PDB-2fkw: Structure of LH2 from Rps. acidophila crystallized in lipidic mes...

ID or keywords:

Entry

Database: PDB / ID: 2fkw

Title

Structure of LH2 from Rps. acidophila crystallized in lipidic mesophases

Components

(Light-harvesting protein B-800/850, ...) x 2

Keywords

MEMBRANE PROTEIN / PHOTOSYNTHESIS / Light Harvesting Complex B800-B850 / Lipidic Mesophase / crystallization / cubic phase / sponge phase / LDAO / rhodopin glucoside carotenoid

Function / homology

Function and homology information

organelle inner membrane / plasma membrane light-harvesting complex / bacteriochlorophyll binding / photosynthesis, light reaction / : / metal ion binding / plasma membrane
Similarity search - Function

Biological species

Rhodoblastus acidophilus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.45 Å

Authors

Papiz, M.Z. / Cherezov, V. / Clogston, J. / Caffrey, M.

Citation

Journal: J.Mol.Biol. / Year: 2006
Title: Room to Move: Crystallizing Membrane Proteins in Swollen Lipidic Mesophases
Authors: Cherezov, V. / Clogston, J. / Papiz, M.Z. / Caffrey, M.

History

Deposition	Jan 5, 2006	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 28, 2006	Provider: repository / Type: Initial release
Revision 1.1	May 1, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Derived calculations / Version format compliance
Revision 1.3	Mar 30, 2016	Group: Non-polymer description
Revision 1.4	Aug 30, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5	Nov 13, 2024	Group: Data collection / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature Item: _chem_comp_atom.pdbx_aromatic_flag / _chem_comp_bond.pdbx_aromatic_flag

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2fkw.cif.gz	260.3 KB	Display	PDBx/mmCIF format
PDB format	pdb2fkw.ent.gz	223.4 KB	Display	PDB format
PDBx/mmJSON format	2fkw.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/fk/2fkw ftp://data.pdbj.org/pub/pdb/validation_reports/fk/2fkw	HTTPS FTP

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Related structure data

Related structure data	1nkzS 1nzu S: Starting model for refinement
Similar structure data	1nkz-1 5oui-d 5kzu-d 5afn-d 5oug-d 3sh1-2 5ke4-d 5afh-d 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: Light-harvesting protein B-800/850, alpha chain

B: Light-harvesting protein B-800/850, beta chain

C: Light-harvesting protein B-800/850, alpha chain

D: Light-harvesting protein B-800/850, beta chain

E: Light-harvesting protein B-800/850, alpha chain

F: Light-harvesting protein B-800/850, beta chain

G: Light-harvesting protein B-800/850, alpha chain

H: Light-harvesting protein B-800/850, beta chain

I: Light-harvesting protein B-800/850, alpha chain

J: Light-harvesting protein B-800/850, beta chain

K: Light-harvesting protein B-800/850, alpha chain

L: Light-harvesting protein B-800/850, beta chain

M: Light-harvesting protein B-800/850, alpha chain

N: Light-harvesting protein B-800/850, beta chain

O: Light-harvesting protein B-800/850, alpha chain

P: Light-harvesting protein B-800/850, beta chain

R: Light-harvesting protein B-800/850, alpha chain

S: Light-harvesting protein B-800/850, beta chain

hetero molecules

130 kDa, 18 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	81.443, 126.384, 129.705
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Component-ID: 1 / Refine code: 3

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	CXM	CXM	LYS	LYS	A	A	1 - 50	1 - 50
2	1	CXM	CXM	LYS	LYS	C	C	1 - 50	1 - 50
3	1	CXM	CXM	LYS	LYS	E	E	1 - 50	1 - 50
4	1	CXM	CXM	LYS	LYS	G	G	1 - 50	1 - 50
5	1	CXM	CXM	LYS	LYS	I	I	1 - 50	1 - 50
6	1	CXM	CXM	LYS	LYS	K	K	1 - 50	1 - 50
7	1	CXM	CXM	LYS	LYS	M	M	1 - 50	1 - 50
8	1	CXM	CXM	LYS	LYS	O	O	1 - 50	1 - 50
9	1	CXM	CXM	LYS	LYS	R	Q	1 - 50	1 - 50
1	2	ALA	ALA	HIS	HIS	B	B	1 - 41	1 - 41
2	2	ALA	ALA	HIS	HIS	D	D	1 - 41	1 - 41
3	2	ALA	ALA	HIS	HIS	F	F	1 - 41	1 - 41
4	2	ALA	ALA	HIS	HIS	H	H	1 - 41	1 - 41
5	2	ALA	ALA	HIS	HIS	J	J	1 - 41	1 - 41
6	2	ALA	ALA	HIS	HIS	L	L	1 - 41	1 - 41
7	2	ALA	ALA	HIS	HIS	N	N	1 - 41	1 - 41
8	2	ALA	ALA	HIS	HIS	P	P	1 - 41	1 - 41
9	2	ALA	ALA	HIS	HIS	S	R	1 - 41	1 - 41
1	3	BCL	BCL	BCL	BCL	A	S - T	1501 - 1701
2	3	BCL	BCL	BCL	BCL	C	Y - Z	1502 - 1702
3	3	BCL	BCL	BCL	BCL	E	FA - GA	1503 - 1703
4	3	BCL	BCL	BCL	BCL	G	MA - NA	1504 - 1704
5	3	BCL	BCL	BCL	BCL	I	TA - UA	1505 - 1705
6	3	BCL	BCL	BCL	BCL	K	BB - CB	1506 - 1706
7	3	BCL	BCL	BCL	BCL	M	IB - JB	1507 - 1707
8	3	BCL	BCL	BCL	BCL	O	PB - QB	1508 - 1708
9	3	BCL	BCL	BCL	BCL	R	WB - XB	1509 - 1709
1	4	RG1	RG1	RG1	RG1	R	VB	1401
2	4	RG1	RG1	RG1	RG1	D	CA	1402
3	4	RG1	RG1	RG1	RG1	F	JA	1403
4	4	RG1	RG1	RG1	RG1	H	QA	1404
5	4	RG1	RG1	RG1	RG1	J	YA	1405
6	4	RG1	RG1	RG1	RG1	L	FB	1406
7	4	RG1	RG1	RG1	RG1	N	MB	1407
8	4	RG1	RG1	RG1	RG1	P	SB	1408
9	4	RG1	RG1	RG1	RG1	S	BC	1409

NCS ensembles :

ID
1
2
3
4

Details

The biological assembly is a nonamer which is also the asymmetric unit of the cell.

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Light-harvesting protein B-800/850, ... , 2 types, 18 molecules ACEGIKMORBDFHJLNPS

#1: Protein	Light-harvesting protein B-800/850, alpha chain / Antenna pigment protein / alpha chain Mass: 5702.733 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Source: (natural) Rhodoblastus acidophilus (bacteria) / Strain: 10050 / References: UniProt: P26789
#2: Protein/peptide	Light-harvesting protein B-800/850, beta chain / Antenna pigment protein / beta chain Mass: 4559.203 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Source: (natural) Rhodoblastus acidophilus (bacteria) / Strain: 10050 / References: UniProt: P26790

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Sugars , 1 types, 9 molecules

#5: Sugar	ChemComp-RG1 / Rhodopin b-D-glucoside / (3E)-3,4-didehydro-1',2'-dihydro-psi,psi-caroten-1'-yl beta-D-glucopyranoside Type: D-saccharide / Mass: 715.013 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C₄₆H₆₆O₆

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Non-polymers , 3 types, 667 molecules

#3: Chemical	... ChemComp-BCL / BACTERIOCHLOROPHYLL A Mass: 911.504 Da / Num. of mol.: 27 / Source method: obtained synthetically / Formula: C₅₅H₇₄MgN₄O₆
#4: Chemical	... ChemComp-LDA / LAURYL DIMETHYLAMINE-N-OXIDE Mass: 229.402 Da / Num. of mol.: 27 / Source method: obtained synthetically / Formula: C₁₄H₃₁NO / Comment: LDAO, detergent*YM
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 613 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has protein modification	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.61 Å³/Da / Density % sol: 65.95 %
Crystal grow	Temperature: 293 K / pH: 8 Details: 200 microlitres of 40 %(w/w) protein, 0.05 %(w/v) LDAO, 20mM Tris/HCl and 60 %(w/w) monoolein mixed with 2 microlitres of precipitant: 20 %(w/v) pentaerythritol propoxylate, 0.1 M potassium ...Details: 200 microlitres of 40 %(w/w) protein, 0.05 %(w/v) LDAO, 20mM Tris/HCl and 60 %(w/w) monoolein mixed with 2 microlitres of precipitant: 20 %(w/v) pentaerythritol propoxylate, 0.1 M potassium formate, 0.1 M Tris/HCl, pH 8.0, Mesophase crystallization, lipidic cubic phase, temperature 293K

Crystal

Density Matthews: 3.61 Å³/Da / Density % sol: 65.95 %

Crystal grow

Temperature: 293 K / pH: 8
Details: 200 microlitres of 40 %(w/w) protein, 0.05 %(w/v) LDAO, 20mM Tris/HCl and 60 %(w/w) monoolein mixed with 2 microlitres of precipitant: 20 %(w/v) pentaerythritol propoxylate, 0.1 M potassium ...

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9124 Å
Detector	Type: ADSC QUANTUM 4 / Detector: CCD
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9124 Å / Relative weight: 1
Reflection	Resolution: 2.449→90.536 Å / Num. all: 49999 / Num. obs: 49795 / % possible obs: 99.8 % / Redundancy: 3.9 % / R_sym value: 0.066 / Net I/σ(I): 20.9
Reflection shell	Resolution: 2.45→2.54 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 2.3 / Num. unique all: 3208 / R_sym value: 0.568 / % possible all: 98.25

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0005	refinement
HKL-2000		data reduction
SCALEPACK		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 1NKZ

1nkz

Resolution: 2.45→10 Å / Cor.coef. F_o:F_c: 0.957 / Cor.coef. F_o:F_c free: 0.924 / SU B: 9.103 / SU ML: 0.209 / Cross valid method: THROUGHOUT / ESU R: 0.575 / ESU R Free: 0.294 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.25367	2498	5.1 %	RANDOM
R_work	0.18282	-	-	-
obs	0.18651	48989	99.78 %	-
all	-	49999	-	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 41.842 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	2.97 Å²	0 Å²	0 Å²
2-	-	-4.14 Å²	0 Å²
3-	-	-	1.17 Å²

Refinement step

Cycle: LAST / Resolution: 2.45→10 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6534	0	2682	613	9829

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.03	0.021	9594
X-RAY DIFFRACTION	r_bond_other_d	0.005	0.02	9774
X-RAY DIFFRACTION	r_angle_refined_deg	1.414	2.259	13347
X-RAY DIFFRACTION	r_angle_other_deg	0.849	3	22401
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	8.963	5	819
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.173	23.2	225
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	18.044	15	972
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	10.639	15	9
X-RAY DIFFRACTION	r_chiral_restr	0.784	0.2	1449
X-RAY DIFFRACTION	r_gen_planes_refined	0.015	0.02	9639
X-RAY DIFFRACTION	r_gen_planes_other	0.019	0.02	1791
X-RAY DIFFRACTION	r_nbd_refined	0.334	0.2	3517
X-RAY DIFFRACTION	r_nbd_other	0.247	0.2	12911
X-RAY DIFFRACTION	r_nbtor_refined	0.195	0.2	4346
X-RAY DIFFRACTION	r_nbtor_other	0.101	0.2	5296
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.353	0.2	774
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined	0.382	0.2	4
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.232	0.2	25
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.175	0.2	47
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.325	0.2	26
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	1.26	1.5	4277
X-RAY DIFFRACTION	r_mcbond_other	0.319	1.5	1737
X-RAY DIFFRACTION	r_mcangle_it	2.016	2	6732
X-RAY DIFFRACTION	r_scbond_it	2.866	3	5817
X-RAY DIFFRACTION	r_scangle_it	4.217	4.5	6561
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	292	tight positional	0.08	0.05
1	2	C	292	tight positional	0.07	0.05
1	3	E	292	tight positional	0.08	0.05
1	4	G	292	tight positional	0.09	0.05
1	5	I	292	tight positional	0.1	0.05
1	6	K	292	tight positional	0.08	0.05
1	7	M	292	tight positional	0.09	0.05
1	8	O	292	tight positional	0.08	0.05
1	9	R	292	tight positional	0.09	0.05
2	1	B	242	tight positional	0.07	0.05
2	2	D	242	tight positional	0.06	0.05
2	3	F	242	tight positional	0.08	0.05
2	4	H	242	tight positional	0.06	0.05
2	5	J	242	tight positional	0.07	0.05
2	6	L	242	tight positional	0.07	0.05
2	7	N	242	tight positional	0.06	0.05
2	8	P	242	tight positional	0.07	0.05
2	9	S	242	tight positional	0.07	0.05
1	1	A	468	loose positional	0.49	5
1	2	C	468	loose positional	0.54	5
1	3	E	468	loose positional	0.5	5
1	4	G	468	loose positional	0.51	5
1	5	I	468	loose positional	0.63	5
1	6	K	468	loose positional	0.41	5
1	7	M	468	loose positional	0.6	5
1	8	O	468	loose positional	0.47	5
1	9	R	468	loose positional	0.45	5
2	1	B	387	loose positional	0.38	5
2	2	D	387	loose positional	0.45	5
2	3	F	387	loose positional	0.49	5
2	4	H	387	loose positional	0.33	5
2	5	J	387	loose positional	0.45	5
2	6	L	387	loose positional	0.43	5
2	7	N	387	loose positional	0.41	5
2	8	P	387	loose positional	0.43	5
2	9	S	387	loose positional	0.34	5
3	1	A	423	loose positional	0.68	5
3	2	C	423	loose positional	0.69	5
3	3	E	423	loose positional	0.57	5
3	4	G	423	loose positional	0.83	5
3	5	I	423	loose positional	0.67	5
3	6	K	423	loose positional	0.82	5
3	7	M	423	loose positional	0.76	5
3	8	O	423	loose positional	0.73	5
3	9	R	423	loose positional	0.72	5
4	4	B	115	loose positional	0.42	5
4	2	D	115	loose positional	0.47	5
4	3	F	115	loose positional	0.41	5
4	4	H	115	loose positional	0.45	5
4	5	J	115	loose positional	0.31	5
4	6	L	115	loose positional	0.4	5
4	7	N	115	loose positional	0.33	5
4	8	P	115	loose positional	0.43	5
4	9	S	115	loose positional	0.39	5
1	1	A	292	tight thermal	0.3	0.5
1	2	C	292	tight thermal	0.31	0.5
1	3	E	292	tight thermal	0.26	0.5
1	4	G	292	tight thermal	0.3	0.5
1	5	I	292	tight thermal	0.3	0.5
1	6	K	292	tight thermal	0.3	0.5
1	7	M	292	tight thermal	0.26	0.5
1	8	O	292	tight thermal	0.24	0.5
1	9	R	292	tight thermal	0.31	0.5
2	1	B	242	tight thermal	0.32	0.5
2	2	D	242	tight thermal	0.29	0.5
2	3	F	242	tight thermal	0.34	0.5
2	4	H	242	tight thermal	0.24	0.5
2	5	J	242	tight thermal	0.26	0.5
2	6	L	242	tight thermal	0.4	0.5
2	7	N	242	tight thermal	0.27	0.5
2	8	P	242	tight thermal	0.23	0.5
2	9	S	242	tight thermal	0.31	0.5
1	1	A	468	loose thermal	2.3	10
1	2	C	468	loose thermal	1.87	10
1	3	E	468	loose thermal	1.78	10
1	4	G	468	loose thermal	1.65	10
1	5	I	468	loose thermal	2.3	10
1	6	K	468	loose thermal	1.77	10
1	7	M	468	loose thermal	1.67	10
1	8	O	468	loose thermal	1.7	10
1	9	R	468	loose thermal	1.78	10
2	1	B	387	loose thermal	2.36	10
2	2	D	387	loose thermal	2.72	10
2	3	F	387	loose thermal	2.95	10
2	4	H	387	loose thermal	2.24	10
2	5	J	387	loose thermal	1.99	10
2	6	L	387	loose thermal	3.28	10
2	7	N	387	loose thermal	1.69	10
2	8	P	387	loose thermal	2.46	10
2	9	S	387	loose thermal	2.3	10
3	1	A	423	loose thermal	5.12	10
3	2	C	423	loose thermal	2.8	10
3	3	E	423	loose thermal	5.17	10
3	4	G	423	loose thermal	3.53	10
3	5	I	423	loose thermal	4.15	10
3	6	K	423	loose thermal	4.49	10
3	7	M	423	loose thermal	3.28	10
3	8	O	423	loose thermal	3.9	10
3	9	R	423	loose thermal	4.96	10
4	4	B	115	loose thermal	2.58	10
4	2	D	115	loose thermal	4.47	10
4	3	F	115	loose thermal	2.05	10
4	4	H	115	loose thermal	3.46	10
4	5	J	115	loose thermal	2.79	10
4	6	L	115	loose thermal	3.97	10
4	7	N	115	loose thermal	3.08	10
4	8	P	115	loose thermal	3.66	10
4	9	S	115	loose thermal	2.76	10

LS refinement shell

Resolution: 2.45→2.51 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.346	170	-
R_work	0.242	3208	-
obs	-	-	98.25 %

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Components

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Light-harvesting protein B-800/850, ... , 2 types, 18 molecules ACEGIKMORBDFHJLNPS

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Sugars , 1 types, 9 molecules

-
Non-polymers , 3 types, 667 molecules

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Details

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Experimental details

-
Experiment

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Sample preparation

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-Light-harvesting protein B-800/850, ... , 2 types, 18 molecules ACEGIKMORBDFHJLNPS

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-Yorodumi

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Movie

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Structure viewers

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Open data

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Light-harvesting protein B-800/850, ... , 2 types, 18 molecules ACEGIKMORBDFHJLNPS

-
Sugars , 1 types, 9 molecules

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Non-polymers , 3 types, 667 molecules

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Details

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Experimental details

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Experiment

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Sample preparation

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Data collection

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Processing

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About Yorodumi

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Feb 9, 2022. New format data for meta-information of EMDB entries

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Aug 12, 2020. Covid-19 info

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Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

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Yorodumi