6z02

Photosynthetic Reaction Center From Rhodobacter Sphaeroides strain RV in surfo crystallization

Method: X-RAY DIFFRACTION

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

Reaction center protein H 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 L chain × 1 （P0C0Y8） Reaction center protein M chain × 1 （P0C0Y9） LAURYL DIMETHYLAMINE-N-OXIDE × 7 DODECANE × 6 PENTADECANE × 3 PHOSPHATE ION × 3 1,2-ETHANEDIOL × 13 SODIUM ION × 1 POTASSIUM ION × 1 BACTERIOCHLOROPHYLL A × 4 BACTERIOPHEOPHYTIN A × 2 UBIQUINONE-10 × 2 DECANE × 1 1,4-DIETHYLENE DIOXIDE × 1 HEPTANE-1,2,3-TRIOL × 3 FE (III) ION × 1 SPEROIDENONE × 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	1
Chains and sequence ranges	Author chain H； PDBConstruct 1–241； UniProt 10–250

Reaction center protein L chain

Rhodobacter sphaeroides

UniProt P0C0Y8

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 H chain × 1 （P0C0Y7） Reaction center protein M chain × 1 （P0C0Y9） LAURYL DIMETHYLAMINE-N-OXIDE × 7 DODECANE × 6 PENTADECANE × 3 PHOSPHATE ION × 3 1,2-ETHANEDIOL × 13 SODIUM ION × 1 POTASSIUM ION × 1 BACTERIOCHLOROPHYLL A × 4 BACTERIOPHEOPHYTIN A × 2 UBIQUINONE-10 × 2 DECANE × 1 1,4-DIETHYLENE DIOXIDE × 1 HEPTANE-1,2,3-TRIOL × 3 FE (III) ION × 1 SPEROIDENONE × 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	2
Chains and sequence ranges	Author chain L； PDBConstruct 1–281； UniProt 2–282

Reaction center protein M chain

Rhodobacter sphaeroides

UniProt P0C0Y9

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 H chain × 1 （P0C0Y7） Reaction center protein L chain × 1 （P0C0Y8） LAURYL DIMETHYLAMINE-N-OXIDE × 7 DODECANE × 6 PENTADECANE × 3 PHOSPHATE ION × 3 1,2-ETHANEDIOL × 13 SODIUM ION × 1 POTASSIUM ION × 1 BACTERIOCHLOROPHYLL A × 4 BACTERIOPHEOPHYTIN A × 2 UBIQUINONE-10 × 2 DECANE × 1 1,4-DIETHYLENE DIOXIDE × 1 HEPTANE-1,2,3-TRIOL × 3 FE (III) ION × 1 SPEROIDENONE × 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	3
Chains and sequence ranges	Author chain M； PDBConstruct 1–302； UniProt 2–303

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	6z02
Deposition date deposition_date	2020-05-07
Structure title title	Photosynthetic Reaction Center From Rhodobacter Sphaeroides strain RV in surfo crystallization
Keywords keywords	;Photosynthetic reaction center, bacteriochlorophyll, Rhodobacter sphaeroides, serial crystallography, mesophase crystallization, lipid sponge phase, lipid cubic phase, spheroidene, ubiquinone, 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.

6z02__assembly_1__model_1

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

Download this curve (.dat)

6z02__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6z02__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	29.65 Å
Rg (electron density)	28.19 Å
Total Rg	29.15 Å
Atom count	7429
Residues	823
Excluded volume	138090 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6z02__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 (20)

Entity 1 Entity 1 polymer

Description description	Reaction center protein H chain
Molecular weight formula_weight	26170.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H
Atom count atom_count	7930

FDLASLAIYSFWIFLAGLIYYLQTENMREGYPLENEDGTPAANQGPFPLPKPKTFILPHGRGTLTVPGPESEDRPIALARTAVSEGFPHAPTGDPMKDGVGPASWVARRDLPELDGHGHNKIKPMKAAAGFHVSAGKNPIGLPVRGCDLEIAGKVVDIWVDIPEQMARFLEVELKDGSTRLLPMQMVKVQSNRVHVNALSSDLFAGIPTIKSPTEVTLLEEDKICGYVAGGLMYAAPKRKS

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 L chain
Molecular weight formula_weight	31360.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L

ALLSFERKYRVPGGTLVGGNLFDFWVGPFYVGFFGVATFFFAALGIILIAWSAVLQGTWNPQLISVYPPALEYGLGGAPLAKGGLWQIITICATGAFVSWALREVEICRKLGIGYHIPFAFAFAILAYLTLVLFRPVMMGAWGYAFPYGIWTHLDWVSNTGYTYGNFHYNPAHMIAITFFFTNALALALHGALVLSAANPEKGKEMRTPDHEDTFFRDLVGYSIGTLGIHRLGLLLSLSAVFFSALCMIITGTIWFDQWVDWWQWWVKLPWWANIPGGING

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 M chain
Molecular weight formula_weight	33885.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	M

AEYQNIFTQVQVRGPADLGMTEDVNLANRSGVGPFSTLLGWFGNAQLGPIYLGSLGVLSLFSGLMWFFTIGIWFWYQAGWNPAVFLRDLFFFSLEPPAPEYGLSFAAPLKEGGLWLIASFFMFVAVWSWWGRTYLRAQALGMGKHTAWAFLSAIWLWMVLGFIRPILMGSWSEAVPYGIFSHLDWTNNFSLVHGNLFYNPFHGLSIAFLYGSALLFAMHGATILAVSRFGGERELEQIADRGTAAERAALFWRWTMGFNATMEGIHRWAIWMAVLVTLTGGIGILLSGTVVDNWYVWGQNHG

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	LAURYL DIMETHYLAMINE-N-OXIDE
Molecular weight formula_weight	229.4 kDa
Source method src_method	syn
Copy count entity_count	7

Entity 5 Entity 5 non-polymer

Description description	DODECANE
Molecular weight formula_weight	170.3 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 6 Entity 6 non-polymer

Description description	PENTADECANE
Molecular weight formula_weight	212.4 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 7 Entity 7 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 8 Entity 8 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	13

Entity 9 Entity 9 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 10 Entity 10 non-polymer

Description description	POTASSIUM ION
Molecular weight formula_weight	39.1 kDa
Source method src_method	nat
Copy count entity_count	1

Entity 11 Entity 11 non-polymer

Description description	BACTERIOCHLOROPHYLL A
Molecular weight formula_weight	911.5 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 12 Entity 12 non-polymer

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

Entity 13 Entity 13 non-polymer

Description description	UBIQUINONE-10
Molecular weight formula_weight	863.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 14 Entity 14 non-polymer

Description description	DECANE
Molecular weight formula_weight	142.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 15 Entity 15 non-polymer

Description description	1,4-DIETHYLENE DIOXIDE
Molecular weight formula_weight	88.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 16 Entity 16 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	3

Entity 17 Entity 17 non-polymer

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

Entity 18 Entity 18 non-polymer

Description description	SPEROIDENONE
Molecular weight formula_weight	595.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 19 Entity 19 non-polymer

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

Entity 20 Entity 20 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	444

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d6z02h1
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	d6z02h2
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	d6z02l_
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	d6z02m_
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

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Unit-cell length a length_a	139.850 Å
Unit-cell length b length_b	139.850 Å
Unit-cell length c length_c	185.370 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	trigonal

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	43.200 Å
R factor r_factor	0.2025
R_work r_work	0.2012
R_free r_free	0.2262

Photosynthetic Reaction Center From Rhodobacter Sphaeroides strain RV in surfo crystallization

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

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

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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

6z02__assembly_1__model_1

6z02__assembly_1__model_1 | I(q)

6z02__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 (20)

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 non-polymer

Entity 16 Entity 16 non-polymer

Entity 17 Entity 17 non-polymer

Entity 18 Entity 18 non-polymer

Entity 19 Entity 19 non-polymer

Entity 20 Entity 20 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (4 domains)

7. Citations (1)