PDB-9b1q: Crystal Structure of human Tryptophan 2,3-dioxygenase in complex ...

ID or keywords:

Entry

Database: PDB / ID: 9b1q

Title

Crystal Structure of human Tryptophan 2,3-dioxygenase in complex with PYN1 inhibitor

Components

Tryptophan 2,3-dioxygenase

Keywords

OXIDOREDUCTASE/INHIBITOR / Inhibitor / OXIDOREDUCTASE / OXIDOREDUCTASE-INHIBITOR complex

Function / homology

Function and homology information

response to nitroglycerin / tryptophan catabolic process to acetyl-CoA / tryptophan 2,3-dioxygenase / tryptophan 2,3-dioxygenase activity / tryptophan catabolic process to kynurenine / Tryptophan catabolism / amino acid binding / oxygen binding / protein homotetramerization / heme binding ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.624 Å

Authors

Geeraerts, Z. / Yeh, S.-R.

Funding support

United States, 2items

Organization	Grant number	Country
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	GM115773	United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	GM151419	United States

Citation

Journal: J.Med.Chem. / Year: 2024
Title: Structural Insights into Protein-Inhibitor Interactions in Human Tryptophan Dioxygenase.
Authors: Geeraerts, Z. / Ishigami, I. / Lewis-Ballester, A. / Pham, K.N. / Kozlova, A. / Mathieu, C. / Frederick, R. / Yeh, S.R.

History

Deposition	Mar 13, 2024	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 21, 2024	Provider: repository / Type: Initial release
Revision 1.1	Sep 4, 2024	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2	Sep 11, 2024	Group: Database references / Category: citation_author / Item: _citation_author.identifier_ORCID

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	9b1q.cif.gz	722.4 KB	Display	PDBx/mmCIF format
PDB format	pdb9b1q.ent.gz		Display	PDB format
PDBx/mmJSON format	9b1q.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	9b1q_validation.pdf.gz	2.6 MB	Display	wwPDB validaton report
Full document	9b1q_full_validation.pdf.gz	2.7 MB	Display
Data in XML	9b1q_validation.xml.gz	52.1 KB	Display
Data in CIF	9b1q_validation.cif.gz	68.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/b1/9b1q ftp://data.pdbj.org/pub/pdb/validation_reports/b1/9b1q	HTTPS FTP

-
Related structure data

Related structure data	7lu7C 8vtqC 8vugC 8vzvC 8w1hC 8w2kC 9at2C 9b17C C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Tryptophan 2,3-dioxygenase

B: Tryptophan 2,3-dioxygenase

C: Tryptophan 2,3-dioxygenase

D: Tryptophan 2,3-dioxygenase

hetero molecules

185 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	142.959, 154.17, 88.277
Angle α, β, γ (deg.)	90, 90, 90
Int Tables number	18
Space group name H-M	P2₁2₁2

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	A
3	2	A
4	2	A
5	3	A
6	3	A
7	4	A
8	4	A
9	5	A
10	5	A
11	6	A
12	6	A

NCS domain segments:

Beg auth comp-ID: LEU / Beg label comp-ID: LEU / Auth asym-ID: A / Label asym-ID: A

Dom-ID	Component-ID	Ens-ID	End auth comp-ID	End label comp-ID	Auth seq-ID	Label seq-ID
1	1	1	HIS	HIS	40 - 391	24 - 375
2	1	1	HIS	HIS	40 - 391	24 - 375
3	2	2	PHE	PHE	40 - 388	24 - 372
4	2	2	PHE	PHE	40 - 388	24 - 372
5	3	3	PHE	PHE	40 - 388	24 - 372
6	3	3	PHE	PHE	40 - 388	24 - 372
7	4	4	PHE	PHE	40 - 388	24 - 372
8	4	4	PHE	PHE	40 - 388	24 - 372
9	5	5	PHE	PHE	40 - 388	24 - 372
10	5	5	PHE	PHE	40 - 388	24 - 372
11	6	6	PHE	PHE	40 - 388	24 - 372
12	6	6	PHE	PHE	40 - 388	24 - 372

NCS ensembles :

ID	Details
1	Local NCS retraints between domains: 1 2
2	Local NCS retraints between domains: 3 4
3	Local NCS retraints between domains: 5 6
4	Local NCS retraints between domains: 7 8
5	Local NCS retraints between domains: 9 10
6	Local NCS retraints between domains: 11 12

#1: Protein	Tryptophan 2,3-dioxygenase / TDO / Tryptamin 2 / 3-dioxygenase / Tryptophan oxygenase / TRPO / Tryptophan pyrrolase / Tryptophanase Mass: 45182.535 Da / Num. of mol.: 4 / Fragment: UNP residues 18-389 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TDO2, TDO / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P48775, tryptophan 2,3-dioxygenase
#2: Chemical	ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₃₄H₃₂FeN₄O₄
#3: Chemical	ChemComp-A1AH8 / (5P)-1-[(imidazolidin-1-yl)methyl]-5-(1H-indol-3-yl)-1H-1,2,3-benzotriazole Mass: 318.376 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₈H₁₈N₆ / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-ZIQ / alpha-methyl-L-tryptophan Type: L-peptide linking / Mass: 218.252 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₂H₁₄N₂O₂
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 12 / 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: 2.69 Å³/Da / Density % sol: 54.3 %
Crystal grow	Temperature: 298 K / Method: microbatch Details: 50 mM Sodium Citrate pH 5.6, 2.0% Tacsimate pH 5.0, 5.0% PEG 3350

-
Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

NSLS-II

/ Beamline: 17-ID-2 / Wavelength: 0.97934 Å

Detector

Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 10, 2024

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97934 Å / Relative weight: 1

Reflection

Resolution: 2.624→34.291 Å / Num. obs: 31809 / % possible obs: 93.7 % / Redundancy: 6.38 %
Details: Some remarks regarding the mmCIF items written, the PDB Exchange Dictionary (PDBx/mmCIF) Version 5.0 supporting the data files in the current PDB archive (dictionary version 5.325, last ...Details: Some remarks regarding the mmCIF items written, the PDB Exchange Dictionary (PDBx/mmCIF) Version 5.0 supporting the data files in the current PDB archive (dictionary version 5.325, last updated 2020-04-13: http://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Index/) and the actual quantities provided by MRFANA (https://github.com/githubgphl/MRFANA) from the autoPROC package (https://www.globalphasing.com/autoproc/). In general, the mmCIF categories here should provide items that are currently used in the PDB archive. If there are alternatives, the one recommended by the PDB developers has been selected. The distinction between *_all and *_obs quantities is not always clear: often only one version is actively used within the PDB archive (or is the one recommended by PDB developers). The intention of distinguishing between classes of reflections before and after some kind of observation criterion was applied, can in principle be useful - but such criteria change in various ways throughout the data processing steps (rejection of overloaded or too partial reflections, outlier/misfit rejections during scaling etc) and there is no retrospect computation of data scaling/merging statistics for the reflections used in the final refinement (where another observation criterion might have been applied). Typical data processing will usually only provide one version of statistics at various stages and these are given in the recommended item here, irrespective of the "_all" and "_obs" connotation, see e.g. the use of _reflns.pdbx_Rmerge_I_obs, _reflns.pdbx_Rrim_I_all and _reflns.pdbx_Rpim_I_all. Please note that all statistics related to "merged intensities" (or "merging") are based on inverse-variance weighting of the individual measurements making up a symmetry-unique reflection. This is standard for several decades now, even if some of the dictionary definitions seem to suggest that a simple "mean" or "average" intensity is being used instead. R-values are always given for all symmetry-equivalent reflections following Friedel's law, i.e. Bijvoet pairs are not treated separately (since we want to describe the overall mean intensity and not the mean I(+) and I(-) here). The Rrim metric is identical to the Rmeas R-value and only differs in name. _reflns.pdbx_number_measured_all is the number of measured intensities just before the final merging step (at which point no additional rejection takes place). _reflns.number_obs is the number of symmetry-unique observations, i.e. the result of merging those measurements via inverse-variance weighting. _reflns.pdbx_netI_over_sigmaI is based on the merged intensities (_reflns.number_obs) as expected. _reflns.pdbx_redundancy is synonymous with "multiplicity". The per-shell item _reflns_shell.number_measured_all corresponds to the overall value _reflns.pdbx_number_measured_all. The per-shell item _reflns_shell.number_unique_all corresponds to the overall value _reflns.number_obs. The per-shell item _reflns_shell.percent_possible_all corresponds to the overall value _reflns.percent_possible_obs. The per-shell item _reflns_shell.meanI_over_sigI_obs corresponds to the overall value given as _reflns.pdbx_netI_over_sigmaI. But be aware of the incorrect definition of the former in the current dictionary!
CC_1/2: 0.998 / CC_1/2 anomalous: -0.177 / R_merge(I) obs: 0.1357 / R_pim(I) all: 0.0582 / R_rim(I) all: 0.148 / AbsDiff over sigma anomalous: 0.784 / B_aniso tensor eigenvalue 1: 52.6 Å² / B_aniso tensor eigenvalue 2: 104.1 Å² / B_aniso tensor eigenvalue 3: 135.3 Å² / B_aniso tensor eigenvector 1 ortho1: 1 / B_aniso tensor eigenvector 1 ortho2: 0 / B_aniso tensor eigenvector 1 ortho3: 0 / B_aniso tensor eigenvector 2 ortho1: 0 / B_aniso tensor eigenvector 2 ortho2: 1 / B_aniso tensor eigenvector 2 ortho3: 0 / B_aniso tensor eigenvector 3 ortho1: 0 / B_aniso tensor eigenvector 3 ortho2: 0 / B_aniso tensor eigenvector 3 ortho3: 1 / Aniso diffraction limit 1: 2.608 Å / Aniso diffraction limit 2: 3.336 Å / Aniso diffraction limit 3: 3.666 Å / Aniso diffraction limit axis 1 ortho1: 1 / Aniso diffraction limit axis 1 ortho2: 0 / Aniso diffraction limit axis 1 ortho3: 0 / Aniso diffraction limit axis 2 ortho1: 0 / Aniso diffraction limit axis 2 ortho2: 1 / Aniso diffraction limit axis 2 ortho3: 0 / Aniso diffraction limit axis 3 ortho1: 0 / Aniso diffraction limit axis 3 ortho2: 0 / Aniso diffraction limit axis 3 ortho3: 1 / Net I/σ(I): 9.62 / Num. measured all: 203088 / Observed signal threshold: 1.2 / Orthogonalization convention: pdb / % possible anomalous: 93.4 / % possible ellipsoidal: 93.7 / % possible ellipsoidal anomalous: 93.4 / % possible spherical: 53.8 / % possible spherical anomalous: 52.4 / Redundancy anomalous: 3.39 / Signal type: local

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured all	Num. measured obs	Num. unique all	Num. unique obs	CC_1/2	CC_1/2 anomalous	R_pim(I) all	R_rim(I) all	AbsDiff over sigma anomalous	% possible anomalous	% possible ellipsoidal	% possible ellipsoidal anomalous	% possible spherical	% possible spherical anomalous	Redundancy anomalous	% possible all
8.96-34.291	5.7	0.0482	28.4	9063	9063	1590	1590	0.998	-0.298	0.0218	0.0531	0.72	99.6	99.1	99.6	99.1	99.6	3.29	99.1
7.081-8.96	5.75	0.0481	23.12	9146	9146	1590	1590	0.999	-0.18	0.0215	0.0528	0.78	99.8	99.5	99.8	99.5	99.8	3.15	99.5
6.162-7.081	5.68	0.0767	17.3	9033	9033	1590	1590	0.996	0.015	0.0347	0.0844	0.837	98.7	99.6	98.7	99.6	98.7	3.09	99.6
5.586-6.162	6.01	0.104	13.91	9561	9561	1591	1591	0.995	-0.115	0.0459	0.114	0.783	98.9	99.5	98.9	99.5	98.9	3.23	99.5
5.177-5.586	6.23	0.1132	13.68	9901	9901	1590	1590	0.994	-0.087	0.049	0.1237	0.792	99.2	99.4	99.2	99.4	99.2	3.34	99.4
4.866-5.177	6.31	0.1212	13.23	10042	10042	1591	1591	0.994	-0.005	0.052	0.1321	0.821	99.4	99.6	99.4	99.6	99.4	3.37	99.6
4.618-4.866	6.4	0.128	12.54	10179	10179	1591	1591	0.994	-0.115	0.0546	0.1394	0.787	99.9	99.7	99.9	99.7	99.9	3.4	99.7
4.412-4.618	6.54	0.1329	11.94	10394	10394	1590	1590	0.995	-0.055	0.0559	0.1444	0.775	99.9	99.9	99.9	99.9	99.9	3.46	99.9
4.24-4.412	6.58	0.1545	10.61	10462	10462	1591	1591	0.993	-0.065	0.0651	0.1679	0.817	99.9	99.9	99.9	99.9	99.9	3.47	99.9
4.091-4.24	6.59	0.2147	8.43	10477	10477	1590	1590	0.991	-0.055	0.0911	0.2336	0.793	99.9	99.9	99.9	99.9	99.9	3.47	99.9
3.959-4.091	6.66	0.2441	7.52	10598	10598	1591	1591	0.984	-0.13	0.1026	0.2652	0.752	99.3	98.8	99.3	98.8	99.3	3.49	98.8
3.841-3.959	6.55	0.3347	5.93	10406	10406	1589	1589	0.967	-0.054	0.1419	0.3641	0.785	98.2	97.9	98.2	97.9	98.2	3.42	97.9
3.733-3.841	5.96	0.4195	4.49	9486	9486	1591	1591	0.948	0.023	0.1846	0.4592	0.809	94	94.7	94	94.7	94	3.15	94.7
3.636-3.733	6.31	0.415	4.65	10034	10034	1591	1591	0.957	-0.017	0.1786	0.4526	0.76	92.9	93.3	92.9	92.2	92	3.31	93.3
3.538-3.636	6.58	0.5396	3.77	10467	10467	1590	1590	0.932	-0.01	0.2277	0.5865	0.781	92.2	92.1	92.2	85.1	85.5	3.42	92.1
3.438-3.538	6.25	0.6348	3.18	9938	9938	1591	1591	0.891	0.029	0.2742	0.6926	0.812	89.9	90.2	89.9	74.1	74.4	3.25	90.2
3.321-3.438	6.35	0.6481	2.98	10096	10096	1590	1590	0.895	-0.001	0.2768	0.7057	0.791	79.9	79.9	79.9	55.3	55.3	3.31	79.9
3.175-3.321	6.87	0.7514	2.58	10931	10931	1591	1591	0.816	-0.012	0.3081	0.813	0.766	82.5	83	82.5	38.5	38	3.59	83
2.997-3.175	7.08	0.7795	2.46	11258	11258	1591	1591	0.817	-0.042	0.3148	0.8414	0.744	82.8	83.3	82.8	25.3	24.7	3.71	83.3
2.624-2.997	7.31	1.0604	1.79	11616	11616	1590	1590	0.647	-0.009	0.42	1.1417	0.76	76.3	77.1	76.3	8.3	7.6	3.92	77.1

-
Processing

Software

Name	Version	Classification
REFMAC	5.8.0425	refinement
autoPROC		data reduction
STARANISO		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.624→34.291 Å / Cor.coef. F_o:F_c: 0.928 / Cor.coef. F_o:F_c free: 0.874 / SU B: 40.36 / SU ML: 0.356 / Cross valid method: FREE R-VALUE / ESU R Free: 0.533
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2583	1625	5.109 %
R_work	0.2023	30183	-
all	0.205	-	-
obs	-	31808	53.781 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 75.541 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.094 Å²	0 Å²	-0 Å²
2-	-	-0.289 Å²	-0 Å²
3-	-	-	-0.805 Å²

Refinement step

Cycle: LAST / Resolution: 2.624→34.291 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11596	0	332	12	11940

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.012	12251
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	11562
X-RAY DIFFRACTION	r_angle_refined_deg	1.417	1.891	16558
X-RAY DIFFRACTION	r_angle_other_deg	0.481	1.79	26505
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.747	5	1354
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	18.277	6.121	107
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.554	10	2254
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	10.713	10	647
X-RAY DIFFRACTION	r_chiral_restr	0.06	0.2	1699
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	14383
X-RAY DIFFRACTION	r_gen_planes_other	0.003	0.02	3113
X-RAY DIFFRACTION	r_nbd_refined	0.241	0.2	3124
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.204	0.2	11752
X-RAY DIFFRACTION	r_nbtor_refined	0.198	0.2	6091
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.077	0.2	6350
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.149	0.2	334
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.092	0.2	2
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.159	0.2	13
X-RAY DIFFRACTION	r_nbd_other	0.201	0.2	35
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.148	0.2	4
X-RAY DIFFRACTION	r_mcbond_it	3.37	4.022	5454
X-RAY DIFFRACTION	r_mcbond_other	3.365	4.021	5452
X-RAY DIFFRACTION	r_mcangle_it	5.641	7.21	6794
X-RAY DIFFRACTION	r_mcangle_other	5.642	7.21	6794
X-RAY DIFFRACTION	r_scbond_it	3.628	4.416	6797
X-RAY DIFFRACTION	r_scbond_other	3.624	4.415	6796
X-RAY DIFFRACTION	r_scangle_it	6.086	7.998	9764
X-RAY DIFFRACTION	r_scangle_other	6.085	7.999	9765
X-RAY DIFFRACTION	r_lrange_it	11.897	49.014	53556
X-RAY DIFFRACTION	r_lrange_other	11.897	49.014	53555
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.112	0.05	12070
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.12	0.05	11413
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.115	0.05	11913
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.121	0.05	11454
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.12	0.05	11921
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.123	0.05	11417

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	A	X-RAY DIFFRACTION	Local ncs	0.11203	0.0501
1	2	A	X-RAY DIFFRACTION	Local ncs	0.11203	0.0501
2	3	A	X-RAY DIFFRACTION	Local ncs	0.11978	0.05009
2	4	A	X-RAY DIFFRACTION	Local ncs	0.11978	0.05009
3	5	A	X-RAY DIFFRACTION	Local ncs	0.11515	0.0501
3	6	A	X-RAY DIFFRACTION	Local ncs	0.11515	0.0501
4	7	A	X-RAY DIFFRACTION	Local ncs	0.12134	0.05009
4	8	A	X-RAY DIFFRACTION	Local ncs	0.12134	0.05009
5	9	A	X-RAY DIFFRACTION	Local ncs	0.11971	0.0501
5	10	A	X-RAY DIFFRACTION	Local ncs	0.11971	0.0501
6	11	A	X-RAY DIFFRACTION	Local ncs	0.12318	0.05009
6	12	A	X-RAY DIFFRACTION	Local ncs	0.12318	0.05009

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.624-2.692	0.15	3	0.327	63	X-RAY DIFFRACTION	1.5363
2.692-2.765	0.386	10	0.321	193	X-RAY DIFFRACTION	4.8507
2.765-2.844	0.188	14	0.344	336	X-RAY DIFFRACTION	8.5721
2.844-2.931	0.388	21	0.314	493	X-RAY DIFFRACTION	13.0292
2.931-3.027	0.386	45	0.296	634	X-RAY DIFFRACTION	17.71
3.027-3.132	0.412	38	0.277	885	X-RAY DIFFRACTION	24.732
3.132-3.249	0.316	73	0.255	1154	X-RAY DIFFRACTION	34.1497
3.249-3.381	0.338	70	0.256	1502	X-RAY DIFFRACTION	45.3287
3.381-3.53	0.282	128	0.248	2154	X-RAY DIFFRACTION	68.5697
3.53-3.7	0.299	127	0.241	2653	X-RAY DIFFRACTION	86.8479
3.7-3.897	0.277	150	0.228	2746	X-RAY DIFFRACTION	95.546
3.897-4.131	0.247	159	0.193	2696	X-RAY DIFFRACTION	98.8231
4.131-4.411	0.197	144	0.164	2588	X-RAY DIFFRACTION	99.9268
4.411-4.758	0.222	103	0.148	2429	X-RAY DIFFRACTION	99.8029
4.758-5.202	0.229	128	0.159	2236	X-RAY DIFFRACTION	99.6627
5.202-5.8	0.266	104	0.193	2025	X-RAY DIFFRACTION	99.4395
5.8-6.665	0.266	91	0.222	1809	X-RAY DIFFRACTION	99.5285
6.665-8.087	0.269	99	0.2	1566	X-RAY DIFFRACTION	99.5813
8.087-11.132	0.196	58	0.177	1251	X-RAY DIFFRACTION	99.4681
11.132-34.291	0.289	60	0.235	770	X-RAY DIFFRACTION	98.8095

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	1.8022	-1.7226	-0.6804	4.0495	0.3882	0.945	-0.0276	-0.024	-0.1149	-0.2993	0.0231	0.452	-0.1033	-0.2468	0.0045	0.0764	0.0546	-0.0461	0.1334	-0.0004	0.1907	-39.0171	37.1873	-0.9285
2	4.0641	-0.4801	-2.1791	1.1053	0.3598	1.8617	-0.3185	-0.3525	-0.4393	0.0537	0.0984	-0.1661	0.1637	0.4956	0.2201	0.069	0.0198	-0.0459	0.1668	0.0375	0.2281	-5.2086	16.726	-10.7042
3	1.9552	0.621	0.4066	3.1582	1.7719	2.4251	0.0212	0.6709	0.0096	-0.5765	-0.2574	0.9214	-0.0645	-0.6393	0.2362	0.2702	0.0623	-0.2169	0.548	-0.0242	0.3446	-27.8101	32.9069	-28.4245
4	1.8224	-0.125	-0.215	1.4306	0.0954	3.4401	-0.0457	-0.5759	0.2052	0.2108	0.0682	-0.2431	0.0224	0.3348	-0.0225	0.0331	0.0153	-0.0543	0.2117	-0.0324	0.2122	-6.8853	42.4262	4.4299

Refinement TLS group

Selection: ALL

-
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