835 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9662	1577	0	205	11444
B_iso mean	-	-	-	52.5	-
Num. residues	-	-	-	-	1328

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	11595
X-RAY DIFFRACTION	f_angle_d	1.05	16057
X-RAY DIFFRACTION	f_chiral_restr	0.044	1833
X-RAY DIFFRACTION	f_plane_restr	0.006	1796
X-RAY DIFFRACTION	f_dihedral_angle_d	18.349	4416

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Number	Refine-ID	Rms	Type
1	1	A	5145	X-RAY DIFFRACTION	10.032	TORSIONAL
1	2	B	5145	X-RAY DIFFRACTION	10.032	TORSIONAL
1	3	C	5145	X-RAY DIFFRACTION	10.032	TORSIONAL
1	4	D	5145	X-RAY DIFFRACTION	10.032	TORSIONAL
2	1	E	716	X-RAY DIFFRACTION	10.032	TORSIONAL
2	2	F	716	X-RAY DIFFRACTION	10.032	TORSIONAL

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 26

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
2.5978-2.6319	0.2692	39	0.2326	687	726	24
2.6319-2.668	0.3068	50	0.2592	980	1030	33
2.668-2.7061	0.313	76	0.2514	1392	1468	47
2.7061-2.7465	0.2805	84	0.2501	1903	1987	64
2.7465-2.7894	0.2577	106	0.2587	2271	2377	76
2.7894-2.8351	0.3114	122	0.2526	2481	2603	84
2.8351-2.884	0.3007	161	0.2539	2781	2942	93
2.884-2.9364	0.2557	151	0.2464	2815	2966	95
2.9364-2.9929	0.2742	159	0.2388	2910	3069	99
2.9929-3.0539	0.2856	151	0.2406	2982	3133	99
3.0539-3.1203	0.2326	137	0.2235	2966	3103	100
3.1203-3.1929	0.2413	99	0.2277	3029	3128	100
3.1929-3.2727	0.2713	182	0.2198	2968	3150	100
3.2727-3.3611	0.2223	138	0.2008	2992	3130	100
3.3611-3.46	0.2128	148	0.1855	2993	3141	100
3.46-3.5716	0.2338	162	0.1784	2957	3119	100
3.5716-3.6991	0.2119	172	0.1622	2992	3164	100
3.6991-3.8471	0.1887	167	0.1653	2966	3133	100
3.8471-4.0221	0.2195	131	0.1568	3022	3153	100
4.0221-4.2339	0.1476	147	0.1361	3002	3149	100
4.2339-4.4988	0.1519	186	0.1334	3015	3201	100
4.4988-4.8456	0.1573	187	0.1335	2990	3177	100
4.8456-5.3322	0.1741	174	0.1496	3034	3208	100
5.3322-6.1014	0.186	125	0.1629	3096	3221	100
6.1014-7.6781	0.1887	169	0.1679	3102	3271	100
7.6781-39.84	0.1783	177	0.1549	3213	3390	99

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	2.4551	0.486	0.6239	1.6372	0.8943	1.4775	-0.0271	-0.1806	-0.398	0.2162	0.0324	0.2505	0.2078	-0.0945	-0.0996	0.2367	-0.0233	0.0644	0.1655	0.1022	0.2963	-60.6058	-127.0788	78.0375
2	0.9939	0.8039	1.0353	6.8726	1.5919	1.4988	-0.1827	0.1056	0.5027	0.0369	0.0482	1.2476	0.0494	-0.4818	-0.0758	0.2446	-0.0469	0.0352	0.5389	0.0308	0.8323	-89.313	-122.8993	73.9137
3	2.2972	-0.8476	-0.0117	3.8017	2.4168	3.8887	-0.1082	0.638	1.2414	-0.9173	-0.1536	0.7907	-1.0206	-0.088	0.031	0.5825	0.2325	-0.0434	0.6478	0.1002	0.7982	-83.667	-107.3057	71.8142
4	2.8898	-0.0432	-0.219	3.0993	1.4161	3.0123	0.037	-0.2967	-0.2438	0.0891	-0.0242	0.3801	-0.0593	-0.3783	-0.0183	0.1771	-0.0109	0.0605	0.2423	0.0871	0.3571	-73.1779	-121.3166	77.9188
5	3.0905	0.3855	0.1314	6.2889	0.4987	5.737	0.3265	-0.0846	-0.0738	-0.0287	-0.0366	-0.1457	-0.4492	0.174	-0.0814	0.2732	-0.0601	0.0683	0.2148	0.0837	0.1607	-46.733	-109.395	65.6953
6	2.7319	0.8938	0.0796	5.6321	-0.6754	3.7622	-0.0171	0.2201	0.071	0.0198	-0.2003	-0.2555	-0.7648	0.6589	-0.0549	0.2709	-0.0939	0.0334	0.2039	0.0438	0.168	-43.2488	-112.5583	67.573
7	0.512	0.4309	-0.7345	4.7082	0.2307	4.4507	0.0741	0.0913	-0.1424	0.0362	0.0733	-0.0824	0.3836	-0.0237	-0.1646	0.1464	0.0058	-0.0117	0.1448	0.003	0.1343	-47.9418	-119.7161	68.8943
8	3.3622	0.4295	1.0158	1.2221	0.6907	3.8207	-0.0437	-0.0748	0.1202	-0.6566	-0.6792	1.3997	-0.6572	-0.5765	0.421	0.3181	0.0679	-0.173	0.3215	-0.0658	0.5713	-63.8883	-131.4463	58.5794
9	4.057	0.4538	-0.0847	4.912	1.8462	2.9339	-0.4134	0.7543	-0.2998	-1.0621	0.1931	0.2978	0.4809	0.0246	0.1938	0.6181	0.0593	-0.1359	0.2795	-0.1127	0.408	-52.5711	-144.6023	46.7492
10	5.5029	5.4849	0.938	5.4515	0.8699	1.5782	0.5014	0.2514	-0.4707	-0.0649	-0.4062	-0.3591	0.1596	0.3679	0.0601	0.5176	0.1196	0.1218	0.336	-0.0194	0.5382	-37.4998	-143.7053	50.2855
11	3.1872	-1.5824	0.567	2.3116	-0.3211	1.3752	-0.105	-0.1554	-0.0278	-0.0112	0.047	-0.3176	-0.0367	0.3426	0.1304	0.2917	-0.0017	0.068	0.2122	0.0211	0.436	-35.4067	-132.8441	62.2459
12	2.2967	-0.8019	-0.8371	3.308	0.325	2.7627	0.1034	-0.0868	0.0103	-0.2878	-0.0965	-0.4731	0.1098	0.2588	-0.0057	0.3103	0.0212	0.0005	0.1537	0.0003	0.3283	-41.9207	-132.8392	56.1602
13	8.4903	0.4119	4.5212	9.4728	-0.6997	7.4137	-0.358	0.5325	0.8472	-0.6759	0.1624	-0.8003	-0.7313	0.1948	0.226	0.2528	0.0269	0.1035	0.4194	0.0242	0.4748	-35.619	-120.8063	54.2076
14	1.7893	0.6659	1.1272	0.5235	0.8395	1.2815	0.377	0.7614	-0.5438	-0.8246	-0.1013	0.0478	-0.2995	-0.0424	-0.016	0.4851	0.1735	-0.2251	0.2846	0.0258	0.2866	-57.8439	-130.2785	48.0112
15	3.5367	0.3441	0.4371	3.3105	1.6073	2.8394	-0.0972	0.4427	0.4683	-0.4732	-0.1209	0.2272	-0.7273	0.1118	0.2293	0.3605	-0.0379	-0.0497	0.2283	0.1169	0.3167	-37.7792	-57.7942	23.8019
16	2.6937	-0.3946	-0.5126	1.5673	0.676	1.3942	-0.0406	0.6156	0.1658	-0.2116	0.0542	-0.1729	-0.0342	0.3026	-0.0598	0.1919	-0.0297	0.0559	0.414	0.0858	0.143	-21.2213	-72.1334	15.3021
17	1.2783	-0.8313	-0.6532	0.7951	1.1309	5.3916	-0.0754	-0.4007	-0.2407	0.0202	0.1112	-0.3012	0.1313	1.2488	-0.0483	0.2509	-0.0626	-0.0179	0.8924	0.0158	0.6014	1.7429	-70.6054	23.0434
18	3.8987	1.0284	1.1883	2.7254	1.7896	3.5331	0.109	-0.2054	-0.0515	0.5725	-0.0064	-0.5127	0.3592	0.5106	-0.0487	0.2635	-0.0194	-0.0696	0.4498	0.0516	0.2919	-10.4285	-70.7691	29.0991
19	2.1616	-0.2395	-0.1205	3.3677	0.9949	2.474	0.1493	0.3737	0.432	-0.2686	-0.0536	-0.2663	-0.6096	0.3512	0.0777	0.1775	-0.0809	0.0184	0.369	0.1026	0.3072	-17.248	-63.9566	19.9088
20	2.3512	-0.0858	-0.2131	5.0326	0.0856	5.9454	0.1476	-0.0466	-0.1086	0.5328	-0.0865	0.2714	0.0554	-0.1242	0.0048	0.1842	-0.0384	0.0448	0.1441	0.0484	0.1699	-40.6188	-78.5202	33.6695
21	3.5028	-0.1622	-0.0787	3.5695	1.9251	3.6956	-0.0335	0.4336	-0.3172	-0.0609	0.2663	-0.2246	0.4247	0.5101	-0.249	0.3659	0.102	-0.0469	0.274	0.0075	0.1504	-32.6728	-90.8746	8.0918
22	5.1468	-0.4038	-5.3238	2.1035	0.3848	5.61	0.3411	0.8324	-0.0303	-0.0862	0.0226	0.3199	-0.0149	-0.5802	-0.3356	0.4965	-0.0714	-0.0863	0.527	-0.0294	0.3179	-49.8699	-95.0417	1.5424
23	5.4978	-0.16	1.4454	1.0057	-0.1193	1.6626	0.1101	0.0756	0.0053	-0.0484	-0.0088	0.1136	0.2034	-0.2349	-0.0796	0.2553	-0.0355	0.0105	0.3431	0	0.1243	-46.1407	-85.2116	11.5021
24	4.7263	-0.1442	1.5335	2.5539	-0.1124	5.278	0.0248	-0.6295	-0.3706	0.3285	-0.008	0.2683	0.5683	-0.5136	-0.1205	0.351	-0.041	-0.0326	0.2369	0.0582	0.2801	-45.9148	-93.3283	18.8528
25	2.3457	2.0942	0.0225	6.0801	3.8355	3.5421	0.0657	0.5841	0.2329	-0.5366	-0.1425	1.4661	-0.0121	0.4974	0.0323	0.4005	-0.0675	-0.0984	0.4717	-0.0247	0.6375	-31.66	-41.2717	31.3924
26	-0.7284	1.2585	-2.1737	0.1083	-1.0594	1.4748	0.7784	-0.0223	0.5776	0.6609	-0.2692	0.9794	-0.6987	0.4609	-0.0862	0.7099	-0.153	0.1751	0.5816	0.272	0.7951	-54.388	-88.4082	66.3321
27	2.2465	-0.4197	-1.5405	3.8692	4.0463	5.5717	0.0821	-0.3341	-0.985	0.2182	0.5202	1.0092	0.483	1.2071	-0.2581	0.4262	0.1236	0.0549	0.6777	-0.041	0.502	-55.7584	-113.8605	104.1767
28	-0.7876	2.4067	-1.15	1.6477	-1.3382	-0.0713	0.7249	-0.6871	0.0455	0.6292	-0.5477	0.5108	-0.5109	1.197	-0.2342	0.7125	-0.1863	0.1968	0.8679	0.2824	0.5746	-32.9248	-78.9838	56.8558
29	3.3566	2.3786	0.2368	6.8303	0.1276	3.5154	0.0968	-0.2401	0.0086	0.1881	-0.4573	0.075	0.0389	0.5788	-0.0578	0.5471	-0.3868	0.32	0.0875	0.5816	-0.3371	-39.0428	-93.5071	47.9236
30	3.618	0.7875	0.1137	4.6624	1.3121	6.4273	0.2492	-0.2831	0.2499	0.3855	-0.3432	0.511	-0.1562	0.4731	0.0182	0.4334	-0.0571	0.0759	0.238	0.0891	0.2107	-38.1481	-85.4002	46.8408
31	3.5084	2.6031	2.4061	7.1121	5.8904	5.0146	-0.3279	-0.173	-0.4854	-0.0476	-0.1411	-0.7899	0.2428	1.4834	0.0893	0.5233	-0.0356	0.0379	0.5254	0.2032	0.2832	-28.8383	-91.8775	44.6612
32	3.6392	-1.0486	-0.3082	0.8391	1.4054	8.5623	0.3244	-0.6273	-0.3384	1.2825	-1.2684	-0.0153	0.4869	0.4531	0.3374	0.6494	-0.1758	-0.0812	0.5397	0.1572	0.3777	-34.5846	-96.7426	54.5334
33	2.8155	-0.454	-2.0668	2.0412	-0.8248	6.0416	0.6487	-0.0626	0.1789	0.1013	0.2774	0.4139	-0.5245	0.2626	0.2701	0.5047	-0.544	0.4633	-0.9369	0.9873	-0.2347	-48.3474	-97.3542	51.7979
34	3.5595	0.5944	-0.6938	5.2687	3.1334	4.4381	0.2994	-0.0064	0.2314	0.0989	-0.0205	0.3744	-0.5754	0.6221	-0.2267	0.4562	-0.0802	0.0702	0.19	0.0905	0.2465	-49.2223	-98.4455	59.9227
35	3.7711	-4.0305	-2.345	7.6108	5.5772	4.4918	-0.069	0.5527	-0.0772	-0.665	0.5076	1.5594	-0.3789	-0.8182	-0.2217	0.4633	-0.0611	0.0038	0.2968	0.2761	0.5655	-58.4869	-100.668	53.4524
36	7.0726	-0.1016	-1.1562	6.2889	0.832	2.5328	0.4143	0.2599	0.0492	-0.5875	0.8063	0.7143	-0.9294	0.2857	-0.5523	0.6133	-0.0738	0.18	0.1986	0.1993	0.4669	-52.3505	-93.6976	47.8672
37	7.1185	-0.8208	-2.2346	3.8392	2.2547	3.8464	0.1706	0.238	0.911	-0.0373	1.1626	0.258	-0.8281	-0.2368	-0.1007	0.834	0.3368	0.1815	0.3823	0.2525	0.752	-53.2791	-87.4912	48.9578

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'D' and (resid 15 through 133 )	D	15 - 133
2	X-RAY DIFFRACTION	2	chain 'D' and (resid 134 through 155 )	D	134 - 155
3	X-RAY DIFFRACTION	3	chain 'D' and (resid 156 through 174 )	D	156 - 174
4	X-RAY DIFFRACTION	4	chain 'D' and (resid 175 through 281 )	D	175 - 281
5	X-RAY DIFFRACTION	5	chain 'C' and (resid 2 through 40 )	C	2 - 40
6	X-RAY DIFFRACTION	6	chain 'C' and (resid 41 through 61 )	C	41 - 61
7	X-RAY DIFFRACTION	7	chain 'C' and (resid 62 through 88 )	C	62 - 88
8	X-RAY DIFFRACTION	8	chain 'C' and (resid 89 through 108 )	C	89 - 108
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 109 through 133 )	C	109 - 133
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 134 through 156 )	C	134 - 156
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 157 through 198 )	C	157 - 198
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 199 through 242 )	C	199 - 242
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 243 through 259 )	C	243 - 259
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 260 through 281 )	C	260 - 281
15	X-RAY DIFFRACTION	15	chain 'A' and (resid 15 through 54 )	A	15 - 54
16	X-RAY DIFFRACTION	16	chain 'A' and (resid 55 through 133 )	A	55 - 133
17	X-RAY DIFFRACTION	17	chain 'A' and (resid 134 through 156 )	A	134 - 156
18	X-RAY DIFFRACTION	18	chain 'A' and (resid 157 through 242 )	A	157 - 242
19	X-RAY DIFFRACTION	19	chain 'A' and (resid 243 through 281 )	A	243 - 281
20	X-RAY DIFFRACTION	20	chain 'B' and (resid 2 through 78 )	B	2 - 78
21	X-RAY DIFFRACTION	21	chain 'B' and (resid 79 through 133 )	B	79 - 133
22	X-RAY DIFFRACTION	22	chain 'B' and (resid 134 through 156 )	B	134 - 156
23	X-RAY DIFFRACTION	23	chain 'B' and (resid 157 through 227 )	B	157 - 227
24	X-RAY DIFFRACTION	24	chain 'B' and (resid 228 through 281 )	B	228 - 281
25	X-RAY DIFFRACTION	25	chain 'G' and (resid 1 through 5 )	G	1 - 5
26	X-RAY DIFFRACTION	26	chain 'G' and (resid 6 through 39 )	G	6 - 39
27	X-RAY DIFFRACTION	27	chain 'H' and (resid 1 through 5 )	H	1 - 5
28	X-RAY DIFFRACTION	28	chain 'H' and (resid 6 through 39 )	H	6 - 39
29	X-RAY DIFFRACTION	29	chain 'F' and (resid 1 through 9 )	F	1 - 9
30	X-RAY DIFFRACTION	30	chain 'F' and (resid 10 through 36 )	F	10 - 36
31	X-RAY DIFFRACTION	31	chain 'F' and (resid 37 through 50 )	F	37 - 50
32	X-RAY DIFFRACTION	32	chain 'F' and (resid 51 through 78 )	F	51 - 78
33	X-RAY DIFFRACTION	33	chain 'E' and (resid 1 through 9 )	E	1 - 9
34	X-RAY DIFFRACTION	34	chain 'E' and (resid 10 through 36 )	E	10 - 36
35	X-RAY DIFFRACTION	35	chain 'E' and (resid 37 through 50 )	E	37 - 50
36	X-RAY DIFFRACTION	36	chain 'E' and (resid 51 through 67 )	E	51 - 67
37	X-RAY DIFFRACTION	37	chain 'E' and (resid 68 through 78 )	E	68 - 78

-
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