1pyh

Crystal structure of RC-LH1 core complex from Rhodopseudomonas palustris

Method: X-RAY DIFFRACTION

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1. Protein Identity and Related Structures Protein Identity & Related Structures

No usable UniProt protein identity is available for this entry.

The relationship tables retain this entry's assembly and composition data, but cross-PDB links for the same protein cannot be established reliably without a unified protein identity.

Assembly Composition of the Current Entry

Assembly	Physical composition	Protein state	蛋白 / DNA / RNA / 其他Polymer	Data consistency
1	Protein heterocomplex	Heteromer	34 / 0 / 0 / 0	Consistent with protein count

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1pyh
Deposition date deposition_date	2003-07-08
Structure title title	Crystal structure of RC-LH1 core complex from Rhodopseudomonas palustris
Keywords keywords	bacterial photosynthetic core complex, integral membrane proteins, light harvesting complex, reaction centre, PHOTOSYNTHESIS; PHOTOSYNTHESIS
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

1pyh__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

1pyh__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1pyh__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	40.25 Å
Rg (electron density)	39.81 Å
Total Rg	40.21 Å
Atom count	10100
Residues	1690
Excluded volume	168270 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1pyh__assembly_1__model_1`	34-meric （34）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (8)

Entity 1 Entity 1 polymer

Description description	Reaction center protein L chain
Molecular weight formula_weight	23932.4 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	10100

XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

Entity 2 Entity 2 polymer

Description description	Reaction center protein M chain
Molecular weight formula_weight	25719.6 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

Entity 3 Entity 3 polymer

Description description	Reaction center protein H chain
Molecular weight formula_weight	20528.2 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

Entity 4 Entity 4 polymer

Description description	Light-harvesting protein B-800/850, alpha chain
Molecular weight formula_weight	2230.7 kDa
Source method src_method	nat
Copy count entity_count	16

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,F,H,J,L,N,P,R,T,V,X,Z,1,3,5,7

XXXXXXXXXXXXXXXXXXXXXXXXXX

Entity 5 Entity 5 polymer

Description description	Light-harvesting protein B-800/850, beta chain
Molecular weight formula_weight	2571.2 kDa
Source method src_method	nat
Copy count entity_count	15

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E,G,I,K,M,O,Q,S,U,W,Y,2,4,6,8

XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

Entity 6 Entity 6 non-polymer

Description description	BACTERIOCHLOROPHYLL A
Molecular weight formula_weight	911.5 kDa
Source method src_method	syn
Copy count entity_count	34

Entity 7 Entity 7 non-polymer

Description description	BACTERIOPHEOPHYTIN A
Molecular weight formula_weight	889.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 8 Entity 8 non-polymer

Description description	FE (III) ION
Molecular weight formula_weight	55.8 kDa
Source method src_method	syn
Copy count entity_count	1

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6. Fold Classification (SCOP + CATH) 34 domains

SCOP 2.08 (34 domains)

Domain ID domain_id	d1pyh1_
Class class	i — Low resolution protein structures
Fold Fold fold	i.5 — Photosystems
Superfamily Superfamily superfamily	i.5.1 — Photosystems
Family Family family	i.5.1.1 — Photosystems

Domain ID domain_id	d1pyh2_
Class class	i — Low resolution protein structures
Fold Fold fold	i.5 — Photosystems
Superfamily Superfamily superfamily	i.5.1 — Photosystems
Family Family family	i.5.1.1 — Photosystems

Domain ID domain_id	d1pyh3_
Class class	i — Low resolution protein structures
Fold Fold fold	i.5 — Photosystems
Superfamily Superfamily superfamily	i.5.1 — Photosystems
Family Family family	i.5.1.1 — Photosystems

Domain ID domain_id	d1pyh4_
Class class	i — Low resolution protein structures
Fold Fold fold	i.5 — Photosystems
Superfamily Superfamily superfamily	i.5.1 — Photosystems
Family Family family	i.5.1.1 — Photosystems

Domain ID domain_id	d1pyh5_
Class class	i — Low resolution protein structures
Fold Fold fold	i.5 — Photosystems
Superfamily Superfamily superfamily	i.5.1 — Photosystems
Family Family family	i.5.1.1 — Photosystems

Domain ID domain_id	d1pyh6_
Class class	i — Low resolution protein structures
Fold Fold fold	i.5 — Photosystems
Superfamily Superfamily superfamily	i.5.1 — Photosystems
Family Family family	i.5.1.1 — Photosystems

Domain ID domain_id	d1pyh7_
Class class	i — Low resolution protein structures
Fold Fold fold	i.5 — Photosystems
Superfamily Superfamily superfamily	i.5.1 — Photosystems
Family Family family	i.5.1.1 — Photosystems

Domain ID domain_id	d1pyh8_
Class class	i — Low resolution protein structures
Fold Fold fold	i.5 — Photosystems
Superfamily Superfamily superfamily	i.5.1 — Photosystems
Family Family family	i.5.1.1 — Photosystems

Domain ID domain_id	d1pyha_
Class class	i — Low resolution protein structures
Fold Fold fold	i.5 — Photosystems
Superfamily Superfamily superfamily	i.5.1 — Photosystems
Family Family family	i.5.1.1 — Photosystems

Domain ID domain_id	d1pyhb_
Class class	i — Low resolution protein structures
Fold Fold fold	i.5 — Photosystems
Superfamily Superfamily superfamily	i.5.1 — Photosystems
Family Family family	i.5.1.1 — Photosystems

Domain ID domain_id	d1pyhc_
Class class	i — Low resolution protein structures
Fold Fold fold	i.5 — Photosystems
Superfamily Superfamily superfamily	i.5.1 — Photosystems
Family Family family	i.5.1.1 — Photosystems

Domain ID domain_id	d1pyhd_
Class class	i — Low resolution protein structures
Fold Fold fold	i.5 — Photosystems
Superfamily Superfamily superfamily	i.5.1 — Photosystems
Family Family family	i.5.1.1 — Photosystems

Domain ID domain_id	d1pyhe_
Class class	i — Low resolution protein structures
Fold Fold fold	i.5 — Photosystems
Superfamily Superfamily superfamily	i.5.1 — Photosystems
Family Family family	i.5.1.1 — Photosystems

Domain ID domain_id	d1pyhf_
Class class	i — Low resolution protein structures
Fold Fold fold	i.5 — Photosystems
Superfamily Superfamily superfamily	i.5.1 — Photosystems
Family Family family	i.5.1.1 — Photosystems

Domain ID domain_id	d1pyhg_
Class class	i — Low resolution protein structures
Fold Fold fold	i.5 — Photosystems
Superfamily Superfamily superfamily	i.5.1 — Photosystems
Family Family family	i.5.1.1 — Photosystems

Domain ID domain_id	d1pyhh_
Class class	i — Low resolution protein structures
Fold Fold fold	i.5 — Photosystems
Superfamily Superfamily superfamily	i.5.1 — Photosystems
Family Family family	i.5.1.1 — Photosystems

Domain ID domain_id	d1pyhi_
Class class	i — Low resolution protein structures
Fold Fold fold	i.5 — Photosystems
Superfamily Superfamily superfamily	i.5.1 — Photosystems
Family Family family	i.5.1.1 — Photosystems

Domain ID domain_id	d1pyhj_
Class class	i — Low resolution protein structures
Fold Fold fold	i.5 — Photosystems
Superfamily Superfamily superfamily	i.5.1 — Photosystems
Family Family family	i.5.1.1 — Photosystems

Domain ID domain_id	d1pyhk_
Class class	i — Low resolution protein structures
Fold Fold fold	i.5 — Photosystems
Superfamily Superfamily superfamily	i.5.1 — Photosystems
Family Family family	i.5.1.1 — Photosystems

Domain ID domain_id	d1pyhl_
Class class	i — Low resolution protein structures
Fold Fold fold	i.5 — Photosystems
Superfamily Superfamily superfamily	i.5.1 — Photosystems
Family Family family	i.5.1.1 — Photosystems

Domain ID domain_id	d1pyhm_
Class class	i — Low resolution protein structures
Fold Fold fold	i.5 — Photosystems
Superfamily Superfamily superfamily	i.5.1 — Photosystems
Family Family family	i.5.1.1 — Photosystems

Domain ID domain_id	d1pyhn_
Class class	i — Low resolution protein structures
Fold Fold fold	i.5 — Photosystems
Superfamily Superfamily superfamily	i.5.1 — Photosystems
Family Family family	i.5.1.1 — Photosystems

Domain ID domain_id	d1pyho_
Class class	i — Low resolution protein structures
Fold Fold fold	i.5 — Photosystems
Superfamily Superfamily superfamily	i.5.1 — Photosystems
Family Family family	i.5.1.1 — Photosystems

Domain ID domain_id	d1pyhp_
Class class	i — Low resolution protein structures
Fold Fold fold	i.5 — Photosystems
Superfamily Superfamily superfamily	i.5.1 — Photosystems
Family Family family	i.5.1.1 — Photosystems

Domain ID domain_id	d1pyhq_
Class class	i — Low resolution protein structures
Fold Fold fold	i.5 — Photosystems
Superfamily Superfamily superfamily	i.5.1 — Photosystems
Family Family family	i.5.1.1 — Photosystems

Domain ID domain_id	d1pyhr_
Class class	i — Low resolution protein structures
Fold Fold fold	i.5 — Photosystems
Superfamily Superfamily superfamily	i.5.1 — Photosystems
Family Family family	i.5.1.1 — Photosystems

Domain ID domain_id	d1pyhs_
Class class	i — Low resolution protein structures
Fold Fold fold	i.5 — Photosystems
Superfamily Superfamily superfamily	i.5.1 — Photosystems
Family Family family	i.5.1.1 — Photosystems

Domain ID domain_id	d1pyht_
Class class	i — Low resolution protein structures
Fold Fold fold	i.5 — Photosystems
Superfamily Superfamily superfamily	i.5.1 — Photosystems
Family Family family	i.5.1.1 — Photosystems

Domain ID domain_id	d1pyhu_
Class class	i — Low resolution protein structures
Fold Fold fold	i.5 — Photosystems
Superfamily Superfamily superfamily	i.5.1 — Photosystems
Family Family family	i.5.1.1 — Photosystems

Domain ID domain_id	d1pyhv_
Class class	i — Low resolution protein structures
Fold Fold fold	i.5 — Photosystems
Superfamily Superfamily superfamily	i.5.1 — Photosystems
Family Family family	i.5.1.1 — Photosystems

Domain ID domain_id	d1pyhw_
Class class	i — Low resolution protein structures
Fold Fold fold	i.5 — Photosystems
Superfamily Superfamily superfamily	i.5.1 — Photosystems
Family Family family	i.5.1.1 — Photosystems

Domain ID domain_id	d1pyhx_
Class class	i — Low resolution protein structures
Fold Fold fold	i.5 — Photosystems
Superfamily Superfamily superfamily	i.5.1 — Photosystems
Family Family family	i.5.1.1 — Photosystems

Domain ID domain_id	d1pyhy_
Class class	i — Low resolution protein structures
Fold Fold fold	i.5 — Photosystems
Superfamily Superfamily superfamily	i.5.1 — Photosystems
Family Family family	i.5.1.1 — Photosystems

Domain ID domain_id	d1pyhz_
Class class	i — Low resolution protein structures
Fold Fold fold	i.5 — Photosystems
Superfamily Superfamily superfamily	i.5.1 — Photosystems
Family Family family	i.5.1.1 — Photosystems

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Unit-cell length a length_a	76.037 Å
Unit-cell length b length_b	119.024 Å
Unit-cell length c length_c	130.432 Å
Unit-cell angle α angle_alpha	69.32 °
Unit-cell angle β angle_beta	72.69 °
Unit-cell angle γ angle_gamma	66.52 °
Molecules per unit cell Z z_pdb	16

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	4.800 Å
Low-resolution limit resolution_low	60.000 Å
R factor r_factor	0.4687
R_work r_work	0.4674
R_free r_free	0.4913

Crystal structure of RC-LH1 core complex from Rhodopseudomonas palustris

1. Protein Identity and Related Structures Protein Identity & Related Structures

Assembly Composition of the Current Entry

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

1pyh__assembly_1__model_1

1pyh__assembly_1__model_1 | I(q)

1pyh__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (8)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

Entity 5 Entity 5 polymer

Polymer Polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

6. Fold Classification (SCOP + CATH) 34 domains

SCOP 2.08 (34 domains)

7. Citations (1)