PDB-2wes: Crystal structures of mutant E46Q of tryptophan 5-halogenase (PyrH)

ID or keywords:

Entry

Database: PDB / ID: 2wes

Title

Crystal structures of mutant E46Q of tryptophan 5-halogenase (PyrH)

Components

TRYPTOPHAN 5-HALOGENASE

Keywords

ANTIFUNGAL PROTEIN / REGIOSELECTIVITY / TRYPTOPHAN 5-HALOGENASE

Function / homology

Function and homology information

tryptophan 5-halogenase / antibiotic biosynthetic process / monooxygenase activity / nucleotide binding
Similarity search - Function

Biological species

STREPTOMYCES RUGOSPORUS (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.5 Å

Authors

Zhu, X. / Naismith, J.H.

Citation

Journal: J.Mol.Biol. / Year: 2009
Title: Structural Insights in the Regioselectivity in the Enzymatic Chlorination of Tryptophan.
Authors: Zhu, X. / De Laurentis, W. / Leang, K. / Herrmann, J. / Ihlefeld, K. / Van Pee, K.H. / Naismith, J.H.

History

Deposition	Apr 1, 2009	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Apr 21, 2009	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Dec 13, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2wes.cif.gz	425.2 KB	Display	PDBx/mmCIF format
PDB format	pdb2wes.ent.gz	347.5 KB	Display	PDB format
PDBx/mmJSON format	2wes.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	2wes_validation.pdf.gz	1.4 MB	Display	wwPDB validaton report
Full document	2wes_full_validation.pdf.gz	1.4 MB	Display
Data in XML	2wes_validation.xml.gz	80.1 KB	Display
Data in CIF	2wes_validation.cif.gz	113.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/we/2wes ftp://data.pdbj.org/pub/pdb/validation_reports/we/2wes	HTTPS FTP

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Related structure data

Related structure data	2wetC 2weuC 2aqjS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	2wet-2 2wet-1 5hy5-d 2weu-1 2weu-2 5lv9-d 6slt-d 6nsd-d 2wcg-d 2vt0-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) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: TRYPTOPHAN 5-HALOGENASE

B: TRYPTOPHAN 5-HALOGENASE

C: TRYPTOPHAN 5-HALOGENASE

D: TRYPTOPHAN 5-HALOGENASE

hetero molecules

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

1

A: TRYPTOPHAN 5-HALOGENASE

D: TRYPTOPHAN 5-HALOGENASE

hetero molecules

defined by author&software
118 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: TRYPTOPHAN 5-HALOGENASE

C: TRYPTOPHAN 5-HALOGENASE

hetero molecules

defined by author&software
118 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	137.570, 137.570, 309.121
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	96
Space group name H-M	P4₃2₁2

Components on special symmetry positions

ID	Model	Components
1	1	C-2066- HOH

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Refine code	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	1	MET	MET	TRP	TRP	1	A	A	1 - 83	1 - 83
2	1	1	MET	MET	TRP	TRP	1	B	B	1 - 83	1 - 83
3	1	1	MET	MET	TRP	TRP	1	C	C	1 - 83	1 - 83
4	1	1	MET	MET	TRP	TRP	1	D	D	1 - 83	1 - 83
1	2	1	TYR	TYR	ASP	ASP	1	A	A	89 - 201	89 - 201
2	2	1	TYR	TYR	ASP	ASP	1	B	B	89 - 201	89 - 201
3	2	1	TYR	TYR	ASP	ASP	1	C	C	89 - 201	89 - 201
4	2	1	TYR	TYR	ASP	ASP	1	D	D	89 - 201	89 - 201
1	3	1	ARG	ARG	LEU	LEU	1	A	A	203 - 256	203 - 256
2	3	1	ARG	ARG	LEU	LEU	1	B	B	203 - 256	203 - 256
3	3	1	ARG	ARG	LEU	LEU	1	C	C	203 - 256	203 - 256
4	3	1	ARG	ARG	LEU	LEU	1	D	D	203 - 256	203 - 256
1	4	1	MET	MET	PHE	PHE	1	A	A	266 - 286	266 - 286
2	4	1	MET	MET	PHE	PHE	1	B	B	266 - 286	266 - 286
3	4	1	MET	MET	PHE	PHE	1	C	C	266 - 286	266 - 286
4	4	1	MET	MET	PHE	PHE	1	D	D	266 - 286	266 - 286
1	5	1	ASP	ASP	GLY	GLY	1	A	A	289 - 374	289 - 374
2	5	1	ASP	ASP	GLY	GLY	1	B	B	289 - 374	289 - 374
3	5	1	ASP	ASP	GLY	GLY	1	C	C	289 - 374	289 - 374
4	5	1	ASP	ASP	GLY	GLY	1	D	D	289 - 374	289 - 374
1	6	1	TRP	TRP	CL	CL	1	A	A - F	377 - 700	377
2	6	1	TRP	TRP	CL	CL	1	B	B - H	377 - 700	377
3	6	1	TRP	TRP	CL	CL	1	C	C - J	377 - 700	377
4	6	1	TRP	TRP	CL	CL	1	D	D - L	377 - 700	377
1	1	2	SER	SER	GLU	GLU	4	A	A	84 - 88	84 - 88
2	1	2	SER	SER	GLU	GLU	4	B	B	84 - 88	84 - 88
3	1	2	SER	SER	GLU	GLU	4	C	C	84 - 88	84 - 88
4	1	2	SER	SER	GLU	GLU	4	D	D	84 - 88	84 - 88
1	1	3	ARG	ARG	ASP	ASP	4	C	C	257 - 265	257 - 265
2	1	3	ARG	ARG	ASP	ASP	4	D	D	257 - 265	257 - 265
1	1	4	LYS	LYS	LYS	LYS	4	A	A	287	287
2	1	4	LYS	LYS	LYS	LYS	4	B	B	287	287
3	1	4	LYS	LYS	LYS	LYS	4	C	C	287	287
4	1	4	LYS	LYS	LYS	LYS	4	D	D	287	287
1	1	5	GLU	GLU	GLU	GLU	4	A	A	202	202
2	1	5	GLU	GLU	GLU	GLU	4	B	B	202	202
3	1	5	GLU	GLU	GLU	GLU	4	C	C	202	202
4	1	5	GLU	GLU	GLU	GLU	4	D	D	202	202
1	1	6	GLU	GLU	ARG	ARG	4	A	A	375 - 376	375 - 376
2	1	6	GLU	GLU	ARG	ARG	4	B	B	375 - 376	375 - 376
3	1	6	GLU	GLU	ARG	ARG	4	C	C	375 - 376	375 - 376
4	1	6	GLU	GLU	ARG	ARG	4	D	D	375 - 376	375 - 376

NCS ensembles :

ID
1
2
3
4
5
6

#1: Protein	TRYPTOPHAN 5-HALOGENASE / TRYPTOPHAN 5-HALOGENASE PYRH Mass: 58217.508 Da / Num. of mol.: 4 / Mutation: YES Source method: isolated from a genetically manipulated source Details: FAD / Source: (gene. exp.) STREPTOMYCES RUGOSPORUS (bacteria) / Strain: LL-42D005 / Production host: PSEUDOMONAS FLUORESCENS (bacteria) / Strain (production host): BL915 / References: UniProt: A4D0H5
#2: Chemical	ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂₇H₃₃N₉O₁₅P₂ / Comment: FAD*YM
#3: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 941 / Source method: isolated from a natural source / Formula: H₂O
Compound details	ENGINEERED RESIDUE IN CHAIN A, GLU 46 TO GLN ENGINEERED RESIDUE IN CHAIN B, GLU 46 TO GLN ...ENGINEERED RESIDUE IN CHAIN A, GLU 46 TO GLN ENGINEERED RESIDUE IN CHAIN B, GLU 46 TO GLN ENGINEERED RESIDUE IN CHAIN C, GLU 46 TO GLN ENGINEERED RESIDUE IN CHAIN D, GLU 46 TO GLN
Sequence details	SITE-DIRECTED MUTAGENESIS(E46Q)

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.18 Å³/Da / Density % sol: 61.35 % / Description: NONE
Crystal grow	pH: 6.2 Details: 0.05MM SODIUM CACODYLATE BUFFER, PH 6.2 1.4M LI2SO4, 0.01M MGCL2

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.98
Detector	Type: ADSC CCD / Detector: CCD
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.98 Å / Relative weight: 1
Reflection	Resolution: 2.5→50 Å / Num. obs: 103328 / % possible obs: 99 % / Observed criterion σ(I): 2 / Redundancy: 9.6 % / R_merge(I) obs: 0.07 / Net I/σ(I): 43.6
Reflection shell	Resolution: 2.5→2.54 Å / Redundancy: 9.4 % / R_merge(I) obs: 0.35 / Mean I/σ(I) obs: 6 / % possible all: 99.9

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Processing

Software

Name	Version	Classification
REFMAC	5.5.0070	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2AQJ

2aqj

Resolution: 2.5→48.25 Å / Cor.coef. F_o:F_c: 0.946 / Cor.coef. F_o:F_c free: 0.925 / SU B: 16.647 / SU ML: 0.169 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.373 / ESU R Free: 0.244 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.22972	5181	5 %	RANDOM
R_work	0.19344	-	-	-
obs	0.19524	98115	99.85 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 37.889 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.14 Å²	0 Å²	0 Å²
2-	-	-1.14 Å²	0 Å²
3-	-	-	2.28 Å²

Refinement step

Cycle: LAST / Resolution: 2.5→48.25 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	15948	0	215	941	17104

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.021	16605
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.317	1.954	22555
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.69	5	1971
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.947	22.594	848
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.824	15	2589
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	20.38	15	164
X-RAY DIFFRACTION	r_chiral_restr	0.092	0.2	2331
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.021	13004
X-RAY DIFFRACTION	r_gen_planes_other
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	0.728	1.5	9843
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	1.508	2	15767
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	2.324	3	6762
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	4.034	4.5	6788
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
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

Ens-ID	Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	1	A	3875	tight positional	0.07	0.05
1	2	B	3875	tight positional	0.07	0.05
1	3	C	3875	tight positional	0.05	0.05
1	4	D	3875	tight positional	0.05	0.05
2	1	A	35	medium positional	0.76	0.5
2	2	B	35	medium positional	0.36	0.5
2	3	C	35	medium positional	0.48	0.5
2	4	D	35	medium positional	0.34	0.5
3	1	C	78	medium positional	0.43	0.5
3	2	D	78	medium positional	0.43	0.5
4	1	A	9	medium positional	0.25	0.5
4	2	B	9	medium positional	0.43	0.5
4	3	C	9	medium positional	0.48	0.5
4	4	D	9	medium positional	0.37	0.5
5	1	A	9	medium positional	0.39	0.5
5	2	B	9	medium positional	0.42	0.5
5	3	C	9	medium positional	0.55	0.5
5	4	D	9	medium positional	0.54	0.5
6	1	A	20	medium positional	1.05	0.5
6	2	B	20	medium positional	0.86	0.5
6	3	C	20	medium positional	0.63	0.5
6	4	D	20	medium positional	0.58	0.5
1	1	A	3875	tight thermal	0.14	0.5
1	2	B	3875	tight thermal	0.12	0.5
1	3	C	3875	tight thermal	0.11	0.5
1	4	D	3875	tight thermal	0.12	0.5
2	1	A	35	medium thermal	0.98	2
2	2	B	35	medium thermal	0.43	2
2	3	C	35	medium thermal	0.47	2
2	4	D	35	medium thermal	0.52	2
3	1	C	78	medium thermal	0.24	2
3	2	D	78	medium thermal	0.24	2
4	1	A	9	medium thermal	1.37	2
4	2	B	9	medium thermal	2.12	2
4	3	C	9	medium thermal	0.99	2
4	4	D	9	medium thermal	0.59	2
5	1	A	9	medium thermal	2.03	2
5	2	B	9	medium thermal	3.02	2
5	3	C	9	medium thermal	2.94	2
5	4	D	9	medium thermal	2.15	2
6	1	A	20	medium thermal	0.79	2
6	2	B	20	medium thermal	0.98	2
6	3	C	20	medium thermal	1.15	2
6	4	D	20	medium thermal	0.57	2

LS refinement shell

Resolution: 2.5→2.562 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.281	384	-
R_work	0.245	7028	-
obs	-	-	98.58 %

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	0.4592	-0.0191	0.3155	0.3271	-0.1138	0.4879	-0.0576	0.0057	0.0078	0.0224	-0.0151	-0.0514	-0.037	0.0329	0.0727	0.0208	-0.0152	-0.0234	0.0206	0.0333	0.0567	-1.5097	34.4647	-26.6829
2	0.1686	-0.0258	0.135	0.7272	0.2386	0.2486	0.042	-0.0198	-0.0396	0.09	-0.006	-0.0305	0.0288	0.0015	-0.036	0.127	-0.0342	-0.0962	0.0127	0.0208	0.0901	0.848	85.75	-4.6329
3	1.3369	0.1345	0.1425	0.3886	0.0337	0.2496	-0.0452	0.3098	0.1171	-0.0608	-0.0005	0.0476	-0.067	0.0184	0.0456	0.1037	-0.0035	-0.0539	0.082	0.0256	0.036	-26.4147	108.0075	-24.2072
4	0.7973	0.192	0.4492	0.386	0.111	0.4508	0.0557	0.2329	-0.0916	-0.0416	-0.0071	-0.132	0.1153	0.2317	-0.0487	0.0754	0.0539	-0.0313	0.1515	0.0364	0.1395	28.0773	8.2573	-18.6126
5	0.3702	-0.8627	0.9988	2.0121	-2.325	2.6978	-0.0814	-0.0869	-0.0581	0.1844	0.2147	0.1518	-0.2334	-0.2197	-0.1334	0.0541	-0.0301	-0.061	0.0889	0.116	0.1621	-14.9564	33.5587	-25.3938
6	0.4355	-0.6087	-1.1661	0.8616	1.5556	3.6465	-0.063	0.0007	0.0236	0.1012	0.0409	-0.0492	0.367	-0.1631	0.0221	0.2267	-0.0438	-0.1499	0.0819	0.023	0.2265	12.3081	89.0112	1.8491
7	9.853	4.7901	-2.6995	2.4901	-0.8228	2.2849	-0.6972	0.2955	-0.3518	-0.3085	0.2837	-0.0758	0.2206	0.2936	0.4135	0.1413	0.0526	-0.0067	0.1681	0.0543	0.105	-39.764	109.0208	-23.2978
8	8.5572	0.3298	-2.0143	0.0154	-0.0785	0.4759	-0.1104	0.6319	-0.8142	-0.0018	-0.0358	-0.055	0.0286	-0.1282	0.1462	0.1635	0.1002	-0.1089	0.3312	-0.0118	0.3839	39.499	9.5262	-11.4753

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 511
2	X-RAY DIFFRACTION	2	B	1 - 511
3	X-RAY DIFFRACTION	3	C	1 - 511
4	X-RAY DIFFRACTION	4	D	1 - 511
5	X-RAY DIFFRACTION	5	A	650
6	X-RAY DIFFRACTION	6	B	650
7	X-RAY DIFFRACTION	7	C	650
8	X-RAY DIFFRACTION	8	D	650

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+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