PDB-7zp2: Crystal Structure of truncated aspartate transcarbamoylase from P...

ID or keywords:

Entry

Database: PDB / ID: 7zp2

Title

Crystal Structure of truncated aspartate transcarbamoylase from Plasmodium falciparum in complex with BDA-04

Components

Aspartate carbamoyltransferase

Keywords

TRANSFERASE /

Aspartate transcarbamoylase /

Plasmodium falciparum / fragment-based screening /

inhibitor /

malaria

Function / homology

Function and homology information

aspartate carbamoyltransferase /

aspartate carbamoyltransferase activity / amino acid metabolic process /

amino acid binding / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process /

membrane
Similarity search - Function

Biological species

Plasmodium falciparum 3D7 (eukaryote)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.292 Å

Authors

Wang, C. / Zhang, B. / Groves, M.R.

Funding support

China, 1items

Citation

Journal: J.Am.Chem.Soc. / Year: 2022
Title: Discovery of Small-Molecule Allosteric Inhibitors of Pf ATC as Antimalarials.
Authors: Wang, C. / Zhang, B. / Kruger, A. / Du, X. / Visser, L. / Domling, A.S.S. / Wrenger, C. / Groves, M.R.

History

Deposition	Apr 26, 2022	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Aug 24, 2022	Provider: repository / Type: Initial release
Revision 1.1	Sep 7, 2022	Group: Structure summary / Category: struct_keywords / Item: _struct_keywords.text
Revision 1.2	Oct 26, 2022	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3	Nov 2, 2022	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.4	Jan 31, 2024	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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	7zp2.cif.gz	1.4 MB	Display	PDBx/mmCIF format
PDB format	pdb7zp2.ent.gz	1.2 MB	Display	PDB format
PDBx/mmJSON format	7zp2.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/zp/7zp2 ftp://data.pdbj.org/pub/pdb/validation_reports/zp/7zp2	HTTPS FTP

-
Related structure data

Related structure data	7zczC 7zeaC 7zgsC 7zhiC 7zidC 7zstC 5ilqS S: Starting model for refinement 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
Related items in Molecule of the Month	#215 - Nov 2017 Aspartate Transcarbamoylase similarity (10)

Deposited unit

A: Aspartate carbamoyltransferase

B: Aspartate carbamoyltransferase

C: Aspartate carbamoyltransferase

D: Aspartate carbamoyltransferase

E: Aspartate carbamoyltransferase

F: Aspartate carbamoyltransferase

hetero molecules

243 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Aspartate carbamoyltransferase

B: Aspartate carbamoyltransferase

C: Aspartate carbamoyltransferase

hetero molecules

defined by author&software
Evidence: gel filtration
122 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

D: Aspartate carbamoyltransferase

E: Aspartate carbamoyltransferase

F: Aspartate carbamoyltransferase

hetero molecules

defined by author&software
121 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	87.065, 87.360, 104.636
Angle α, β, γ (deg.)	89.981, 90.036, 117.724
Int Tables number	1
Space group name H-M	P1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

End auth comp-ID: PHE / End label comp-ID: PHE

Dom-ID	Component-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	1	TYR	TYR	A	A	39 - 383	3 - 347
2	1	1	TYR	TYR	B	B	39 - 383	3 - 347
3	2	2	TYR	TYR	A	A	39 - 383	3 - 347
4	2	2	TYR	TYR	C	C	39 - 383	3 - 347
5	3	3	TYR	TYR	A	A	39 - 383	3 - 347
6	3	3	TYR	TYR	D	D	39 - 383	3 - 347
7	4	4	TYR	TYR	A	A	39 - 383	3 - 347
8	4	4	TYR	TYR	E	E	39 - 383	3 - 347
9	5	5	TYR	TYR	A	A	39 - 383	3 - 347
10	5	5	TYR	TYR	F	F	39 - 383	3 - 347
11	6	6	PHE	PHE	B	B	38 - 383	2 - 347
12	6	6	PHE	PHE	C	C	38 - 383	2 - 347
13	7	7	TYR	TYR	B	B	39 - 383	3 - 347
14	7	7	TYR	TYR	D	D	39 - 383	3 - 347
15	8	8	PHE	PHE	B	B	38 - 383	2 - 347
16	8	8	PHE	PHE	E	E	38 - 383	2 - 347
17	9	9	PHE	PHE	B	B	38 - 383	2 - 347
18	9	9	PHE	PHE	F	F	38 - 383	2 - 347
19	10	10	TYR	TYR	C	C	39 - 383	3 - 347
20	10	10	TYR	TYR	D	D	39 - 383	3 - 347
21	11	11	PHE	PHE	C	C	38 - 383	2 - 347
22	11	11	PHE	PHE	E	E	38 - 383	2 - 347
23	12	12	PHE	PHE	C	C	38 - 383	2 - 347
24	12	12	PHE	PHE	F	F	38 - 383	2 - 347
25	13	13	TYR	TYR	D	D	39 - 383	3 - 347
26	13	13	TYR	TYR	E	E	39 - 383	3 - 347
27	14	14	TYR	TYR	D	D	39 - 383	3 - 347
28	14	14	TYR	TYR	F	F	39 - 383	3 - 347
29	15	15	PHE	PHE	E	E	38 - 383	2 - 347
30	15	15	PHE	PHE	F	F	38 - 383	2 - 347

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
7	Local NCS retraints between domains: 13 14
8	Local NCS retraints between domains: 15 16
9	Local NCS retraints between domains: 17 18
10	Local NCS retraints between domains: 19 20
11	Local NCS retraints between domains: 21 22
12	Local NCS retraints between domains: 23 24
13	Local NCS retraints between domains: 25 26
14	Local NCS retraints between domains: 27 28
15	Local NCS retraints between domains: 29 30

#1: Protein	Aspartate carbamoyltransferase / Mass: 40350.762 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium falciparum 3D7 (eukaryote) / Strain: isolate 3D7 / Gene: PF3D7_1344800 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: A0A5K1K910, aspartate carbamoyltransferase
#2: Chemical	ChemComp-EJG / tert-butyl N-[5-phenyl-3-(2-phenylethylcarbamoyl)thiophen-2-yl]carbamate / (2S)-2-[[(2S)-4-methyl-2-(phenylmethoxycarbonylamino)pentanoyl]amino]-1-oxidanyl-hexane-1-sulfonic acid Mass: 422.540 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂₄H₂₆N₂O₃S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO₄
#4: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 195 / 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: 2.18 Å³/Da / Density % sol: 43.74 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 200mM NaCl, 15%(w/v)PEG3350, 100mM bis-tris propane, 2%(v/v)DMSO

-
Data collection

Diffraction

Mean temperature: 291 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

PETRA III, DESY

/ Beamline: P11 / Wavelength: 1.0332 Å

Detector

Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 13, 2019

Radiation

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

Radiation wavelength

Wavelength: 1.0332 Å / Relative weight: 1

Reflection twin

Type	Crystal-ID	ID	Operator	Domain-ID	Fraction
pseudo-merohedral	1	1	H, K, L	1	0.3999
pseudo-merohedral	2	2	-h,-k,l	2	0.3668
pseudo-merohedral	3	3	K, H, -L	3	0.0808
pseudo-merohedral	4	4	-K, -H, -L	4	0.1525

Reflection

Resolution: 2.292→62.192 Å / Num. obs: 117783 / % possible obs: 97.1 % / Redundancy: 1.7 % / CC_1/2: 0.992 / R_merge(I) obs: 0.056 / R_pim(I) all: 0.056 / R_rim(I) all: 0.079 / Net I/σ(I): 9.4

Reflection shell

Resolution: 2.3→2.34 Å / Redundancy: 1.8 % / R_merge(I) obs: 0.303 / Num. unique obs: 5756 / CC_1/2: 0.931 / R_pim(I) all: 0.303 / R_rim(I) all: 0.429

-
Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
REFMAC	5.8.0267	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5ILQ

5ilq

Resolution: 2.292→62.192 Å / Cor.coef. F_o:F_c: 0.966 / Cor.coef. F_o:F_c free: 0.952 / WR_factor R_free: 0.191 / WR_factor R_work: 0.164 / SU B: 8.177 / SU ML: 0.104 / Average fsc free: 0.9736 / Average fsc work: 0.9819 / Cross valid method: FREE R-VALUE / ESU R: 0.05 / ESU R Free: 0.037
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.1914	6216	5.282 %
R_work	0.1636	111456	-
all	0.165	-	-
obs	-	117672	95.99 %

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: 54.772 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	3.212 Å²	-1.142 Å²	-3.002 Å²
2-	-	-3.233 Å²	2.366 Å²
3-	-	-	0.021 Å²

Refinement step

Cycle: LAST / Resolution: 2.292→62.192 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	16344	0	52	195	16591

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.014	0.013	16704
X-RAY DIFFRACTION	r_bond_other_d	0.003	0.015	15954
X-RAY DIFFRACTION	r_angle_refined_deg	2.037	1.641	22566
X-RAY DIFFRACTION	r_angle_other_deg	1.392	1.586	36836
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	8.087	5	2004
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.162	23.96	851
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	18.767	15	3098
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	24.94	15	62
X-RAY DIFFRACTION	r_chiral_restr	0.097	0.2	2259
X-RAY DIFFRACTION	r_gen_planes_refined	0.011	0.02	18627
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	3785
X-RAY DIFFRACTION	r_nbd_refined	0.228	0.2	3589
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.205	0.2	15798
X-RAY DIFFRACTION	r_nbtor_refined	0.176	0.2	8223
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.087	0.2	8670
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.256	0.2	438
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.141	0.2	6
X-RAY DIFFRACTION	r_metal_ion_refined	0.026	0.2	1
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.172	0.2	29
X-RAY DIFFRACTION	r_nbd_other	0.239	0.2	86
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.334	0.2	3
X-RAY DIFFRACTION	r_mcbond_it	3.825	4.179	8052
X-RAY DIFFRACTION	r_mcbond_other	3.825	4.179	8051
X-RAY DIFFRACTION	r_mcangle_it	5.232	6.26	10044
X-RAY DIFFRACTION	r_mcangle_other	5.232	6.26	10045
X-RAY DIFFRACTION	r_scbond_it	3.713	4.339	8652
X-RAY DIFFRACTION	r_scbond_other	3.659	4.337	8637
X-RAY DIFFRACTION	r_scangle_it	5.04	6.43	12522
X-RAY DIFFRACTION	r_scangle_other	5.007	6.427	12499
X-RAY DIFFRACTION	r_lrange_it	7.021	48.71	18500
X-RAY DIFFRACTION	r_lrange_other	7.017	48.695	18478
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.099	0.05	10654
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.096	0.05	10725
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.098	0.05	10807
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.098	0.05	10691
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.099	0.05	10741
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.103	0.05	10884
X-RAY DIFFRACTION	r_ncsr_local_group_7	0.104	0.05	10672
X-RAY DIFFRACTION	r_ncsr_local_group_8	0.093	0.05	11575
X-RAY DIFFRACTION	r_ncsr_local_group_9	0.103	0.05	10868
X-RAY DIFFRACTION	r_ncsr_local_group_10	0.1	0.05	10737
X-RAY DIFFRACTION	r_ncsr_local_group_11	0.103	0.05	10852
X-RAY DIFFRACTION	r_ncsr_local_group_12	0.086	0.05	11065
X-RAY DIFFRACTION	r_ncsr_local_group_13	0.098	0.05	10698
X-RAY DIFFRACTION	r_ncsr_local_group_14	0.095	0.05	10787
X-RAY DIFFRACTION	r_ncsr_local_group_15	0.097	0.05	10889

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	0.09913	0.05009
1	2	B	X-RAY DIFFRACTION	Local ncs	0.09913	0.05009
2	3	A	X-RAY DIFFRACTION	Local ncs	0.09648	0.05009
2	4	C	X-RAY DIFFRACTION	Local ncs	0.09648	0.05009
3	5	A	X-RAY DIFFRACTION	Local ncs	0.09751	0.05009
3	6	D	X-RAY DIFFRACTION	Local ncs	0.09751	0.05009
4	7	A	X-RAY DIFFRACTION	Local ncs	0.09783	0.05009
4	8	E	X-RAY DIFFRACTION	Local ncs	0.09783	0.05009
5	9	A	X-RAY DIFFRACTION	Local ncs	0.09918	0.05009
5	10	F	X-RAY DIFFRACTION	Local ncs	0.09918	0.05009
6	11	B	X-RAY DIFFRACTION	Local ncs	0.10295	0.05008
6	12	C	X-RAY DIFFRACTION	Local ncs	0.10295	0.05008
7	13	B	X-RAY DIFFRACTION	Local ncs	0.1035	0.05009
7	14	D	X-RAY DIFFRACTION	Local ncs	0.1035	0.05009
8	15	B	X-RAY DIFFRACTION	Local ncs	0.09328	0.05009
8	16	E	X-RAY DIFFRACTION	Local ncs	0.09328	0.05009
9	17	B	X-RAY DIFFRACTION	Local ncs	0.10334	0.05008
9	18	F	X-RAY DIFFRACTION	Local ncs	0.10334	0.05008
10	19	C	X-RAY DIFFRACTION	Local ncs	0.10014	0.05009
10	20	D	X-RAY DIFFRACTION	Local ncs	0.10014	0.05009
11	21	C	X-RAY DIFFRACTION	Local ncs	0.10345	0.05008
11	22	E	X-RAY DIFFRACTION	Local ncs	0.10345	0.05008
12	23	C	X-RAY DIFFRACTION	Local ncs	0.08567	0.05009
12	24	F	X-RAY DIFFRACTION	Local ncs	0.08567	0.05009
13	25	D	X-RAY DIFFRACTION	Local ncs	0.09816	0.05009
13	26	E	X-RAY DIFFRACTION	Local ncs	0.09816	0.05009
14	27	D	X-RAY DIFFRACTION	Local ncs	0.09507	0.05009
14	28	F	X-RAY DIFFRACTION	Local ncs	0.09507	0.05009
15	29	E	X-RAY DIFFRACTION	Local ncs	0.09748	0.05009
15	30	F	X-RAY DIFFRACTION	Local ncs	0.09748	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 (%)
2.292-2.351	0.269	360	0.238	7097	X-RAY DIFFRACTION	81.9001
2.351-2.416	0.265	382	0.222	8156	X-RAY DIFFRACTION	96.704
2.416-2.486	0.274	430	0.221	7829	X-RAY DIFFRACTION	95.8009
2.486-2.562	0.23	453	0.212	7577	X-RAY DIFFRACTION	96.2138
2.562-2.646	0.274	408	0.203	7275	X-RAY DIFFRACTION	95.3936
2.646-2.739	0.227	461	0.204	7104	X-RAY DIFFRACTION	96.3817
2.739-2.842	0.247	366	0.192	6897	X-RAY DIFFRACTION	96.9046
2.842-2.958	0.225	401	0.191	6698	X-RAY DIFFRACTION	97.2466
2.958-3.09	0.21	413	0.188	6349	X-RAY DIFFRACTION	97.0994
3.09-3.24	0.207	305	0.19	6211	X-RAY DIFFRACTION	97.5595
3.24-3.415	0.214	378	0.179	5681	X-RAY DIFFRACTION	96.4809
3.415-3.622	0.172	315	0.166	5602	X-RAY DIFFRACTION	98.3217
3.622-3.872	0.176	313	0.154	5226	X-RAY DIFFRACTION	98.2092
3.872-4.182	0.156	329	0.138	4827	X-RAY DIFFRACTION	98.0415
4.182-4.58	0.146	195	0.115	4516	X-RAY DIFFRACTION	98.0845
4.58-5.12	0.157	163	0.12	4117	X-RAY DIFFRACTION	98.4814
5.12-5.909	0.187	266	0.171	3508	X-RAY DIFFRACTION	98.5893
5.909-7.232	0.181	130	0.161	3093	X-RAY DIFFRACTION	98.1126
7.232-10.203	0.131	90	0.128	2363	X-RAY DIFFRACTION	98.3561

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	2.5876	-0.0531	0.5649	1.1184	-0.0423	0.7525	-0.0425	-0.133	-0.0883	0.1124	-0.0019	-0.1244	-0.0318	-0.0032	0.0444	0.0613	0.0255	-0.0329	0.0545	0.0436	0.0934	51.058	13.0652	-0.4339
2	1.1404	-0.4551	-0.0716	1.918	0.8688	1.0307	-0.0089	-0.0907	-0.0297	0.1439	-0.0115	0.0683	-0.0624	-0.0844	0.0204	0.0857	0.0202	-0.0005	0.0846	0.034	0.0207	21.586	45.2267	4.0193
3	0.8538	0.676	-0.1899	2.1366	-0.1059	0.6428	-0.0027	0.0195	-0.2072	0.0856	-0.0522	0.1081	0.1324	-0.2371	0.0548	0.0491	-0.0153	0.0052	0.2045	-0.0022	0.1718	9.0642	5.902	-9.6381
4	2.4558	-0.2757	-0.7938	1.1041	0.2017	0.9416	-0.018	-0.1124	0.1082	0.1496	-0.0274	0.1576	0.0286	-0.0189	0.0455	0.0858	-0.0009	-0.0339	0.0718	0.0319	0.1314	-4.2205	63.3477	-52.7972
5	1.4227	-0.3401	-0.0508	1.6132	-0.6916	0.935	-0.002	-0.109	0.038	0.14	0.0109	-0.0236	0.0528	0.067	-0.0089	0.1197	0.0206	-0.0468	0.0702	0.0148	0.0339	25.2857	31.0873	-48.2298
6	0.9783	0.7108	0.1261	2.4155	-0.0134	0.7452	0.0248	-0.044	0.1959	0.0353	-0.0119	-0.1224	-0.1146	0.2371	-0.0129	0.0567	-0.0265	-0.0288	0.2038	0.0404	0.1857	37.979	70.4252	-62.1787

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	A	39 - 383
2	X-RAY DIFFRACTION	2	ALL	B	38 - 383
3	X-RAY DIFFRACTION	3	ALL	C	38 - 383
4	X-RAY DIFFRACTION	4	ALL	D	39 - 383
5	X-RAY DIFFRACTION	5	ALL	E	38 - 383
6	X-RAY DIFFRACTION	6	ALL	F	38 - 383

-
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