8c88

Double mutant G(M19)C/T(L214)C structure of Photosynthetic Reaction Center From Cereibacter sphaeroides strain RV

Method: X-RAY DIFFRACTION

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

Reaction center protein H chain

Cereibacter sphaeroides 2.4.1

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） (2R)-2-hydroxy-3-(phosphonooxy)propyl (9E)-octadec-9-enoate × 2 LAURYL DIMETHYLAMINE-N-OXIDE × 6 UNKNOWN LIGAND × 7 (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate × 1 BACTERIOCHLOROPHYLL A × 4 BACTERIOPHEOPHYTIN A × 2 1,4-DIETHYLENE DIOXIDE × 1 1,2-ETHANEDIOL × 3 FE (III) ION × 1 UBIQUINONE-10 × 1 SPEROIDENONE × 1 PHOSPHATE ION × 2 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RCEH_CERSP
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain H； PDBConstruct 1–242； UniProt 9–250

Reaction center protein L chain

Cereibacter sphaeroides 2.4.1

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） (2R)-2-hydroxy-3-(phosphonooxy)propyl (9E)-octadec-9-enoate × 2 LAURYL DIMETHYLAMINE-N-OXIDE × 6 UNKNOWN LIGAND × 7 (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate × 1 BACTERIOCHLOROPHYLL A × 4 BACTERIOPHEOPHYTIN A × 2 1,4-DIETHYLENE DIOXIDE × 1 1,2-ETHANEDIOL × 3 FE (III) ION × 1 UBIQUINONE-10 × 1 SPEROIDENONE × 1 PHOSPHATE ION × 2 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RCEL_CERSP
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain L； PDBConstruct 1–281； UniProt 2–282

Reaction center protein M chain

Cereibacter sphaeroides 2.4.1

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） (2R)-2-hydroxy-3-(phosphonooxy)propyl (9E)-octadec-9-enoate × 2 LAURYL DIMETHYLAMINE-N-OXIDE × 6 UNKNOWN LIGAND × 7 (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate × 1 BACTERIOCHLOROPHYLL A × 4 BACTERIOPHEOPHYTIN A × 2 1,4-DIETHYLENE DIOXIDE × 1 1,2-ETHANEDIOL × 3 FE (III) ION × 1 UBIQUINONE-10 × 1 SPEROIDENONE × 1 PHOSPHATE ION × 2 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RCEM_CERSP
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain M； PDBConstruct 1–303； UniProt 2–304

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	8c88
Deposition date deposition_date	2023-01-19
Structure title title	Double mutant G(M19)C/T(L214)C structure of Photosynthetic Reaction Center From Cereibacter sphaeroides strain RV
Keywords keywords	;Photosynthetic reaction center, bacteriochlorophyll, Rhodobacter sphaeroides, spheroidene, ubiquinone, disulfide bond, 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.

8c88__assembly_1__model_1

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

Download this curve (.dat)

8c88__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8c88__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	29.87 Å
Rg (electron density)	28.52 Å
Total Rg	29.45 Å
Atom count	7280
Residues	826
Excluded volume	133530 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8c88__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 (16)

Entity 1 Entity 1 polymer

Description description	Reaction center protein H chain
Molecular weight formula_weight	26284.2 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	7341

NFDLASLAIYSFWIFLAGLIYYLQTENMREGYPLENEDGTPAANQGPFPLPKPKTFILPHGRGTLTVPGPESEDRPIALARTAVSEGFPHAPTGDPMKDGVGPASWVARRDLPELDGHGHNKIKPMKAAAGFHVSAGKNPIGLPVRGCDLEIAGKVVDIWVDIPEQMARFLEVELKDGSTRLLPMQMVKVQSNRVHVNALSSDLFAGIPTIKSPTEVTLLEEDKICGYVAGGLMYAAPKRKS

Source Source

Source organism organism	Cereibacter sphaeroides 2.4.1
NCBI taxonomy ID ncbi_taxonomy_id	272943
Host organism host_organism	Cereibacter sphaeroides 2.4.1

Entity 2 Entity 2 polymer

Description description	Reaction center protein L chain
Molecular weight formula_weight	31362.5 kDa
Mutation mutation	S178T, T214C
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L

ALLSFERKYRVPGGTLVGGNLFDFWVGPFYVGFFGVATFFFAALGIILIAWSAVLQGTWNPQLISVYPPALEYGLGGAPLAKGGLWQIITICATGAFVSWALREVEICRKLGIGYHIPFAFAFAILAYLTLVLFRPVMMGAWGYAFPYGIWTHLDWVSNTGYTYGNFHYNPAHMIAITFFFTNALALALHGALVLSAANPEKGKEMRTPDHEDCFFRDLVGYSIGTLGIHRLGLLLSLSAVFFSALCMIITGTIWFDQWVDWWQWWVKLPWWANIPGGING

Source Source

Source organism organism	Cereibacter sphaeroides 2.4.1
NCBI taxonomy ID ncbi_taxonomy_id	272943
Host organism host_organism	Cereibacter sphaeroides 2.4.1

Entity 3 Entity 3 polymer

Description description	Reaction center protein M chain
Molecular weight formula_weight	34063.2 kDa
Mutation mutation	S8T, G19C
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	M

AEYQNIFTQVQVRGPADLCMTEDVNLANRSGVGPFSTLLGWFGNAQLGPIYLGSLGVLSLFSGLMWFFTIGIWFWYQAGWNPAVFLRDLFFFSLEPPAPEYGLSFAAPLKEGGLWLIASFFMFVAVWSWWGRTYLRAQALGMGKHTAWAFLSAIWLWMVLGFIRPILMGSWSEAVPYGIFSHLDWTNNFSLVHGNLFYNPFHGLSIAFLYGSALLFAMHGATILAVSRFGGERELEQIADRGTAAERAALFWRWTMGFNATMEGIHRWAIWMAVLVTLTGGIGILLSGTVVDNWYVWGQNHGM

Source Source

Source organism organism	Cereibacter sphaeroides 2.4.1
NCBI taxonomy ID ncbi_taxonomy_id	272943
Host organism host_organism	Cereibacter sphaeroides 2.4.1

Entity 4 Entity 4 non-polymer

Description description	(2R)-2-hydroxy-3-(phosphonooxy)propyl (9E)-octadec-9-enoate
Molecular weight formula_weight	436.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	LAURYL DIMETHYLAMINE-N-OXIDE
Molecular weight formula_weight	229.4 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 6 Entity 6 non-polymer

Description description	UNKNOWN LIGAND
Source method src_method	syn
Copy count entity_count	7

Entity 7 Entity 7 non-polymer

Description description	(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
Molecular weight formula_weight	356.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 8 Entity 8 non-polymer

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

Entity 9 Entity 9 non-polymer

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

Entity 10 Entity 10 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 11 Entity 11 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 12 Entity 12 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 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	1

Entity 14 Entity 14 non-polymer

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

Entity 15 Entity 15 non-polymer

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

Entity 16 Entity 16 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	23

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Unit-cell length a length_a	100.910 Å
Unit-cell length b length_b	100.910 Å
Unit-cell length c length_c	237.020 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 42 21 2
Space-group number int_tables_number	94
Crystal system crystal_system	tetragonal

Resolution resolution	2.750 Å
Low-resolution limit resolution_low	46.420 Å
R factor r_factor	0.2020
R_work r_work	0.1991
R_free r_free	0.2706

Double mutant G(M19)C/T(L214)C structure of Photosynthetic Reaction Center From Cereibacter sphaeroides strain RV

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

8c88__assembly_1__model_1

8c88__assembly_1__model_1 | I(q)

8c88__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 (16)

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 water

7. Citations (1)