1yf6

Structure of a quintuple mutant of photosynthetic reaction center from rhodobacter sphaeroides

Method: X-RAY DIFFRACTION

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

Reaction center protein L chain

Rhodobacter sphaeroides

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Reaction center protein M chain × 1 （P02953） Reaction center protein H chain × 1 （P11846） BACTERIOCHLOROPHYLL A × 5 BACTERIOPHEOPHYTIN A × 1 UBIQUINONE-10 × 3 HEPTANE-1,2,3-TRIOL × 1 LAURYL DIMETHYLAMINE-N-OXIDE × 3 GLYCEROL × 1 FE (II) ION × 1 CHLORIDE ION × 1 PHOSPHATE ION × 2 SPHEROIDENE × 1 CARDIOLIPIN × 1 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RCEL_RHOSH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain L； PDBConstruct 1–281； UniProt 1–281

Reaction center protein M chain

Rhodobacter sphaeroides

UniProt P02953

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Reaction center protein L chain × 1 （P02954） Reaction center protein H chain × 1 （P11846） BACTERIOCHLOROPHYLL A × 5 BACTERIOPHEOPHYTIN A × 1 UBIQUINONE-10 × 3 HEPTANE-1,2,3-TRIOL × 1 LAURYL DIMETHYLAMINE-N-OXIDE × 3 GLYCEROL × 1 FE (II) ION × 1 CHLORIDE ION × 1 PHOSPHATE ION × 2 SPHEROIDENE × 1 CARDIOLIPIN × 1 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RCEM_RHOSH
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain M； PDBConstruct 1–307； UniProt 1–307

Reaction center protein H chain

Rhodobacter sphaeroides

UniProt P11846

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Reaction center protein L chain × 1 （P02954） Reaction center protein M chain × 1 （P02953） BACTERIOCHLOROPHYLL A × 5 BACTERIOPHEOPHYTIN A × 1 UBIQUINONE-10 × 3 HEPTANE-1,2,3-TRIOL × 1 LAURYL DIMETHYLAMINE-N-OXIDE × 3 GLYCEROL × 1 FE (II) ION × 1 CHLORIDE ION × 1 PHOSPHATE ION × 2 SPHEROIDENE × 1 CARDIOLIPIN × 1 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RCEH_RHOSH
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain H； PDBConstruct 1–260； UniProt 1–260

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	1yf6
Deposition date deposition_date	2004-12-30
Structure title title	Structure of a quintuple mutant of photosynthetic reaction center from rhodobacter sphaeroides
Keywords keywords	;BACTERIAL PHOTOSYNTHESIS, RHODOBACTER SPHAEROIDES, GATED ELECTRON TRANSFER, QUINONE MOVEMENT, INTEGRAL MEMBRANE PROTEIN, 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.

1yf6__assembly_1__model_1

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

Download this curve (.dat)

1yf6__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1yf6__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	29.61 Å
Rg (electron density)	28.41 Å
Total Rg	29.30 Å
Atom count	7086
Residues	820
Excluded volume	129300 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1yf6__assembly_1__model_1`	trimeric （3）	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 (15)

Entity 1 Entity 1 polymer

Description description	Reaction center protein L chain
Molecular weight formula_weight	31362.4 kDa
Mutation mutation	L181Y
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L
Atom count atom_count	7450

ALLSFERKYRVPGGTLVGGNLFDFWVGPFYVGFFGVATFFFAALGIILIAWSAVLQGTWNPQLISVYPPALEYGLGGAPLAKGGLWQIITICATGAFVSWALREVEICRKLGIGYHIPFAFAFAILAYLTLVLFRPVMMGAWGYAFPYGIWTHLDWVSNTGYTYGNFHYNPAHMIAISFFYTNALALALHGALVLSAANPEKGKEMRTPDHEDTFFRDLVGYSIGTLGIHRLGLLLSLSAVFFSALCMIITGTIWFDQWVDWWQWWVKLPWWANIPGGING

Source Source

Source organism organism	Rhodobacter sphaeroides
NCBI taxonomy ID ncbi_taxonomy_id	1063
Host organism host_organism	Rhodobacter sphaeroides

Entity 2 Entity 2 polymer

Description description	Reaction center protein M chain
Molecular weight formula_weight	34580.7 kDa
Mutation mutation	M203D, M210F, M214H, M260W
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	M

AEYQNIFSQVQVRGPADLGMTEDVNLANRSGVGPFSTLLGWFGNAQLGPIYLGSLGVLSLFSGLMWFFTIGIWFWYQAGWNPAVFLRDLFFFSLEPPAPEYGLSFAAPLKEGGLWLIASFFMFVAVWSWWGRTYLRAQALGMGKHTAWAFLSAIWLWMVLGFIRPILMGSWSEAVPYGIFSHLDWTNNFSLVHGNLFYNPFHDLSIAFLFGSAHLFAMHGATILAVSRFGGERELEQIADRGTAAERAALFWRWTMGFNWTMEGIHRWAIWMAVLVTLTGGIGILLSGTVVDNWYVWGQNHGMAPLN

Source Source

Source organism organism	Rhodobacter sphaeroides
NCBI taxonomy ID ncbi_taxonomy_id	1063
Host organism host_organism	Rhodobacter sphaeroides

Entity 3 Entity 3 polymer

Description description	Reaction center protein H chain
Molecular weight formula_weight	28066.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H

MVGVTAFGNFDLASLAIYSFWIFLAGLIYYLQTENMREGYPLENEDGTPAANQGPFPLPKPKTFILPHGRGTLTVPGPESEDRPIALARTAVSEGFPHAPTGDPMKDGVGPASWVARRDLPELDGHGHNKIKPMKAAAGFHVSAGKNPIGLPVRGCDLEIAGKVVDIWVDIPEQMARFLEVELKDGSTRLLPMQMVKVQSNRVHVNALSSDLFAGIPTIKSPTEVTLLEEDKICGYVAGGLMYAAPKRKSVVAAMLAEYA

Source Source

Source organism organism	Rhodobacter sphaeroides
NCBI taxonomy ID ncbi_taxonomy_id	1063
Host organism host_organism	Rhodobacter sphaeroides

Entity 4 Entity 4 non-polymer

Description description	BACTERIOCHLOROPHYLL A
Molecular weight formula_weight	911.5 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 5 Entity 5 non-polymer

Description description	BACTERIOPHEOPHYTIN A
Molecular weight formula_weight	889.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 non-polymer

Description description	UBIQUINONE-10
Molecular weight formula_weight	863.3 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 7 Entity 7 non-polymer

Description description	HEPTANE-1,2,3-TRIOL
Molecular weight formula_weight	148.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 8 Entity 8 non-polymer

Description description	LAURYL DIMETHYLAMINE-N-OXIDE
Molecular weight formula_weight	229.4 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 9 Entity 9 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 10 Entity 10 non-polymer

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

Entity 11 Entity 11 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 12 Entity 12 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 13 Entity 13 non-polymer

Description description	SPHEROIDENE
Molecular weight formula_weight	568.9 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 14 Entity 14 non-polymer

Description description	CARDIOLIPIN
Molecular weight formula_weight	1464.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 15 Entity 15 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	364

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6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1yf6h1
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.23 — Single transmembrane helix
Superfamily Superfamily superfamily	f.23.10 — Photosystem II reaction centre subunit H, transmembrane region
Family Family family	f.23.10.1 — Photosystem II reaction centre subunit H, transmembrane region

Domain ID domain_id	d1yf6h2
Class class	b — All beta proteins
Fold Fold fold	b.41 — PRC-barrel domain
Superfamily Superfamily superfamily	b.41.1 — PRC-barrel domain
Family Family family	b.41.1.1 — Photosynthetic reaction centre, H-chain, cytoplasmic domain

Domain ID domain_id	d1yf6l_
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.26 — Bacterial photosystem II reaction centre, L and M subunits
Superfamily Superfamily superfamily	f.26.1 — Bacterial photosystem II reaction centre, L and M subunits
Family Family family	f.26.1.1 — Bacterial photosystem II reaction centre, L and M subunits

Domain ID domain_id	d1yf6m_
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.26 — Bacterial photosystem II reaction centre, L and M subunits
Superfamily Superfamily superfamily	f.26.1 — Bacterial photosystem II reaction centre, L and M subunits
Family Family family	f.26.1.1 — Bacterial photosystem II reaction centre, L and M subunits

CATH v4.4 (6 domains)

Domain ID domain_id	1yf6H01
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	540 — Photosynthetic Reaction Center; Chain H, domain 1
Homologous superfamily homologous superfamily	10 — Photosynthetic reaction centre, H subunit, N-terminal domain

Domain ID domain_id	1yf6H02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	50 — Photosynthetic Reaction Center; Chain H, domain 2
Homologous superfamily homologous superfamily	10 — Photosynthetic Reaction Center, subunit H, domain 2

Domain ID domain_id	1yf6L01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	85 — Photosynthetic Reaction Center, subunit M; domain 1
Homologous superfamily homologous superfamily	10 — Photosystem II protein D1-like

Domain ID domain_id	1yf6L02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	85 — Photosynthetic Reaction Center, subunit M; domain 1
Homologous superfamily homologous superfamily	10 — Photosystem II protein D1-like

Domain ID domain_id	1yf6M01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	85 — Photosynthetic Reaction Center, subunit M; domain 1
Homologous superfamily homologous superfamily	10 — Photosystem II protein D1-like

Domain ID domain_id	1yf6M02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	85 — Photosynthetic Reaction Center, subunit M; domain 1
Homologous superfamily homologous superfamily	10 — Photosystem II protein D1-like

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Unit-cell length a length_a	139.442 Å
Unit-cell length b length_b	139.442 Å
Unit-cell length c length_c	185.460 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 31 2 1
Space-group number int_tables_number	152
Crystal system crystal_system	—

Resolution resolution	2.250 Å
Low-resolution limit resolution_low	39.340 Å
R factor r_factor	0.1970
R_work r_work	0.1970
R_free r_free	0.2160

Structure of a quintuple mutant of photosynthetic reaction center from rhodobacter sphaeroides

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

Reaction center protein L chain

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Reaction center protein M chain

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Reaction center protein H chain

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

1yf6__assembly_1__model_1

1yf6__assembly_1__model_1 | I(q)

1yf6__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 (15)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 non-polymer

Entity 10 Entity 10 non-polymer

Entity 11 Entity 11 non-polymer

Entity 12 Entity 12 non-polymer

Entity 13 Entity 13 non-polymer

Entity 14 Entity 14 non-polymer

Entity 15 Entity 15 water

6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (4 domains)

CATH v4.4 (6 domains)

7. Citations (2)