8vtk

Crystal structure of R.sphaeroides Photosynthetic Reaction Center variant Y(M210)2-chlorophenylalanine

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

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） FE (III) ION × 1 BACTERIOPHEOPHYTIN A × 2 BACTERIOCHLOROPHYLL A × 4 UBIQUINONE-10 × 1 CHLORIDE ION × 1 LAURYL DIMETHYLAMINE-N-OXIDE × 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	1
Chains and sequence ranges	Author chain H； PDBConstruct 1–240； UniProt 11–250

Reaction center protein L chain

Cereibacter 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） FE (III) ION × 1 BACTERIOPHEOPHYTIN A × 2 BACTERIOCHLOROPHYLL A × 4 UBIQUINONE-10 × 1 CHLORIDE ION × 1 LAURYL DIMETHYLAMINE-N-OXIDE × 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	2
Chains and sequence ranges	Author chain L； PDBConstruct 1–281； UniProt 2–282

Reaction center protein M chain

Cereibacter 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） FE (III) ION × 1 BACTERIOPHEOPHYTIN A × 2 BACTERIOCHLOROPHYLL A × 4 UBIQUINONE-10 × 1 CHLORIDE ION × 1 LAURYL DIMETHYLAMINE-N-OXIDE × 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_CERSP
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain M； PDBConstruct 1–301； UniProt 3–303

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	8vtk
Deposition date deposition_date	2024-01-26
Structure title title	Crystal structure of R.sphaeroides Photosynthetic Reaction Center variant Y(M210)2-chlorophenylalanine
Keywords keywords	Photosynthesis, membrane protein, electron transfer; 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.

8vtk__assembly_1__model_1

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

Download this curve (.dat)

8vtk__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8vtk__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	29.68 Å
Rg (electron density)	28.45 Å
Total Rg	29.31 Å
Atom count	6989
Residues	821
Excluded volume	127430 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8vtk__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 (12)

Entity 1 Entity 1 polymer

Description description	Reaction center protein H chain
Molecular weight formula_weight	26022.9 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	7024

DLASLAIYSFWIFLAGLIYYLQTENMREGYPLENEDGTPAANQGPFPLPKPKTFILPHGRGTLTVPGPESEDRPIALARTAVSEGFPHAPTGDPMKDGVGPASWVARRDLPELDGHGHNKIKPMKAAAGFHVSAGKNPIGLPVRGCDLEIAGKVVDIWVDIPEQMARFLEVELKDGSTRLLPMQMVKVQSNRVHVNALSSDLFAGIPTIKSPTEVTLLEEDKICGYVAGGLMYAAPKRKS

Source Source

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

Entity 2 Entity 2 polymer

Description description	Reaction center protein L chain
Molecular weight formula_weight	31346.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L

ALLSFERKYRVPGGTLVGGNLFDFWVGPFYVGFFGVATFFFAALGIILIAWSAVLQGTWNPQLISVYPPALEYGLGGAPLAKGGLWQIITICATGAFVSWALREVEICRKLGIGYHIPFAFAFAILAYLTLVLFRPVMMGAWGYAFPYGIWTHLDWVSNTGYTYGNFHYNPAHMIAISFFFTNALALALHGALVLSAANPEKGKEMRTPDHEDTFFRDLVGYSIGTLGIHRLGLLLSLSAVFFSALCMIITGTIWFDQWVDWWQWWVKLPWWANIPGGING

Source Source

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

Entity 3 Entity 3 polymer

Description description	Reaction center protein M chain
Molecular weight formula_weight	33732.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	M

EYQNIFSQVQVRGPADLGMTEDVNLANRSGVGPFSTLLGWFGNAQLGPIYLGSLGVLSLFSGLMWFFTIGIWFWYQAGWNPAVFLRDLFFFSLEPPAPEYGLSFAAPLKEGGLWLIASFFMFVAVWSWWGRTYLRAQALGMGKHTAWAFLSAIWLWMVLGFIRPILMGSWSEAVPYGIFSHLDWTNNFSLVHGNLFYNPFHGLSIAFLXGSALLFAMHGATILAVSRFGGERELEQIADRGTAAERAALFVRWTMGFNATMEGIHRWAIWMAVLVTLTGGIGILLSGTVVDNWYVWGQNHG

Source Source

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

Entity 4 Entity 4 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 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	2

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	4

Entity 7 Entity 7 non-polymer

Description description	UBIQUINONE-10
Molecular weight formula_weight	863.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 8 Entity 8 non-polymer

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

Entity 9 Entity 9 non-polymer

Description description	LAURYL DIMETHYLAMINE-N-OXIDE
Molecular weight formula_weight	229.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 10 Entity 10 non-polymer

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

Entity 11 Entity 11 non-polymer

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

Entity 12 Entity 12 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	19

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Unit-cell length a length_a	140.950 Å
Unit-cell length b length_b	140.950 Å
Unit-cell length c length_c	186.720 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	3.070 Å
Low-resolution limit resolution_low	39.760 Å
R factor r_factor	0.1789
R_work r_work	0.1771
R_free r_free	0.2127

Crystal structure of R.sphaeroides Photosynthetic Reaction Center variant Y(M210)2-chlorophenylalanine

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

8vtk__assembly_1__model_1

8vtk__assembly_1__model_1 | I(q)

8vtk__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 (12)

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 water

7. Citations (1)