1dv3

PHOTOSYNTHETIC REACTION CENTER FROM RHODOBACTER SPHAEROIDES IN THE CHARGE-SEPARATED D+QAQB-STATE WITH THE PROTON TRANSFER INHIBITOR CD2+

Method: X-RAY DIFFRACTION

▼

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

PHOTOSYNTHETIC REACTION CENTER REACTION CENTER

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	PHOTOSYNTHETIC REACTION CENTER REACTION CENTER × 1 （P02953） PHOTOSYNTHETIC REACTION CENTER REACTION CENTER × 1 （P11846） BACTERIOCHLOROPHYLL A × 4 BACTERIOPHEOPHYTIN A × 2 UBIQUINONE-10 × 2 FE (II) ION × 1 CHLORIDE ION × 1 LAURYL DIMETHYLAMINE-N-OXIDE × 2 CADMIUM ION × 1 water × 3	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	PHOTOSYNTHETIC REACTION CENTER REACTION CENTER × 1 （P02953） PHOTOSYNTHETIC REACTION CENTER REACTION CENTER × 1 （P11846） BACTERIOCHLOROPHYLL A × 4 BACTERIOPHEOPHYTIN A × 2 UBIQUINONE-10 × 2 FE (II) ION × 1 CHLORIDE ION × 1 CADMIUM ION × 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 Author chain R； PDBConstruct 1–281； UniProt 1–281

PHOTOSYNTHETIC REACTION CENTER REACTION CENTER

OrganismNot specified

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	PHOTOSYNTHETIC REACTION CENTER REACTION CENTER × 1 （P02954） PHOTOSYNTHETIC REACTION CENTER REACTION CENTER × 1 （P11846） BACTERIOCHLOROPHYLL A × 4 BACTERIOPHEOPHYTIN A × 2 UBIQUINONE-10 × 2 FE (II) ION × 1 CHLORIDE ION × 1 LAURYL DIMETHYLAMINE-N-OXIDE × 2 CADMIUM ION × 1 water × 3	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	PHOTOSYNTHETIC REACTION CENTER REACTION CENTER × 1 （P02954） PHOTOSYNTHETIC REACTION CENTER REACTION CENTER × 1 （P11846） BACTERIOCHLOROPHYLL A × 4 BACTERIOPHEOPHYTIN A × 2 UBIQUINONE-10 × 2 FE (II) ION × 1 CHLORIDE ION × 1 CADMIUM ION × 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 Author chain S； PDBConstruct 1–307； UniProt 1–307

PHOTOSYNTHETIC REACTION CENTER REACTION CENTER

OrganismNot specified

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	PHOTOSYNTHETIC REACTION CENTER REACTION CENTER × 1 （P02954） PHOTOSYNTHETIC REACTION CENTER REACTION CENTER × 1 （P02953） BACTERIOCHLOROPHYLL A × 4 BACTERIOPHEOPHYTIN A × 2 UBIQUINONE-10 × 2 FE (II) ION × 1 CHLORIDE ION × 1 LAURYL DIMETHYLAMINE-N-OXIDE × 2 CADMIUM ION × 1 water × 3	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	PHOTOSYNTHETIC REACTION CENTER REACTION CENTER × 1 （P02954） PHOTOSYNTHETIC REACTION CENTER REACTION CENTER × 1 （P02953） BACTERIOCHLOROPHYLL A × 4 BACTERIOPHEOPHYTIN A × 2 UBIQUINONE-10 × 2 FE (II) ION × 1 CHLORIDE ION × 1 CADMIUM ION × 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 Author chain T； 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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	1dv3
Deposition date deposition_date	2000-01-19
Structure title title	PHOTOSYNTHETIC REACTION CENTER FROM RHODOBACTER SPHAEROIDES IN THE CHARGE-SEPARATED D+QAQB-STATE WITH THE PROTON TRANSFER INHIBITOR CD2+
Keywords keywords	;Bacterial Photosynthesis, Rhodobacter sphaeroides, Metal Ion Binding, Cation Binding, Proton Transfer, Integral Membrane Protein, PHOTOSYNTHESIS ;; PHOTOSYNTHESIS
Experimental Method method	X-RAY DIFFRACTION

▼

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.

1dv3__assembly_1__model_1

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

Download this curve (.dat)

1dv3__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1dv3__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	29.75 Å
Rg (electron density)	28.48 Å
Total Rg	29.37 Å
Atom count	6954
Residues	826
Excluded volume	126610 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1dv3__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1dv3__assembly_2__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (11)

Entity 1 Entity 1 polymer

Description description	PHOTOSYNTHETIC REACTION CENTER REACTION CENTER
Molecular weight formula_weight	31346.4 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L,R
Atom count atom_count	14271

ALLSFERKYRVPGGTLVGGNLFDFWVGPFYVGFFGVATFFFAALGIILIAWSAVLQGTWNPQLISVYPPALEYGLGGAPLAKGGLWQIITICATGAFVSWALREVEICRKLGIGYHIPFAFAFAILAYLTLVLFRPVMMGAWGYAFPYGIWTHLDWVSNTGYTYGNFHYNPAHMIAISFFFTNALALALHGALVLSAANPEKGKEMRTPDHEDTFFRDLVGYSIGTLGIHRLGLLLSLSAVFFSALCMIITGTIWFDQWVDWWQWWVKLPWWANIPGGING

Entity 2 Entity 2 polymer

Description description	PHOTOSYNTHETIC REACTION CENTER REACTION CENTER
Molecular weight formula_weight	34355.5 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	M,S

AEYQNIFSQVQVRGPADLGMTEDVNLANRSGVGPFSTLLGWFGNAQLGPIYLGSLGVLSLFSGLMWFFTIGIWFWYQAGWNPAVFLRDLFFFSLEPPAPEYGLSFAAPLKEGGLWLIASFFMFVAVWSWWGRTYLRAQALGMGKHTAWAFLSAIWLWMVLGFIRPILMGSWSEAVPYGIFSHLDWTNNFSLVHGNLFYNPFHGLSIAFLYGSALLFAMHGATILAVSRFGGERELEQIADRGTAAERAALFWRWTMGFNATMEGIHRWAIWMAVLVTLTGGIGILLSGTVVDNWYVWGQNHGMAPLA

Entity 3 Entity 3 polymer

Description description	PHOTOSYNTHETIC REACTION CENTER REACTION CENTER
Molecular weight formula_weight	28137.4 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H,T

MVGVTAFQNFDLASLAIYSFWIFLAGLIYYLQTENMREGYPLENEDGTPAANQGPFPLPKPKTFILPHGRGTLTVPGPESEDRPIALARTAVSEGFPHAPTGDPMKDGVGPASWVARRDLPELDGHGHNKIKPMKAAAGFHVSAGKNPIGLPVRGCDLEIAGKVVDIWVDIPEQMARFLEVELKDGSTRLLPMQMVKVQSNRVHVNALSSDLFAGIPTIKSPTEVTLLEEDKICGYVAGGLMYAAPKRKSVVAAMLAEYA

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	8

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	4

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	4

Entity 7 Entity 7 non-polymer

Description description	FE (II) ION
Molecular weight formula_weight	55.8 kDa
Source method src_method	syn
Copy count entity_count	2

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	2

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	CADMIUM ION
Molecular weight formula_weight	112.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 11 Entity 11 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	406

▼

6. Fold Classification (SCOP + CATH) 20 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d1dv3h1
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	d1dv3h2
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	d1dv3l_
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	d1dv3m_
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	d1dv3r_
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	d1dv3s_
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	d1dv3t1
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	d1dv3t2
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

CATH v4.4 (12 domains)

Domain ID domain_id	1dv3H01
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	1dv3H02
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	1dv3L01
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	1dv3L02
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	1dv3M01
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	1dv3M02
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	1dv3R01
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	1dv3R02
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	1dv3S01
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	1dv3S02
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	1dv3T01
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	1dv3T02
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

▶

Unit-cell length a length_a	141.250 Å
Unit-cell length b length_b	141.250 Å
Unit-cell length c length_c	275.330 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	16

Space group space_group	P 43 21 2
Space-group number int_tables_number	96
Crystal system crystal_system	—

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	27.800 Å
R factor r_factor	0.2270
R_work r_work	0.2260
R_free r_free	0.2520

PHOTOSYNTHETIC REACTION CENTER FROM RHODOBACTER SPHAEROIDES IN THE CHARGE-SEPARATED D+QAQB-STATE WITH THE PROTON TRANSFER INHIBITOR CD2+

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

PHOTOSYNTHETIC REACTION CENTER REACTION CENTER

State in the Current Structure

Other States of the Same Protein in the Database

PHOTOSYNTHETIC REACTION CENTER REACTION CENTER

State in the Current Structure

Other States of the Same Protein in the Database

PHOTOSYNTHETIC REACTION CENTER REACTION CENTER

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

1dv3__assembly_1__model_1

1dv3__assembly_1__model_1 | I(q)

1dv3__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 (11)

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 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 water

6. Fold Classification (SCOP + CATH) 20 domains

SCOP 2.08 (8 domains)

CATH v4.4 (12 domains)

7. Citations (4)

PHOTOSYNTHETIC REACTION CENTER FROM RHODOBACTER SPHAEROIDES IN THE CHARGE-SEPARATED D+QAQB-STATE WITH THE PROTON TRANSFER INHIBITOR CD2+

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

PHOTOSYNTHETIC REACTION CENTER REACTION CENTER

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

PHOTOSYNTHETIC REACTION CENTER REACTION CENTER

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

PHOTOSYNTHETIC REACTION CENTER REACTION CENTER

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

1dv3__assembly_1__model_1

1dv3__assembly_1__model_1 | I(q)

1dv3__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 (11)

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 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 water

6. Fold Classification (SCOP + CATH) 20 domains

SCOP 2.08 (8 domains)

CATH v4.4 (12 domains)

7. Citations (4)