PDB-6s7m: Structure of parasitic PEX14 in complex with a benzo[b]thiophene-...

ID or keywords:

Entry

Database: PDB / ID: 6s7m

Title

Structure of parasitic PEX14 in complex with a benzo[b]thiophene-7-carboxylic acid.

Components

Peroxin 14

Keywords

SIGNALING PROTEIN / PEX14 / PPI / PEX14/PEX5 / Trypanosomes / FBDD

Function / homology

Function and homology information

glycosome membrane / peroxisomal importomer complex / protein import into peroxisome matrix, docking / protein targeting to vacuole / glycosome / post-transcriptional regulation of gene expression / signaling receptor binding
Similarity search - Function

Biological species

Trypanosoma brucei brucei (eukaryote)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.75845964621 Å

Authors

Hassaan, E. / Heine, A. / Klebe, G.

Funding support

Germany, 1items

Citation

Journal: To Be Published
Title: Structure of parasitic PEX14 in complex with a benzo[b]thiophene-7-carboxylic acid.
Authors: Hassaan, E. / Heine, A. / Klebe, G.

History

Deposition	Jul 5, 2019	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jul 15, 2020	Provider: repository / Type: Initial release
Revision 1.1	May 15, 2024	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	6s7m.cif.gz	263.7 KB	Display	PDBx/mmCIF format
PDB format	pdb6s7m.ent.gz	176.8 KB	Display	PDB format
PDBx/mmJSON format	6s7m.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/s7/6s7m ftp://data.pdbj.org/pub/pdb/validation_reports/s7/6s7m	HTTPS FTP

-
Related structure data

Similar structure data	3bs9-1 3mx7-d 1d8b-d 5o3j-d 3hi9-1 1zw8-d 2rjw-2 2ru9-d 4zka-3 4ljm-1 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) 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

Similar structure data

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Peroxin 14

B: Peroxin 14

C: Peroxin 14

D: Peroxin 14

E: Peroxin 14

F: Peroxin 14

G: Peroxin 14

H: Peroxin 14

hetero molecules

63.9 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Peroxin 14

hetero molecules

defined by author
8.11 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Peroxin 14

hetero molecules

defined by author
8 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: Peroxin 14

hetero molecules

defined by author
8 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

D: Peroxin 14

hetero molecules

defined by author
8.11 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

5

E: Peroxin 14

hetero molecules

defined by author
8.18 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

6

F: Peroxin 14

defined by author
7.83 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

7

G: Peroxin 14

defined by author
7.83 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

8

H: Peroxin 14

defined by author
7.83 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	79.786, 39.712, 81.100
Angle α, β, γ (deg.)	90.000, 90.082, 90.000
Int Tables number	4
Space group name H-M	P12₁1
Space group name Hall	P2yb

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID
1	1
2	1
3	1
4	1
5	1
6	1
7	1
8	1

NCS domain segments:

Ens-ID: 1

Dom-ID	Component-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	ARG	ARG	VAL	VAL	(chain A and ((resid 7 and (name N or name...	A	A	7 - 11	9 - 13
1	2	ASN	ASN	SER	SER	(chain A and ((resid 7 and (name N or name...	A	A	13 - 29	15 - 31
1	3	LYS	LYS	ILE	ILE	(chain A and ((resid 7 and (name N or name...	A	A	31 - 45	33 - 47
1	4	GLU	GLU	PHE	PHE	(chain A and ((resid 7 and (name N or name...	A	A	47 - 49	49 - 51
1	5	LYS	LYS	ASN	ASN	(chain A and ((resid 7 and (name N or name...	A	A	51 - 59	53 - 61
1	6	ILE	ILE	ILE	ILE	(chain A and ((resid 7 and (name N or name...	A	A	61	63
1	7	ILE	ILE	ILE	ILE	(chain A and ((resid 7 and (name N or name...	A	A	64	66
2	8	ARG	ARG	VAL	VAL	(chain B and ((resid 7 and (name N or name...	B	B	7 - 11	9 - 13
2	9	ASN	ASN	SER	SER	(chain B and ((resid 7 and (name N or name...	B	B	13 - 29	15 - 31
2	10	LYS	LYS	ILE	ILE	(chain B and ((resid 7 and (name N or name...	B	B	31 - 45	33 - 47
2	11	GLU	GLU	PHE	PHE	(chain B and ((resid 7 and (name N or name...	B	B	47 - 49	49 - 51
2	12	LYS	LYS	ASN	ASN	(chain B and ((resid 7 and (name N or name...	B	B	51 - 59	53 - 61
2	13	ILE	ILE	ILE	ILE	(chain B and ((resid 7 and (name N or name...	B	B	61	63
2	14	ILE	ILE	ILE	ILE	(chain B and ((resid 7 and (name N or name...	B	B	64	66
3	15	ARG	ARG	VAL	VAL	(chain C and ((resid 7 and (name N or name...	C	C	7 - 11	9 - 13
3	16	ASN	ASN	SER	SER	(chain C and ((resid 7 and (name N or name...	C	C	13 - 29	15 - 31
3	17	LYS	LYS	ILE	ILE	(chain C and ((resid 7 and (name N or name...	C	C	31 - 45	33 - 47
3	18	GLU	GLU	PHE	PHE	(chain C and ((resid 7 and (name N or name...	C	C	47 - 49	49 - 51
3	19	LYS	LYS	ASN	ASN	(chain C and ((resid 7 and (name N or name...	C	C	51 - 59	53 - 61
3	60	ILE	ILE	ILE	ILE	(chain C and ((resid 7 and (name N or name...	C	C	61	63
3	20	ILE	ILE	ILE	ILE	(chain C and ((resid 7 and (name N or name...	C	C	64	66
4	21	ARG	ARG	VAL	VAL	(chain D and ((resid 7 and (name N or name...	D	D	7 - 11	9 - 13
4	22	ASN	ASN	SER	SER	(chain D and ((resid 7 and (name N or name...	D	D	13 - 29	15 - 31
4	23	LYS	LYS	ILE	ILE	(chain D and ((resid 7 and (name N or name...	D	D	31 - 45	33 - 47
4	24	GLU	GLU	PHE	PHE	(chain D and ((resid 7 and (name N or name...	D	D	47 - 49	49 - 51
4	25	LYS	LYS	ASN	ASN	(chain D and ((resid 7 and (name N or name...	D	D	51 - 59	53 - 61
4	26	ILE	ILE	ILE	ILE	(chain D and ((resid 7 and (name N or name...	D	D	61	63
4	27	ILE	ILE	ILE	ILE	(chain D and ((resid 7 and (name N or name...	D	D	64	66
5	28	ARG	ARG	VAL	VAL	(chain E and ((resid 7 and (name N or name...	E	E	7 - 11	9 - 13
5	29	ASN	ASN	SER	SER	(chain E and ((resid 7 and (name N or name...	E	E	13 - 29	15 - 31
5	30	LYS	LYS	ILE	ILE	(chain E and ((resid 7 and (name N or name...	E	E	31 - 45	33 - 47
5	31	GLU	GLU	PHE	PHE	(chain E and ((resid 7 and (name N or name...	E	E	47 - 49	49 - 51
5	32	LYS	LYS	ASN	ASN	(chain E and ((resid 7 and (name N or name...	E	E	51 - 59	53 - 61
5	33	ILE	ILE	ILE	ILE	(chain E and ((resid 7 and (name N or name...	E	E	61	63
5	34	ILE	ILE	ILE	ILE	(chain E and ((resid 7 and (name N or name...	E	E	64	66
6	35	ARG	ARG	VAL	VAL	(chain F and (resseq 7:11 or resseq 13:14 or (resid...	F	F	7 - 11	9 - 13
6	36	ASN	ASN	SER	SER	(chain F and (resseq 7:11 or resseq 13:14 or (resid...	F	F	13 - 29	15 - 31
6	37	LYS	LYS	ILE	ILE	(chain F and (resseq 7:11 or resseq 13:14 or (resid...	F	F	31 - 45	33 - 47
6	38	GLU	GLU	PHE	PHE	(chain F and (resseq 7:11 or resseq 13:14 or (resid...	F	F	47 - 49	49 - 51
6	39	LYS	LYS	ASN	ASN	(chain F and (resseq 7:11 or resseq 13:14 or (resid...	F	F	51 - 59	53 - 61
6	40	ILE	ILE	ILE	ILE	(chain F and (resseq 7:11 or resseq 13:14 or (resid...	F	F	61	63
6	41	ILE	ILE	ILE	ILE	(chain F and (resseq 7:11 or resseq 13:14 or (resid...	F	F	64	66
7	42	ARG	ARG	VAL	VAL	(chain G and (resseq 7 or (resid 8 and (name...	G	G	7 - 11	9 - 13
7	43	ASN	ASN	SER	SER	(chain G and (resseq 7 or (resid 8 and (name...	G	G	13 - 29	15 - 31
7	44	LYS	LYS	ILE	ILE	(chain G and (resseq 7 or (resid 8 and (name...	G	G	31 - 45	33 - 47
7	45	GLU	GLU	PHE	PHE	(chain G and (resseq 7 or (resid 8 and (name...	G	G	47 - 49	49 - 51
7	46	LYS	LYS	ASN	ASN	(chain G and (resseq 7 or (resid 8 and (name...	G	G	51 - 59	53 - 61
7	47	ILE	ILE	ILE	ILE	(chain G and (resseq 7 or (resid 8 and (name...	G	G	61	63
7	48	ILE	ILE	ILE	ILE	(chain G and (resseq 7 or (resid 8 and (name...	G	G	64	66
8	49	ARG	ARG	VAL	VAL	(chain H and ((resid 7 and (name N or name...	H	H	7 - 11	9 - 13
8	50	ASN	ASN	SER	SER	(chain H and ((resid 7 and (name N or name...	H	H	13 - 29	15 - 31
8	51	LYS	LYS	ILE	ILE	(chain H and ((resid 7 and (name N or name...	H	H	31 - 45	33 - 47
8	52	GLU	GLU	PHE	PHE	(chain H and ((resid 7 and (name N or name...	H	H	47 - 49	49 - 51
8	53	LYS	LYS	ASN	ASN	(chain H and ((resid 7 and (name N or name...	H	H	51 - 59	53 - 61
8	54	ILE	ILE	ILE	ILE	(chain H and ((resid 7 and (name N or name...	H	H	61	63
8	55	ILE	ILE	ILE	ILE	(chain H and ((resid 7 and (name N or name...	H	H	64	66

#1: Protein	Peroxin 14 Mass: 7826.022 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Gene: PEX14 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8IEW2
#2: Chemical	ChemComp-KZ2 / 1-benzothiophene-7-carboxylic acid Mass: 178.208 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₉H₆O₂S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 151 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.07 Å³/Da / Density % sol: 40.47 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 0.17 M ammonium acetate, 0.085 M sodium citrate pH 5.6, 25.5% PEG4000, 15% glycerol

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 22, 2018
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9184 Å / Relative weight: 1
Reflection	Resolution: 1.758→39.893 Å / Num. obs: 49925 / % possible obs: 97.6 % / Redundancy: 3.7 % / B_iso Wilson estimate: 23.026260966 Å² / CC_1/2: 0.99 / R_sym value: 0.05 / Net I/σ(I): 14.68
Reflection shell	Resolution: 1.758→1.767 Å / Num. unique obs: 7928

-
Processing

Software

Name	Version	Classification
PHENIX	1.10.1_2155	refinement
PHASER		phasing
Coot		model building
XDS		data scaling
XDS		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.75845964621→39.89 Å / SU ML: 0.241096427044 / Cross valid method: FREE R-VALUE / σ(F): 1.3588830167 / Phase error: 28.3646510532

	R_factor	Num. reflection	% reflection
R_free	0.26712042883	2495	5.00531626778 %
R_work	0.230474731299	-	-
obs	0.232337321952	49847	97.4506852261 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Displacement parameters

B_iso mean: 26.3968381408 Å²

Refinement step

Cycle: LAST / Resolution: 1.75845964621→39.89 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3918	0	86	151	4155

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.00668841722139	4216
X-RAY DIFFRACTION	f_angle_d	0.735572183815	5709
X-RAY DIFFRACTION	f_chiral_restr	0.0426568661816	668
X-RAY DIFFRACTION	f_plane_restr	0.0048592097099	796
X-RAY DIFFRACTION	f_dihedral_angle_d	14.3500630118	2626

LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)	Highest resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	% reflection obs (%)
1.7585-1.7923		0.340915707339	133	0.283178642673	2538	94.7835344216
1.7923-1.8289		0.344595924869	139	0.259210738141	2618	97.1801198449
1.8289-1.8686		0.278037900012	136	0.246421570367	2587	97.5985663082
1.8686-1.9121		0.297523454234	138	0.242444336803	2628	98.0155917789
1.9121-1.9599		0.256367222589	138	0.230052478936	2609	97.5497159091
1.9599-2.0129		0.32000508157	136	0.224369389741	2589	96.0183227625
2.0129-2.0721		0.249929440587	138	0.215464822365	2612	98.0741797432
2.0721-2.139		0.25317079366	137	0.207543773442	2615	97.2781901732
2.139-2.2155		0.255430763609	139	0.210509971975	2631	98.2966643009
2.2155-2.3042		0.274422183529	137	0.21417772652	2608	97.5479744136
2.3042-2.409		0.243419259127	140	0.214001308885	2650	98.1703026038
2.409-2.536		0.28697867757	138	0.221164079447	2628	97.3943661972
2.536-2.6948		0.237118458874	137	0.215966881696	2588	96.1877867984
2.6948-2.9029		0.210740777726	139	0.237783954064	2630	97.6031018682
2.9029-3.1949		0.276613175943	141	0.246467889681	2687	99.1584852735
3.1949-3.6569		0.245922582879	143	0.222865876554	2705	98.3425414365
3.6569-4.6062		0.258027733556	140	0.212522621242	2652	97.4860335196
	4.6062	0.311983695289	146	0.268759337559	2777	97.4658219406

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	0.061783895002	0.0113233628733	-0.0372258947895	0.0501158680924	0.0298034636531	0.0259482528239	0.248267793374	-0.0653244389367	-0.0224778281488	-0.117742247958	-0.204595226787	0.0819581533225	-0.0730216882837	-0.40288214657	0.00185947813643	0.232986449214	-0.00981335994975	-0.0632909328897	0.258411343592	0.0013967577164	0.249784164329	108.102850558	0.538291138415	109.23424164
2	-0.00152806571996	-0.018056879325	0.00119801273815	0.0132694757332	-0.0442998454236	0.038256070454	0.102069387739	0.0562535462404	0.142190502943	-0.0683892939728	-0.059876444625	-0.138701646877	-0.183693606535	-0.0455743159444	0.000152565955249	0.202397614944	0.0321227514675	0.0224307331958	0.190309108906	0.0186553543412	0.189331292794	110.532942051	10.5413038564	115.01524476
3	0.0296508586416	0.00899168278951	0.00380433722147	0.00541615526356	-0.00495966543687	0.00646336115125	-0.0899375839421	0.011114543494	0.042608881005	0.00598966721956	-0.117375709446	-0.0527731357265	-0.0274980514338	0.0694224898851	4.40185371419E-5	0.284872139361	0.0499276069756	-0.0734524831797	0.376099685159	0.0615055704176	0.291782963398	109.737445786	16.9611211991	108.010225463
4	0.0124076740041	-0.00626598371103	-0.0102770309106	0.00747966778068	0.00229441974109	0.00419068954167	-0.00975455704586	-0.049071616016	0.0995820382433	-0.0687647048216	0.166946986103	-0.0794203275802	-0.0659936244275	0.146518857061	4.35404117682E-5	0.255530972825	-0.00355743965239	0.0371395109381	0.171454980685	-0.0189855395933	0.220987097497	120.996462531	13.8157995105	111.811204487
5	0.0717459270225	-0.0326478885291	0.0572421638655	0.098794505462	0.0740023925787	0.0944760742565	0.0705244674772	0.0302118259354	-0.0165671652084	0.0432876885201	-0.0776633280264	0.0415587567356	-0.00407639926314	0.066816155751	0.000189780152703	0.142784611103	0.00297270932709	-0.0220598702026	0.104173962134	0.0022658750609	0.190212295301	90.3816496816	21.9682182454	129.644892607
6	0.0326788627578	-0.0485897556796	-0.069518122971	0.0864786110941	0.127478533109	0.289777619028	-0.138332293472	0.0161626247392	-0.183812260625	-0.0300543434154	0.0668451571872	-0.00982083423216	-0.0662527412801	-0.0849147959881	-0.148237842953	0.154357302188	0.0384630274221	-0.0184192237472	0.0910852197679	-0.0171575685267	0.13957562794	83.8008111022	29.041425971	133.676140937
7	0.0590674405145	0.0367539593446	-0.0825773393429	0.105864609768	0.0853927631801	0.047365646539	-0.165869997836	-0.0765265121523	-0.0429937802283	0.0560381091185	0.122595152556	-0.0298758749902	0.206249629615	-0.00496731832016	0.000386287717525	0.183344470806	0.0334222339189	-0.00815745480798	0.158219985951	-0.00644428916144	0.195020973028	116.398019423	10.8600681209	134.090253564
8	0.000537185679069	-0.0205402266325	-0.024109821826	0.0144697553688	-0.0341991873242	0.130239128343	0.0142223118162	-0.0430764297745	0.0291245185679	-0.132075240169	-0.0927861327132	-0.0532897405605	0.0237660857722	-0.147906508407	-0.00146250705403	0.127287997987	0.0406394744324	0.00506815926785	0.161619058914	-0.00515503002014	0.162928440827	109.63854278	16.3569716751	129.49252419
9	0.0576209543523	-0.012870410673	0.0389170570031	0.012236763934	0.0161906052113	0.0513956116102	-0.0550357618497	-0.0661073112177	0.0460718228775	-0.00718466109713	0.0683698009418	0.00614611569328	0.293152547952	-0.101473350435	0.00117371050808	0.21056472969	-0.0111919429443	-0.0209697201088	0.147223533756	0.0222150980548	0.225143670903	76.1714326181	27.9681329435	114.641601292
10	0.0634944643468	-0.0458992706774	0.0763368310803	0.0569339967465	-0.0638313980009	0.118607800624	-0.166384403732	0.0623182528562	-0.235082655836	-0.0378366564866	0.0378809117245	-0.0468195444717	0.0685768665957	0.199804186395	-0.0338485132395	0.211512152304	0.0679999700583	0.0249526275289	0.166971695614	-0.00121262056076	0.201237032965	88.3734299636	28.4732801457	103.469464196
11	0.246593511242	0.0612093658805	0.0304289638888	0.0326598534082	-0.018912892931	0.125857020425	0.146082072717	-0.197176601741	0.0318830885942	0.062680254685	-0.177701096978	-0.0914112179988	-0.174651432313	-0.0464835862514	-0.0319346849073	0.1318069261	-0.00424601898783	-0.018198137916	0.0631908955933	0.00747882460604	0.136638580284	87.9251238084	29.6871184018	114.945792978
12	0.0061348405939	0.00264315395658	-0.00232118413718	0.00287881997997	-0.0043274314192	0.000427843727476	0.00121342912908	-0.0628721229384	-0.21305689108	0.182500410482	0.146265918807	-0.146273810528	-0.0364198600459	0.128945227988	-0.000208971940702	0.172212066752	0.0141126621174	-0.0184633180402	0.186603729064	0.0178450478972	0.252975926735	91.3421610625	39.4925665376	110.952345951
13	0.0459924053819	-0.0331856247042	-0.176495199123	0.0123573619264	0.0804650822401	0.574595971705	0.0302616662537	-0.442130407273	0.0011892004073	0.00550379808519	0.0389090148795	0.0899145612452	-0.0493908088337	0.617438642525	-0.0365996724082	0.136079416518	-0.0197751215894	-0.00574999519382	0.299675784488	-0.0661969692902	0.221486781279	110.480092104	23.9989329799	149.113753955
14	0.334120904837	-0.0372799224664	-0.0746218785266	0.0348844614655	-0.00148543440518	0.0170879039997	0.0339650788407	-0.0119718786704	0.070461930688	0.0247968026933	0.00651094589798	-0.0728128661201	0.0697970658667	0.117945290043	0.0397462117983	0.599686031183	0.361905294817	-0.118123908785	0.594192877071	-0.0774268346802	0.211970289675	117.191688332	9.77282785656	161.267900055
15	0.0604906940491	0.0606793444809	-0.0388157152151	0.0664186281954	-0.0147274995968	0.147605336243	-0.158785515746	-0.0493731045728	-0.0259203445313	0.139718844663	0.149795954281	-0.0174369144853	0.36820089439	0.216741371156	0.0121662875911	0.203774464583	0.0874983235501	-0.0108802069861	0.296695740053	-0.0108673028692	0.109351861341	107.475578408	14.7025133481	153.325834506
16	0.0207602632666	0.0114344927972	0.00187915136302	0.001280883356	0.00141817524156	-0.000121728161548	-0.0187190592698	0.00739062401421	0.0046276763039	0.0719370184599	0.0442434496789	-0.0523993570239	0.0967695249158	0.0522731072512	-1.74222533464E-5	0.204244656652	0.0240460951851	0.0529125792228	0.279049313833	-0.0231581955817	0.265982312657	111.375065391	7.04038607298	148.480686536
17	0.140888984984	0.108769508381	0.0635025240691	0.100229773146	0.0546662067644	0.0667949822655	0.0662579696425	0.0549915257135	-0.242050344281	0.0664146747379	0.077589196369	-0.0881157532626	0.154575830292	-0.00306281712494	0.0243822465918	0.227538766038	0.100592771692	0.0244685901489	0.240581690705	0.06524798036	0.195925446368	99.9989590361	8.473019545	152.11640377
18	0.300203949942	-0.224588956558	-0.16801349761	0.179187451643	0.140086174653	0.118786358768	-0.0622712702391	0.112948597641	-0.0240433465138	0.0852761170538	-0.0349408926162	0.0692807635392	-0.102377508902	-0.189299104556	-0.0678706761017	0.435011668388	0.2383517623	0.0382914958485	0.509089305434	0.0624799578163	0.195215843492	84.7388720197	37.1398161647	90.9949252755
19	0.000628946026347	-0.00136042729704	-0.000977726605714	0.000830986567451	0.00147423953992	0.000953787043072	0.098356813089	0.0290522296687	0.00296591759548	-0.0658599649943	0.0688957108171	-0.125906742588	0.0582869796681	-0.00518492089732	-0.000108858900918	0.517284069876	-0.153957652405	-0.0767497549681	0.708636601366	-0.0415155113826	0.230729214509	81.7592932868	26.1298739928	81.7148625123
20	0.0719873158772	-0.0663216951788	0.0401680379064	0.0739975694352	-0.0381623939473	0.0615854334787	-0.107404438942	-0.229536623606	-0.198536623908	-0.0872851515419	-0.0239869668085	0.118177244821	-0.00476496333674	-0.0622591769125	-0.127763328047	0.37988820957	0.162434817324	0.0370235419444	0.404099595148	0.224192575054	-0.705925954395	91.2489901451	32.1771475984	89.610205812
21	0.0428819082316	-0.0115214777345	0.00155962740046	-3.89720853219E-5	0.000148218158401	-0.00155731354097	0.00897070980907	-0.0123094803947	-0.0214859671888	0.0520284780962	0.0657692830206	0.036054649266	-0.00678623875855	-0.0275736597961	0.000199570980887	0.340888239938	0.0245458956603	0.0269642820922	0.369969275454	0.00302418347939	0.182787089384	88.7098912367	24.5851869312	94.7005893022
22	0.00106710967862	-0.000847268807165	-3.01203513551E-5	0.00475104152477	-0.00133808397487	0.00011706358153	0.0726715881831	-0.0240031285132	-0.017273752109	0.0631847326103	-0.198904257886	-0.0148235913613	0.0765895421063	0.0564268224774	-8.28097680038E-5	0.229985105212	0.0461189046383	-0.0489776882939	0.563254575839	0.0395542265626	0.260761523631	99.4374720479	27.3296452464	90.456132741
23	-0.000554682121197	-0.00488370799189	0.00220415522895	0.0128301982451	-0.00412159504457	0.00365476382036	0.229266760211	-0.0504842532254	0.24515517572	0.0974956327298	0.0388217253161	0.0773333707109	-0.259319546009	0.0925744230691	0.000627248793412	0.405507765524	0.0499983606392	0.00669534980914	0.332882568621	-0.0306733786405	0.2040706906	101.881282877	15.143566984	91.1839729218
24	0.0706558222911	0.0472275909145	-0.0202069489972	0.0481522595992	-0.012321079425	0.0282168342815	-0.141117290506	-0.102393512014	0.0539396763333	0.142682329636	-0.0791934963887	-0.146859990195	-0.247695308606	-0.0330485294093	-0.00169167416684	0.380463776658	-0.00464715251489	-0.0412346218723	0.397098884331	-0.00654411482076	0.180782840861	109.64684398	12.8977906476	99.2226540043
25	0.395340209628	-0.399151457734	-0.155061940334	0.394763209861	0.149136989872	0.0611066977026	0.167483013508	0.0202220255344	0.164503260237	-0.195130178619	-0.0782436497863	-0.254703917683	-0.0782929114553	0.00603673679005	0.0229043183117	0.401213508125	0.0269687466112	-0.0308147952811	0.365304152364	-0.0173806423524	0.122841220387	105.86629989	9.66703476262	89.0675343542
26	0.0276210375929	0.0181018780685	0.0053198590885	0.0931718814257	-0.03103424299	0.0138834759478	-0.019659374189	-0.00587121859308	-0.0784257347103	-0.037135648491	-0.0284320638298	-0.032747740705	-0.0525468078871	0.116856738971	0.0251617373229	0.434260376746	0.127386146745	0.10550194427	0.626502546516	0.237428588766	0.267577472334	114.62209975	12.5664351162	87.5852388871
27	0.0515597741365	0.00195162840043	-0.0174120313678	0.00115040941095	-0.00982723552455	0.0428794344476	-0.10109114124	-0.0395484519442	-0.021384872029	-0.0213918375329	-0.0118132461228	-0.0844428943688	0.119447740143	0.0108692281259	-0.0079791739178	0.551281186785	0.210798042752	-0.00273615373169	0.314801336528	0.021616113792	0.104522156654	113.239751548	1.59164847036	91.7193919745
28	0.235958709606	0.312427296321	-0.226930409069	0.426837885468	-0.280120489984	0.21586744527	0.00793132347579	0.0491856734343	0.333442502003	-0.156823414105	0.184758070814	0.0596762297618	-0.36830467218	-0.0719211965288	0.147041370048	0.239343265397	0.0403722277201	0.034618220743	0.0834403052969	-0.102835807223	0.121012286295	99.7232373902	32.0380164374	154.187434811
29	-0.00278308359397	-0.00141513088869	0.000229089940451	0.00110619395536	-0.000563184957349	-0.00299404611727	0.00643178768025	0.00893840645633	-0.00606332991572	0.0561630603668	0.0290450095014	0.0963548549659	-0.189978636717	0.0801819145055	-0.000224749379309	0.259349309204	0.0334565894029	-0.0407870307572	0.174810575036	-0.000761455051598	0.159655757993	84.1118180242	35.1479139814	142.394030981
30	0.0386418805825	0.021836457607	0.0410902274692	-0.00321203117349	0.0329581242319	0.0397702001685	-0.00594818507311	-0.232037690806	-0.102441580289	0.120230287411	-0.019664845469	0.0730166074991	0.0981030963782	-0.0725844231959	3.0629588847E-5	0.143081560978	-0.0289842315147	-0.0045595958798	0.212316245303	0.0120352217659	0.151439694744	90.2554226267	25.332264116	151.464616633

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 0 through 19 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 20 through 51 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 52 through 57 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 58 through 66 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid -1 through 38 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 39 through 66 )
7	X-RAY DIFFRACTION	7	chain 'C' and (resid 0 through 38 )
8	X-RAY DIFFRACTION	8	chain 'C' and (resid 39 through 66 )
9	X-RAY DIFFRACTION	9	chain 'D' and (resid -1 through 19 )
10	X-RAY DIFFRACTION	10	chain 'D' and (resid 20 through 38 )
11	X-RAY DIFFRACTION	11	chain 'D' and (resid 39 through 57 )
12	X-RAY DIFFRACTION	12	chain 'D' and (resid 58 through 66 )
13	X-RAY DIFFRACTION	13	chain 'E' and (resid 0 through 19 )
14	X-RAY DIFFRACTION	14	chain 'E' and (resid 20 through 27 )
15	X-RAY DIFFRACTION	15	chain 'E' and (resid 28 through 51 )
16	X-RAY DIFFRACTION	16	chain 'E' and (resid 52 through 57 )
17	X-RAY DIFFRACTION	17	chain 'E' and (resid 58 through 66 )
18	X-RAY DIFFRACTION	18	chain 'F' and (resid 6 through 19 )
19	X-RAY DIFFRACTION	19	chain 'F' and (resid 20 through 27 )
20	X-RAY DIFFRACTION	20	chain 'F' and (resid 28 through 51 )
21	X-RAY DIFFRACTION	21	chain 'F' and (resid 52 through 57 )
22	X-RAY DIFFRACTION	22	chain 'F' and (resid 58 through 66 )
23	X-RAY DIFFRACTION	23	chain 'G' and (resid 7 through 19 )
24	X-RAY DIFFRACTION	24	chain 'G' and (resid 20 through 37 )
25	X-RAY DIFFRACTION	25	chain 'G' and (resid 38 through 51 )
26	X-RAY DIFFRACTION	26	chain 'G' and (resid 52 through 57 )
27	X-RAY DIFFRACTION	27	chain 'G' and (resid 58 through 66 )
28	X-RAY DIFFRACTION	28	chain 'H' and (resid 1 through 19 )
29	X-RAY DIFFRACTION	29	chain 'H' and (resid 20 through 27 )
30	X-RAY DIFFRACTION	30	chain 'H' and (resid 28 through 66 )

-
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