PDB-6p02: Crystal structure of Mtb aspartate decarboxylase, 6-Chlorine pyra...

ID or keywords:

Entry

Database: PDB / ID: 6p02

Title

Crystal structure of Mtb aspartate decarboxylase, 6-Chlorine pyrazinoic acid complex

Components

Aspartate 1-decarboxylase alpha chain
Aspartate 1-decarboxylase beta chain

Keywords

LYASE / active / 6-Cl-POA / complex / Structural Genomics / TB Structural Genomics Consortium / TBSGC

Function / homology

Function and homology information

alanine biosynthetic process / aspartate 1-decarboxylase / aspartate 1-decarboxylase activity / pantothenate biosynthetic process / peptidoglycan-based cell wall / cytosol
Similarity search - Function

Biological species

Mycobacterium tuberculosis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.25 Å

Authors

Sun, Q. / Li, X. / Sacchettini, J.C. / TB Structural Genomics Consortium (TBSGC)

Funding support

United States, 2items

Citation

Journal: Nat Commun / Year: 2020
Title: The molecular basis of pyrazinamide activity on Mycobacterium tuberculosis PanD.
Authors: Sun, Q. / Li, X. / Perez, L.M. / Shi, W. / Zhang, Y. / Sacchettini, J.C.

History

Deposition	May 16, 2019	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 5, 2020	Provider: repository / Type: Initial release
Revision 1.1	Oct 11, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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
Revision 2.0	Nov 15, 2023	Group: Atomic model / Data collection / Derived calculations Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / pdbx_validate_main_chain_plane / pdbx_validate_rmsd_angle / struct_conn Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _struct_conn.ptnr1_label_atom_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6p02.cif.gz	280.2 KB	Display	PDBx/mmCIF format
PDB format	pdb6p02.ent.gz	222.6 KB	Display	PDB format
PDBx/mmJSON format	6p02.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6p02_validation.pdf.gz	3.7 MB	Display	wwPDB validaton report
Full document	6p02_full_validation.pdf.gz	3.7 MB	Display
Data in XML	6p02_validation.xml.gz	49.2 KB	Display
Data in CIF	6p02_validation.cif.gz	65.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/p0/6p02 ftp://data.pdbj.org/pub/pdb/validation_reports/p0/6p02	HTTPS FTP

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Related structure data

Related structure data	6oyyC 6oz8C 6p1yC 2c45S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6oyy-1 6oyy-2 6oz8-2 2c45-1 6oz8-1 2c45-2 1pt1-1 1z8p-d 3t30-1 1egy-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

S: Starting model for refinement

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#80 - Aug 2006 AAA+ Proteases similarity (1) #144 - Dec 2011 Complex I similarity (1) #167 - Nov 2013 SNARE Proteins similarity (1)

Deposited unit

A: Aspartate 1-decarboxylase beta chain

B: Aspartate 1-decarboxylase alpha chain

C: Aspartate 1-decarboxylase beta chain

D: Aspartate 1-decarboxylase alpha chain

E: Aspartate 1-decarboxylase beta chain

F: Aspartate 1-decarboxylase alpha chain

G: Aspartate 1-decarboxylase beta chain

H: Aspartate 1-decarboxylase alpha chain

I: Aspartate 1-decarboxylase beta chain

J: Aspartate 1-decarboxylase alpha chain

K: Aspartate 1-decarboxylase beta chain

L: Aspartate 1-decarboxylase alpha chain

M: Aspartate 1-decarboxylase beta chain

N: Aspartate 1-decarboxylase alpha chain

O: Aspartate 1-decarboxylase beta chain

P: Aspartate 1-decarboxylase alpha chain

Q: Aspartate 1-decarboxylase beta chain

R: Aspartate 1-decarboxylase alpha chain

S: Aspartate 1-decarboxylase beta chain

T: Aspartate 1-decarboxylase alpha chain

U: Aspartate 1-decarboxylase beta chain

V: Aspartate 1-decarboxylase alpha chain

W: Aspartate 1-decarboxylase beta chain

X: Aspartate 1-decarboxylase alpha chain

hetero molecules

194 kDa, 24 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Aspartate 1-decarboxylase beta chain

B: Aspartate 1-decarboxylase alpha chain

C: Aspartate 1-decarboxylase beta chain

D: Aspartate 1-decarboxylase alpha chain

E: Aspartate 1-decarboxylase beta chain

F: Aspartate 1-decarboxylase alpha chain

G: Aspartate 1-decarboxylase beta chain

H: Aspartate 1-decarboxylase alpha chain

hetero molecules

defined by author&software
Evidence: gel filtration
64.5 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

I: Aspartate 1-decarboxylase beta chain

J: Aspartate 1-decarboxylase alpha chain

K: Aspartate 1-decarboxylase beta chain

L: Aspartate 1-decarboxylase alpha chain

M: Aspartate 1-decarboxylase beta chain

N: Aspartate 1-decarboxylase alpha chain

O: Aspartate 1-decarboxylase beta chain

P: Aspartate 1-decarboxylase alpha chain

hetero molecules

defined by author&software
Evidence: gel filtration
64.5 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

Q: Aspartate 1-decarboxylase beta chain

R: Aspartate 1-decarboxylase alpha chain

S: Aspartate 1-decarboxylase beta chain

T: Aspartate 1-decarboxylase alpha chain

U: Aspartate 1-decarboxylase beta chain

V: Aspartate 1-decarboxylase alpha chain

W: Aspartate 1-decarboxylase beta chain

X: Aspartate 1-decarboxylase alpha chain

hetero molecules

defined by author&software
Evidence: gel filtration
64.5 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	143.679, 143.679, 59.838
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	144
Space group name H-M	P3₁

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Component-ID: _ / Refine code: _

Dom-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	MET	MET	GLY	GLY	A	A	1 - 24	1 - 24
2	1	MET	MET	GLY	GLY	C	C	1 - 24	1 - 24
1	2	MET	MET	GLY	GLY	A	A	1 - 24	1 - 24
2	2	MET	MET	GLY	GLY	E	E	1 - 24	1 - 24
1	3	MET	MET	GLY	GLY	A	A	1 - 24	1 - 24
2	3	MET	MET	GLY	GLY	G	G	1 - 24	1 - 24
1	4	MET	MET	GLY	GLY	A	A	1 - 24	1 - 24
2	4	MET	MET	GLY	GLY	I	I	1 - 24	1 - 24
1	5	MET	MET	GLY	GLY	A	A	1 - 24	1 - 24
2	5	MET	MET	GLY	GLY	K	K	1 - 24	1 - 24
1	6	MET	MET	GLY	GLY	A	A	1 - 24	1 - 24
2	6	MET	MET	GLY	GLY	M	M	1 - 24	1 - 24
1	7	MET	MET	GLY	GLY	A	A	1 - 24	1 - 24
2	7	MET	MET	GLY	GLY	O	O	1 - 24	1 - 24
1	8	MET	MET	GLY	GLY	A	A	1 - 24	1 - 24
2	8	MET	MET	GLY	GLY	Q	Q	1 - 24	1 - 24
1	9	MET	MET	GLY	GLY	A	A	1 - 24	1 - 24
2	9	MET	MET	GLY	GLY	S	S	1 - 24	1 - 24
1	10	MET	MET	GLY	GLY	A	A	1 - 24	1 - 24
2	10	MET	MET	GLY	GLY	U	U	1 - 24	1 - 24
1	11	MET	MET	GLY	GLY	A	A	1 - 24	1 - 24
2	11	MET	MET	GLY	GLY	W	W	1 - 24	1 - 24
1	12	VAL	VAL	ILE	ILE	B	B	26 - 115	2 - 91
2	12	VAL	VAL	ILE	ILE	D	D	26 - 115	2 - 91
1	13	VAL	VAL	ILE	ILE	B	B	26 - 115	2 - 91
2	13	VAL	VAL	ILE	ILE	F	F	26 - 115	2 - 91
1	14	VAL	VAL	ILE	ILE	B	B	26 - 115	2 - 91
2	14	VAL	VAL	ILE	ILE	H	H	26 - 115	2 - 91
1	15	VAL	VAL	ILE	ILE	B	B	26 - 115	2 - 91
2	15	VAL	VAL	ILE	ILE	J	J	26 - 115	2 - 91
1	16	VAL	VAL	ILE	ILE	B	B	26 - 115	2 - 91
2	16	VAL	VAL	ILE	ILE	L	L	26 - 115	2 - 91
1	17	VAL	VAL	ILE	ILE	B	B	26 - 115	2 - 91
2	17	VAL	VAL	ILE	ILE	N	N	26 - 115	2 - 91
1	18	VAL	VAL	ILE	ILE	B	B	26 - 115	2 - 91
2	18	VAL	VAL	ILE	ILE	P	P	26 - 115	2 - 91
1	19	VAL	VAL	ILE	ILE	B	B	26 - 115	2 - 91
2	19	VAL	VAL	ILE	ILE	R	R	26 - 115	2 - 91
1	20	VAL	VAL	ILE	ILE	B	B	26 - 115	2 - 91
2	20	VAL	VAL	ILE	ILE	T	T	26 - 115	2 - 91
1	21	VAL	VAL	ILE	ILE	B	B	26 - 115	2 - 91
2	21	VAL	VAL	ILE	ILE	V	V	26 - 115	2 - 91
1	22	VAL	VAL	ILE	ILE	B	B	26 - 115	2 - 91
2	22	VAL	VAL	ILE	ILE	X	X	26 - 115	2 - 91
1	23	MET	MET	GLY	GLY	C	C	1 - 24	1 - 24
2	23	MET	MET	GLY	GLY	E	E	1 - 24	1 - 24
1	24	MET	MET	GLY	GLY	C	C	1 - 24	1 - 24
2	24	MET	MET	GLY	GLY	G	G	1 - 24	1 - 24
1	25	MET	MET	GLY	GLY	C	C	1 - 24	1 - 24
2	25	MET	MET	GLY	GLY	I	I	1 - 24	1 - 24
1	26	MET	MET	GLY	GLY	C	C	1 - 24	1 - 24
2	26	MET	MET	GLY	GLY	K	K	1 - 24	1 - 24
1	27	MET	MET	GLY	GLY	C	C	1 - 24	1 - 24
2	27	MET	MET	GLY	GLY	M	M	1 - 24	1 - 24
1	28	MET	MET	GLY	GLY	C	C	1 - 24	1 - 24
2	28	MET	MET	GLY	GLY	O	O	1 - 24	1 - 24
1	29	MET	MET	GLY	GLY	C	C	1 - 24	1 - 24
2	29	MET	MET	GLY	GLY	Q	Q	1 - 24	1 - 24
1	30	MET	MET	GLY	GLY	C	C	1 - 24	1 - 24
2	30	MET	MET	GLY	GLY	S	S	1 - 24	1 - 24
1	31	MET	MET	GLY	GLY	C	C	1 - 24	1 - 24
2	31	MET	MET	GLY	GLY	U	U	1 - 24	1 - 24
1	32	MET	MET	GLY	GLY	C	C	1 - 24	1 - 24
2	32	MET	MET	GLY	GLY	W	W	1 - 24	1 - 24
1	33	VAL	VAL	ILE	ILE	D	D	26 - 115	2 - 91
2	33	VAL	VAL	ILE	ILE	F	F	26 - 115	2 - 91
1	34	VAL	VAL	ILE	ILE	D	D	26 - 115	2 - 91
2	34	VAL	VAL	ILE	ILE	H	H	26 - 115	2 - 91
1	35	VAL	VAL	ILE	ILE	D	D	26 - 115	2 - 91
2	35	VAL	VAL	ILE	ILE	J	J	26 - 115	2 - 91
1	36	VAL	VAL	ILE	ILE	D	D	26 - 115	2 - 91
2	36	VAL	VAL	ILE	ILE	L	L	26 - 115	2 - 91
1	37	VAL	VAL	ILE	ILE	D	D	26 - 115	2 - 91
2	37	VAL	VAL	ILE	ILE	N	N	26 - 115	2 - 91
1	38	VAL	VAL	ILE	ILE	D	D	26 - 115	2 - 91
2	38	VAL	VAL	ILE	ILE	P	P	26 - 115	2 - 91
1	39	VAL	VAL	ILE	ILE	D	D	26 - 115	2 - 91
2	39	VAL	VAL	ILE	ILE	R	R	26 - 115	2 - 91
1	40	VAL	VAL	ILE	ILE	D	D	26 - 115	2 - 91
2	40	VAL	VAL	ILE	ILE	T	T	26 - 115	2 - 91
1	41	VAL	VAL	ILE	ILE	D	D	26 - 115	2 - 91
2	41	VAL	VAL	ILE	ILE	V	V	26 - 115	2 - 91
1	42	VAL	VAL	ILE	ILE	D	D	26 - 115	2 - 91
2	42	VAL	VAL	ILE	ILE	X	X	26 - 115	2 - 91
1	43	MET	MET	GLY	GLY	E	E	1 - 24	1 - 24
2	43	MET	MET	GLY	GLY	G	G	1 - 24	1 - 24
1	44	MET	MET	GLY	GLY	E	E	1 - 24	1 - 24
2	44	MET	MET	GLY	GLY	I	I	1 - 24	1 - 24
1	45	MET	MET	GLY	GLY	E	E	1 - 24	1 - 24
2	45	MET	MET	GLY	GLY	K	K	1 - 24	1 - 24
1	46	MET	MET	GLY	GLY	E	E	1 - 24	1 - 24
2	46	MET	MET	GLY	GLY	M	M	1 - 24	1 - 24
1	47	MET	MET	GLY	GLY	E	E	1 - 24	1 - 24
2	47	MET	MET	GLY	GLY	O	O	1 - 24	1 - 24
1	48	MET	MET	GLY	GLY	E	E	1 - 24	1 - 24
2	48	MET	MET	GLY	GLY	Q	Q	1 - 24	1 - 24
1	49	MET	MET	GLY	GLY	E	E	1 - 24	1 - 24
2	49	MET	MET	GLY	GLY	S	S	1 - 24	1 - 24
1	50	MET	MET	GLY	GLY	E	E	1 - 24	1 - 24
2	50	MET	MET	GLY	GLY	U	U	1 - 24	1 - 24
1	51	MET	MET	GLY	GLY	E	E	1 - 24	1 - 24
2	51	MET	MET	GLY	GLY	W	W	1 - 24	1 - 24
1	52	VAL	VAL	ILE	ILE	F	F	26 - 115	2 - 91
2	52	VAL	VAL	ILE	ILE	H	H	26 - 115	2 - 91
1	53	VAL	VAL	ILE	ILE	F	F	26 - 115	2 - 91
2	53	VAL	VAL	ILE	ILE	J	J	26 - 115	2 - 91
1	54	VAL	VAL	ILE	ILE	F	F	26 - 115	2 - 91
2	54	VAL	VAL	ILE	ILE	L	L	26 - 115	2 - 91
1	55	VAL	VAL	ILE	ILE	F	F	26 - 115	2 - 91
2	55	VAL	VAL	ILE	ILE	N	N	26 - 115	2 - 91
1	56	VAL	VAL	ILE	ILE	F	F	26 - 115	2 - 91
2	56	VAL	VAL	ILE	ILE	P	P	26 - 115	2 - 91
1	57	VAL	VAL	ILE	ILE	F	F	26 - 115	2 - 91
2	57	VAL	VAL	ILE	ILE	R	R	26 - 115	2 - 91
1	58	VAL	VAL	ILE	ILE	F	F	26 - 115	2 - 91
2	58	VAL	VAL	ILE	ILE	T	T	26 - 115	2 - 91
1	59	VAL	VAL	ILE	ILE	F	F	26 - 115	2 - 91
2	59	VAL	VAL	ILE	ILE	V	V	26 - 115	2 - 91
1	60	VAL	VAL	ILE	ILE	F	F	26 - 115	2 - 91
2	60	VAL	VAL	ILE	ILE	X	X	26 - 115	2 - 91
1	61	MET	MET	GLY	GLY	G	G	1 - 24	1 - 24
2	61	MET	MET	GLY	GLY	I	I	1 - 24	1 - 24
1	62	MET	MET	GLY	GLY	G	G	1 - 24	1 - 24
2	62	MET	MET	GLY	GLY	K	K	1 - 24	1 - 24
1	63	MET	MET	GLY	GLY	G	G	1 - 24	1 - 24
2	63	MET	MET	GLY	GLY	M	M	1 - 24	1 - 24
1	64	MET	MET	GLY	GLY	G	G	1 - 24	1 - 24
2	64	MET	MET	GLY	GLY	O	O	1 - 24	1 - 24
1	65	MET	MET	GLY	GLY	G	G	1 - 24	1 - 24
2	65	MET	MET	GLY	GLY	Q	Q	1 - 24	1 - 24
1	66	MET	MET	GLY	GLY	G	G	1 - 24	1 - 24
2	66	MET	MET	GLY	GLY	S	S	1 - 24	1 - 24
1	67	MET	MET	GLY	GLY	G	G	1 - 24	1 - 24
2	67	MET	MET	GLY	GLY	U	U	1 - 24	1 - 24
1	68	MET	MET	GLY	GLY	G	G	1 - 24	1 - 24
2	68	MET	MET	GLY	GLY	W	W	1 - 24	1 - 24
1	69	VAL	VAL	ILE	ILE	H	H	26 - 115	2 - 91
2	69	VAL	VAL	ILE	ILE	J	J	26 - 115	2 - 91
1	70	VAL	VAL	ILE	ILE	H	H	26 - 115	2 - 91
2	70	VAL	VAL	ILE	ILE	L	L	26 - 115	2 - 91
1	71	VAL	VAL	ILE	ILE	H	H	26 - 115	2 - 91
2	71	VAL	VAL	ILE	ILE	N	N	26 - 115	2 - 91
1	72	VAL	VAL	ILE	ILE	H	H	26 - 115	2 - 91
2	72	VAL	VAL	ILE	ILE	P	P	26 - 115	2 - 91
1	73	VAL	VAL	ILE	ILE	H	H	26 - 115	2 - 91
2	73	VAL	VAL	ILE	ILE	R	R	26 - 115	2 - 91
1	74	VAL	VAL	ILE	ILE	H	H	26 - 115	2 - 91
2	74	VAL	VAL	ILE	ILE	T	T	26 - 115	2 - 91
1	75	VAL	VAL	ILE	ILE	H	H	26 - 115	2 - 91
2	75	VAL	VAL	ILE	ILE	V	V	26 - 115	2 - 91
1	76	VAL	VAL	ILE	ILE	H	H	26 - 115	2 - 91
2	76	VAL	VAL	ILE	ILE	X	X	26 - 115	2 - 91
1	77	MET	MET	GLY	GLY	I	I	1 - 24	1 - 24
2	77	MET	MET	GLY	GLY	K	K	1 - 24	1 - 24
1	78	MET	MET	GLY	GLY	I	I	1 - 24	1 - 24
2	78	MET	MET	GLY	GLY	M	M	1 - 24	1 - 24
1	79	MET	MET	GLY	GLY	I	I	1 - 24	1 - 24
2	79	MET	MET	GLY	GLY	O	O	1 - 24	1 - 24
1	80	MET	MET	GLY	GLY	I	I	1 - 24	1 - 24
2	80	MET	MET	GLY	GLY	Q	Q	1 - 24	1 - 24
1	81	MET	MET	GLY	GLY	I	I	1 - 24	1 - 24
2	81	MET	MET	GLY	GLY	S	S	1 - 24	1 - 24
1	82	MET	MET	GLY	GLY	I	I	1 - 24	1 - 24
2	82	MET	MET	GLY	GLY	U	U	1 - 24	1 - 24
1	83	MET	MET	GLY	GLY	I	I	1 - 24	1 - 24
2	83	MET	MET	GLY	GLY	W	W	1 - 24	1 - 24
1	84	VAL	VAL	ILE	ILE	J	J	26 - 115	2 - 91
2	84	VAL	VAL	ILE	ILE	L	L	26 - 115	2 - 91
1	85	VAL	VAL	ILE	ILE	J	J	26 - 115	2 - 91
2	85	VAL	VAL	ILE	ILE	N	N	26 - 115	2 - 91
1	86	VAL	VAL	ILE	ILE	J	J	26 - 115	2 - 91
2	86	VAL	VAL	ILE	ILE	P	P	26 - 115	2 - 91
1	87	VAL	VAL	ILE	ILE	J	J	26 - 115	2 - 91
2	87	VAL	VAL	ILE	ILE	R	R	26 - 115	2 - 91
1	88	VAL	VAL	ILE	ILE	J	J	26 - 115	2 - 91
2	88	VAL	VAL	ILE	ILE	T	T	26 - 115	2 - 91
1	89	VAL	VAL	ILE	ILE	J	J	26 - 115	2 - 91
2	89	VAL	VAL	ILE	ILE	V	V	26 - 115	2 - 91
1	90	VAL	VAL	ILE	ILE	J	J	26 - 115	2 - 91
2	90	VAL	VAL	ILE	ILE	X	X	26 - 115	2 - 91
1	91	MET	MET	GLY	GLY	K	K	1 - 24	1 - 24
2	91	MET	MET	GLY	GLY	M	M	1 - 24	1 - 24
1	92	MET	MET	GLY	GLY	K	K	1 - 24	1 - 24
2	92	MET	MET	GLY	GLY	O	O	1 - 24	1 - 24
1	93	MET	MET	GLY	GLY	K	K	1 - 24	1 - 24
2	93	MET	MET	GLY	GLY	Q	Q	1 - 24	1 - 24
1	94	MET	MET	GLY	GLY	K	K	1 - 24	1 - 24
2	94	MET	MET	GLY	GLY	S	S	1 - 24	1 - 24
1	95	MET	MET	GLY	GLY	K	K	1 - 24	1 - 24
2	95	MET	MET	GLY	GLY	U	U	1 - 24	1 - 24
1	96	MET	MET	GLY	GLY	K	K	1 - 24	1 - 24
2	96	MET	MET	GLY	GLY	W	W	1 - 24	1 - 24
1	97	VAL	VAL	ILE	ILE	L	L	26 - 115	2 - 91
2	97	VAL	VAL	ILE	ILE	N	N	26 - 115	2 - 91
1	98	VAL	VAL	ILE	ILE	L	L	26 - 115	2 - 91
2	98	VAL	VAL	ILE	ILE	P	P	26 - 115	2 - 91
1	99	VAL	VAL	ILE	ILE	L	L	26 - 115	2 - 91
2	99	VAL	VAL	ILE	ILE	R	R	26 - 115	2 - 91
1	100	VAL	VAL	ILE	ILE	L	L	26 - 115	2 - 91
2	100	VAL	VAL	ILE	ILE	T	T	26 - 115	2 - 91
1	101	VAL	VAL	ILE	ILE	L	L	26 - 115	2 - 91
2	101	VAL	VAL	ILE	ILE	V	V	26 - 115	2 - 91
1	102	VAL	VAL	ILE	ILE	L	L	26 - 115	2 - 91
2	102	VAL	VAL	ILE	ILE	X	X	26 - 115	2 - 91
1	103	MET	MET	GLY	GLY	M	M	1 - 24	1 - 24
2	103	MET	MET	GLY	GLY	O	O	1 - 24	1 - 24
1	104	MET	MET	GLY	GLY	M	M	1 - 24	1 - 24
2	104	MET	MET	GLY	GLY	Q	Q	1 - 24	1 - 24
1	105	MET	MET	GLY	GLY	M	M	1 - 24	1 - 24
2	105	MET	MET	GLY	GLY	S	S	1 - 24	1 - 24
1	106	MET	MET	GLY	GLY	M	M	1 - 24	1 - 24
2	106	MET	MET	GLY	GLY	U	U	1 - 24	1 - 24
1	107	MET	MET	GLY	GLY	M	M	1 - 24	1 - 24
2	107	MET	MET	GLY	GLY	W	W	1 - 24	1 - 24
1	108	VAL	VAL	ILE	ILE	N	N	26 - 115	2 - 91
2	108	VAL	VAL	ILE	ILE	P	P	26 - 115	2 - 91
1	109	VAL	VAL	ILE	ILE	N	N	26 - 115	2 - 91
2	109	VAL	VAL	ILE	ILE	R	R	26 - 115	2 - 91
1	110	VAL	VAL	ILE	ILE	N	N	26 - 115	2 - 91
2	110	VAL	VAL	ILE	ILE	T	T	26 - 115	2 - 91
1	111	VAL	VAL	ILE	ILE	N	N	26 - 115	2 - 91
2	111	VAL	VAL	ILE	ILE	V	V	26 - 115	2 - 91
1	112	VAL	VAL	ILE	ILE	N	N	26 - 115	2 - 91
2	112	VAL	VAL	ILE	ILE	X	X	26 - 115	2 - 91
1	113	MET	MET	GLY	GLY	O	O	1 - 24	1 - 24
2	113	MET	MET	GLY	GLY	Q	Q	1 - 24	1 - 24
1	114	MET	MET	GLY	GLY	O	O	1 - 24	1 - 24
2	114	MET	MET	GLY	GLY	S	S	1 - 24	1 - 24
1	115	MET	MET	GLY	GLY	O	O	1 - 24	1 - 24
2	115	MET	MET	GLY	GLY	U	U	1 - 24	1 - 24
1	116	MET	MET	GLY	GLY	O	O	1 - 24	1 - 24
2	116	MET	MET	GLY	GLY	W	W	1 - 24	1 - 24
1	117	VAL	VAL	ILE	ILE	P	P	26 - 115	2 - 91
2	117	VAL	VAL	ILE	ILE	R	R	26 - 115	2 - 91
1	118	VAL	VAL	ILE	ILE	P	P	26 - 115	2 - 91
2	118	VAL	VAL	ILE	ILE	T	T	26 - 115	2 - 91
1	119	VAL	VAL	ILE	ILE	P	P	26 - 115	2 - 91
2	119	VAL	VAL	ILE	ILE	V	V	26 - 115	2 - 91
1	120	VAL	VAL	ILE	ILE	P	P	26 - 115	2 - 91
2	120	VAL	VAL	ILE	ILE	X	X	26 - 115	2 - 91
1	121	MET	MET	GLY	GLY	Q	Q	1 - 24	1 - 24
2	121	MET	MET	GLY	GLY	S	S	1 - 24	1 - 24
1	122	MET	MET	GLY	GLY	Q	Q	1 - 24	1 - 24
2	122	MET	MET	GLY	GLY	U	U	1 - 24	1 - 24
1	123	MET	MET	GLY	GLY	Q	Q	1 - 24	1 - 24
2	123	MET	MET	GLY	GLY	W	W	1 - 24	1 - 24
1	124	VAL	VAL	ILE	ILE	R	R	26 - 115	2 - 91
2	124	VAL	VAL	ILE	ILE	T	T	26 - 115	2 - 91
1	125	VAL	VAL	ILE	ILE	R	R	26 - 115	2 - 91
2	125	VAL	VAL	ILE	ILE	V	V	26 - 115	2 - 91
1	126	VAL	VAL	ILE	ILE	R	R	26 - 115	2 - 91
2	126	VAL	VAL	ILE	ILE	X	X	26 - 115	2 - 91
1	127	MET	MET	GLY	GLY	S	S	1 - 24	1 - 24
2	127	MET	MET	GLY	GLY	U	U	1 - 24	1 - 24
1	128	MET	MET	GLY	GLY	S	S	1 - 24	1 - 24
2	128	MET	MET	GLY	GLY	W	W	1 - 24	1 - 24
1	129	VAL	VAL	ILE	ILE	T	T	26 - 115	2 - 91
2	129	VAL	VAL	ILE	ILE	V	V	26 - 115	2 - 91
1	130	VAL	VAL	ILE	ILE	T	T	26 - 115	2 - 91
2	130	VAL	VAL	ILE	ILE	X	X	26 - 115	2 - 91
1	131	MET	MET	GLY	GLY	U	U	1 - 24	1 - 24
2	131	MET	MET	GLY	GLY	W	W	1 - 24	1 - 24
1	132	VAL	VAL	ILE	ILE	V	V	26 - 115	2 - 91
2	132	VAL	VAL	ILE	ILE	X	X	26 - 115	2 - 91

NCS ensembles :

#1: Protein/peptide	Aspartate 1-decarboxylase beta chain Mass: 2751.341 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria) Strain: ATCC 25618 / H37Rv / Gene: panD, Rv3601c, MTCY07H7B.21 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P9WIL3
#2: Protein	Aspartate 1-decarboxylase alpha chain Mass: 13221.777 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria) Strain: ATCC 25618 / H37Rv / Gene: panD, Rv3601c, MTCY07H7B.21 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P9WIL3, aspartate 1-decarboxylase
#3: Chemical	ChemComp-NMJ / 6-chloropyrazine-2-carboxylic acid Mass: 158.543 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C₅H₃ClN₂O₂ / Feature type: SUBJECT OF INVESTIGATION
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 7 / 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: 1.86 Å³/Da / Density % sol: 33.88 %
Crystal grow	Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: MES, HEPES, PEG 3350, Ammonium Chloride / PH range: 6.5-7

-
Data collection

Diffraction

Mean temperature: 130 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 23-ID-D / Wavelength: 1.033 Å

Detector

Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 15, 2018

Radiation

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

Radiation wavelength

Wavelength: 1.033 Å / Relative weight: 1

Reflection twin

Crystal-ID	ID	Operator	Domain-ID	Fraction
1	1	H, K, L	1	0.086
1	1	-h,-k,l	2	0.074
1	1	K, H, -L	3	0.483
1	1	-K, -H, -L	4	0.357

Reflection

Resolution: 2.25→21.89 Å / Num. obs: 65250 / % possible obs: 99.53 % / Redundancy: 5.7 % / CC_1/2: 0.993 / Net I/σ(I): 8.03

Reflection shell

Resolution: 2.25→2.33 Å / Mean I/σ(I) obs: 1.9 / Num. unique obs: 6314 / CC_1/2: 0.625 / % possible all: 96.47

-
Processing

Software

Name	Version	Classification
REFMAC	5.8.0232	refinement
PROTEUM PLUS		data reduction
PROTEUM PLUS		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2C45

2c45

Resolution: 2.25→21.89 Å / Cor.coef. F_o:F_c: 0.973 / Cor.coef. F_o:F_c free: 0.962 / SU B: 2.63 / SU ML: 0.071 / Cross valid method: THROUGHOUT / ESU R: 0.048 / ESU R Free: 0.033 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.16442	3466	5.3 %	RANDOM
R_work	0.13384	-	-	-
obs	0.13543	61782	99.51 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å

Displacement parameters

B_iso mean: 51.156 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	6.71 Å²	0 Å²	0 Å²
2-	-	6.71 Å²	0 Å²
3-	-	-	-13.42 Å²

Refinement step

Cycle: 1 / Resolution: 2.25→21.89 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10416	0	120	7	10543

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.013	0.013	10668
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	10248
X-RAY DIFFRACTION	r_angle_refined_deg	1.606	1.658	14460
X-RAY DIFFRACTION	r_angle_other_deg	1.401	1.592	23484
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.493	5	1344
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	30.615	21.163	516
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.583	15	1728
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.045	15	84
X-RAY DIFFRACTION	r_chiral_restr	0.073	0.2	1500
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	12036
X-RAY DIFFRACTION	r_gen_planes_other	0.003	0.02	2172
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	6.361	5.13	5448
X-RAY DIFFRACTION	r_mcbond_other	6.357	5.13	5447
X-RAY DIFFRACTION	r_mcangle_it	7.908	7.661	6768
X-RAY DIFFRACTION	r_mcangle_other	7.907	7.662	6769
X-RAY DIFFRACTION	r_scbond_it	7.249	5.866	5220
X-RAY DIFFRACTION	r_scbond_other	7.249	5.866	5221
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	9.587	8.584	7693
X-RAY DIFFRACTION	r_long_range_B_refined	10.768		20682
X-RAY DIFFRACTION	r_long_range_B_other	10.768		20683
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-ID	Dom-ID	Auth asym-ID	Number	Rms dev position (Å)
1	1	A	518	0.07
1	2	C	518	0.07
2	1	A	516	0.09
2	2	E	516	0.09
3	1	A	521	0.03
3	2	G	521	0.03
4	1	A	521	0.06
4	2	I	521	0.06
5	1	A	519	0.08
5	2	K	519	0.08
6	1	A	512	0.09
6	2	M	512	0.09
7	1	A	520	0.03
7	2	O	520	0.03
8	1	A	527	0.01
8	2	Q	527	0.01
9	1	A	519	0.07
9	2	S	519	0.07
10	1	A	520	0.07
10	2	U	520	0.07
11	1	A	518	0.05
11	2	W	518	0.05
12	1	B	2460	0.09
12	2	D	2460	0.09
13	1	B	2468	0.1
13	2	F	2468	0.1
14	1	B	2509	0.07
14	2	H	2509	0.07
15	1	B	2544	0.05
15	2	J	2544	0.05
16	1	B	2478	0.08
16	2	L	2478	0.08
17	1	B	2475	0.09
17	2	N	2475	0.09
18	1	B	2502	0.08
18	2	P	2502	0.08
19	1	B	2532	0.05
19	2	R	2532	0.05
20	1	B	2462	0.08
20	2	T	2462	0.08
21	1	B	2481	0.09
21	2	V	2481	0.09
22	1	B	2505	0.07
22	2	X	2505	0.07
23	1	C	514	0.09
23	2	E	514	0.09
24	1	C	521	0.07
24	2	G	521	0.07
25	1	C	514	0.09
25	2	I	514	0.09
26	1	C	529	0.03
26	2	K	529	0.03
27	1	C	507	0.1
27	2	M	507	0.1
28	1	C	519	0.08
28	2	O	519	0.08
29	1	C	518	0.07
29	2	Q	518	0.07
30	1	C	522	0.02
30	2	S	522	0.02
31	1	C	522	0.08
31	2	U	522	0.08
32	1	C	518	0.07
32	2	W	518	0.07
33	1	D	2472	0.1
33	2	F	2472	0.1
34	1	D	2508	0.06
34	2	H	2508	0.06
35	1	D	2463	0.09
35	2	J	2463	0.09
36	1	D	2537	0.05
36	2	L	2537	0.05
37	1	D	2464	0.09
37	2	N	2464	0.09
38	1	D	2514	0.07
38	2	P	2514	0.07
39	1	D	2488	0.08
39	2	R	2488	0.08
40	1	D	2537	0.04
40	2	T	2537	0.04
41	1	D	2487	0.08
41	2	V	2487	0.08
42	1	D	2515	0.06
42	2	X	2515	0.06
43	1	E	515	0.08
43	2	G	515	0.08
44	1	E	509	0.11
44	2	I	509	0.11
45	1	E	516	0.09
45	2	K	516	0.09
46	1	E	516	0.05
46	2	M	516	0.05
47	1	E	514	0.09
47	2	O	514	0.09
48	1	E	515	0.09
48	2	Q	515	0.09
49	1	E	509	0.09
49	2	S	509	0.09
50	1	E	521	0.04
50	2	U	521	0.04
51	1	E	514	0.1
51	2	W	514	0.1
52	1	F	2488	0.09
52	2	H	2488	0.09
53	1	F	2477	0.1
53	2	J	2477	0.1
54	1	F	2487	0.09
54	2	L	2487	0.09
55	1	F	2549	0.06
55	2	N	2549	0.06
56	1	F	2499	0.09
56	2	P	2499	0.09
57	1	F	2474	0.1
57	2	R	2474	0.1
58	1	F	2484	0.1
58	2	T	2484	0.1
59	1	F	2562	0.06
59	2	V	2562	0.06
60	1	F	2508	0.09
60	2	X	2508	0.09
61	1	G	517	0.07
61	2	I	517	0.07
62	1	G	522	0.08
62	2	K	522	0.08
63	1	G	512	0.09
63	2	M	512	0.09
64	1	G	528	0.04
64	2	O	528	0.04
65	1	G	523	0.02
65	2	Q	523	0.02
66	1	G	516	0.08
66	2	S	516	0.08
67	1	G	525	0.07
67	2	U	525	0.07
68	1	G	522	0.06
68	2	W	522	0.06
69	1	H	2504	0.07
69	2	J	2504	0.07
70	1	H	2523	0.05
70	2	L	2523	0.05
71	1	H	2492	0.09
71	2	N	2492	0.09
72	1	H	2572	0.04
72	2	P	2572	0.04
73	1	H	2529	0.06
73	2	R	2529	0.06
74	1	H	2507	0.06
74	2	T	2507	0.06
75	1	H	2513	0.07
75	2	V	2513	0.07
76	1	H	2570	0.03
76	2	X	2570	0.03
77	1	I	515	0.1
77	2	K	515	0.1
78	1	I	509	0.11
78	2	M	509	0.11
79	1	I	517	0.07
79	2	O	517	0.07
80	1	I	519	0.06
80	2	Q	519	0.06
81	1	I	515	0.09
81	2	S	515	0.09
82	1	I	516	0.1
82	2	U	516	0.1
83	1	I	516	0.08
83	2	W	516	0.08
84	1	J	2483	0.08
84	2	L	2483	0.08
85	1	J	2476	0.09
85	2	N	2476	0.09
86	1	J	2505	0.08
86	2	P	2505	0.08
87	1	J	2542	0.05
87	2	R	2542	0.05
88	1	J	2469	0.08
88	2	T	2469	0.08
89	1	J	2492	0.08
89	2	V	2492	0.08
90	1	J	2511	0.07
90	2	X	2511	0.07
91	1	K	511	0.1
91	2	M	511	0.1
92	1	K	519	0.08
92	2	O	519	0.08
93	1	K	519	0.07
93	2	Q	519	0.07
94	1	K	524	0.03
94	2	S	524	0.03
95	1	K	523	0.08
95	2	U	523	0.08
96	1	K	521	0.08
96	2	W	521	0.08
97	1	L	2483	0.08
97	2	N	2483	0.08
98	1	L	2530	0.05
98	2	P	2530	0.05
99	1	L	2505	0.07
99	2	R	2505	0.07
100	1	L	2526	0.04
100	2	T	2526	0.04
101	1	L	2496	0.07
101	2	V	2496	0.07
102	1	L	2533	0.04
102	2	X	2533	0.04
103	1	M	512	0.1
103	2	O	512	0.1
104	1	M	511	0.09
104	2	Q	511	0.09
105	1	M	509	0.09
105	2	S	509	0.09
106	1	M	516	0.05
106	2	U	516	0.05
107	1	M	509	0.1
107	2	W	509	0.1
108	1	N	2510	0.08
108	2	P	2510	0.08
109	1	N	2473	0.1
109	2	R	2473	0.1
110	1	N	2483	0.09
110	2	T	2483	0.09
111	1	N	2550	0.06
111	2	V	2550	0.06
112	1	N	2499	0.08
112	2	X	2499	0.08
113	1	O	522	0.03
113	2	Q	522	0.03
114	1	O	514	0.08
114	2	S	514	0.08
115	1	O	522	0.08
115	2	U	522	0.08
116	1	O	520	0.04
116	2	W	520	0.04
117	1	P	2529	0.07
117	2	R	2529	0.07
118	1	P	2509	0.06
118	2	T	2509	0.06
119	1	P	2518	0.08
119	2	V	2518	0.08
120	1	P	2576	0.04
120	2	X	2576	0.04
121	1	Q	516	0.07
121	2	S	516	0.07
122	1	Q	522	0.07
122	2	U	522	0.07
123	1	Q	518	0.05
123	2	W	518	0.05
124	1	R	2484	0.08
124	2	T	2484	0.08
125	1	R	2491	0.09
125	2	V	2491	0.09
126	1	R	2532	0.06
126	2	X	2532	0.06
127	1	S	517	0.08
127	2	U	517	0.08
128	1	S	517	0.07
128	2	W	517	0.07
129	1	T	2488	0.08
129	2	V	2488	0.08
130	1	T	2517	0.06
130	2	X	2517	0.06
131	1	U	520	0.09
131	2	W	520	0.09
132	1	V	2520	0.07
132	2	X	2520	0.07

LS refinement shell

Resolution: 2.25→2.308 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.296	208	-
R_work	0.221	4399	-
obs	-	-	94.91 %

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