1dv3

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

Method: X-RAY DIFFRACTION Dmax: 150.5 Å Quality: GOOD

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

PHOTOSYNTHETIC REACTION CENTER REACTION CENTER

OrganismNot specified

UniProt P02954

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain L; UniProt 1–281 Fragment:L CHAIN PHOTOSYNTHETIC REACTION CENTER REACTION CENTER × 1 (P02953) PHOTOSYNTHETIC REACTION CENTER REACTION CENTER × 1 (P11846) BCL BACTERIOCHLOROPHYLL A × 4 BPH BACTERIOPHEOPHYTIN A × 2 U10 UBIQUINONE-10 × 2 FE2 FE (II) ION × 1 CL CHLORIDE ION × 1 LDA LAURYL DIMETHYLAMINE-N-OXIDE × 2 CD CADMIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 8.5;292 K;PEG 4000, heptanetriol, TRIS-HCL, LDAO detergent, sodium chloride, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K Resolution 2.50 Å R-free 0.252
2 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain R; UniProt 1–281 Fragment:L CHAIN PHOTOSYNTHETIC REACTION CENTER REACTION CENTER × 1 (P02953) PHOTOSYNTHETIC REACTION CENTER REACTION CENTER × 1 (P11846) BCL BACTERIOCHLOROPHYLL A × 4 BPH BACTERIOPHEOPHYTIN A × 2 U10 UBIQUINONE-10 × 2 FE2 FE (II) ION × 1 CL CHLORIDE ION × 1 CD CADMIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 8.5;292 K;PEG 4000, heptanetriol, TRIS-HCL, LDAO detergent, sodium chloride, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K Resolution 2.50 Å R-free 0.252

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

39 other PDB entries and 47 assemblies. Open the comparison page and filter oligomeric states

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 Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain M; UniProt 1–307 Fragment:M CHAIN PHOTOSYNTHETIC REACTION CENTER REACTION CENTER × 1 (P02954) PHOTOSYNTHETIC REACTION CENTER REACTION CENTER × 1 (P11846) BCL BACTERIOCHLOROPHYLL A × 4 BPH BACTERIOPHEOPHYTIN A × 2 U10 UBIQUINONE-10 × 2 FE2 FE (II) ION × 1 CL CHLORIDE ION × 1 LDA LAURYL DIMETHYLAMINE-N-OXIDE × 2 CD CADMIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 8.5;292 K;PEG 4000, heptanetriol, TRIS-HCL, LDAO detergent, sodium chloride, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K Resolution 2.50 Å R-free 0.252
2 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain S; UniProt 1–307 Fragment:M CHAIN PHOTOSYNTHETIC REACTION CENTER REACTION CENTER × 1 (P02954) PHOTOSYNTHETIC REACTION CENTER REACTION CENTER × 1 (P11846) BCL BACTERIOCHLOROPHYLL A × 4 BPH BACTERIOPHEOPHYTIN A × 2 U10 UBIQUINONE-10 × 2 FE2 FE (II) ION × 1 CL CHLORIDE ION × 1 CD CADMIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 8.5;292 K;PEG 4000, heptanetriol, TRIS-HCL, LDAO detergent, sodium chloride, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K Resolution 2.50 Å R-free 0.252

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

39 other PDB entries and 47 assemblies. Open the comparison page and filter oligomeric states

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 Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain H; UniProt 1–260 Fragment:H CHAIN PHOTOSYNTHETIC REACTION CENTER REACTION CENTER × 1 (P02954) PHOTOSYNTHETIC REACTION CENTER REACTION CENTER × 1 (P02953) BCL BACTERIOCHLOROPHYLL A × 4 BPH BACTERIOPHEOPHYTIN A × 2 U10 UBIQUINONE-10 × 2 FE2 FE (II) ION × 1 CL CHLORIDE ION × 1 LDA LAURYL DIMETHYLAMINE-N-OXIDE × 2 CD CADMIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 8.5;292 K;PEG 4000, heptanetriol, TRIS-HCL, LDAO detergent, sodium chloride, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K Resolution 2.50 Å R-free 0.252
2 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain T; UniProt 1–260 Fragment:H CHAIN PHOTOSYNTHETIC REACTION CENTER REACTION CENTER × 1 (P02954) PHOTOSYNTHETIC REACTION CENTER REACTION CENTER × 1 (P02953) BCL BACTERIOCHLOROPHYLL A × 4 BPH BACTERIOPHEOPHYTIN A × 2 U10 UBIQUINONE-10 × 2 FE2 FE (II) ION × 1 CL CHLORIDE ION × 1 CD CADMIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 8.5;292 K;PEG 4000, heptanetriol, TRIS-HCL, LDAO detergent, sodium chloride, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K Resolution 2.50 Å R-free 0.252

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

39 other PDB entries and 47 assemblies. Open the comparison page and filter oligomeric states

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.

SAXS scattering curve SAXS Profile

SAXS profile for 1dv3

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1dv3
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1dv3
Deposition date deposition_date2000-01-19
Structure title titlePHOTOSYNTHETIC 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 methodX-RAY DIFFRACTION

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier52.27
Radius of gyration Rg (electron density) rg_electron51.66
Forward intensity I(0) i0434835000.00
Molecular weight molecular_weight195390.0 kDa
Excluded volume excluded_volume252160 ų
Envelope volume envelope_volume338170 ų
Hydration-shell volume shell_volume54026 ų
Envelope diameter envelope_diameter163.5
Shell Rg shell_rg56.42
Envelope Rg envelope_rg49.71
Shape Rg shape_rg51.58
Total Rg total_rg52.12
Total atoms total_atoms13865
Residues n_residues1652
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax150.5
Rg (real space) rg_real52.49
Rg uncertainty (real space) rg_real_error1.30
I(0) (real space) i0_real4.3480e+08
I(0) uncertainty (real space) i0_real_error7.5090e+06
Rg (reciprocal space) rg_reciprocal52.05
I(0) (reciprocal space) i0_reciprocal434600000.0000
Solution quality estimate total_estimate0.7684
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary35.1
Skewness Skewness skewness0.235
Kurtosis Kurtosis kurtosis-1.048
Angular range angular_range— – 0.1500 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha21840000.0000
Real-space data points n_real_points31
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.777; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.654; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (11)

7. Fold Classification (SCOP + CATH) 20 domains

SCOP 2.08 (8 domains)

Domain ID domain_idd1dv3h1
Class classb — All beta proteins
Fold Fold foldb.41 — PRC-barrel domain
Superfamily Superfamily superfamilyb.41.1 — PRC-barrel domain
Family Family familyb.41.1.1 — Photosynthetic reaction centre, H-chain, cytoplasmic domain
Domain ID domain_idd1dv3h2
Class classf — Membrane and cell surface proteins and peptides
Fold Fold foldf.23 — Single transmembrane helix
Superfamily Superfamily superfamilyf.23.10 — Photosystem II reaction centre subunit H, transmembrane region
Family Family familyf.23.10.1 — Photosystem II reaction centre subunit H, transmembrane region
Domain ID domain_idd1dv3l_
Class classf — Membrane and cell surface proteins and peptides
Fold Fold foldf.26 — Bacterial photosystem II reaction centre, L and M subunits
Superfamily Superfamily superfamilyf.26.1 — Bacterial photosystem II reaction centre, L and M subunits
Family Family familyf.26.1.1 — Bacterial photosystem II reaction centre, L and M subunits
Domain ID domain_idd1dv3m_
Class classf — Membrane and cell surface proteins and peptides
Fold Fold foldf.26 — Bacterial photosystem II reaction centre, L and M subunits
Superfamily Superfamily superfamilyf.26.1 — Bacterial photosystem II reaction centre, L and M subunits
Family Family familyf.26.1.1 — Bacterial photosystem II reaction centre, L and M subunits
Domain ID domain_idd1dv3r_
Class classf — Membrane and cell surface proteins and peptides
Fold Fold foldf.26 — Bacterial photosystem II reaction centre, L and M subunits
Superfamily Superfamily superfamilyf.26.1 — Bacterial photosystem II reaction centre, L and M subunits
Family Family familyf.26.1.1 — Bacterial photosystem II reaction centre, L and M subunits
Domain ID domain_idd1dv3s_
Class classf — Membrane and cell surface proteins and peptides
Fold Fold foldf.26 — Bacterial photosystem II reaction centre, L and M subunits
Superfamily Superfamily superfamilyf.26.1 — Bacterial photosystem II reaction centre, L and M subunits
Family Family familyf.26.1.1 — Bacterial photosystem II reaction centre, L and M subunits
Domain ID domain_idd1dv3t1
Class classb — All beta proteins
Fold Fold foldb.41 — PRC-barrel domain
Superfamily Superfamily superfamilyb.41.1 — PRC-barrel domain
Family Family familyb.41.1.1 — Photosynthetic reaction centre, H-chain, cytoplasmic domain
Domain ID domain_idd1dv3t2
Class classf — Membrane and cell surface proteins and peptides
Fold Fold foldf.23 — Single transmembrane helix
Superfamily Superfamily superfamilyf.23.10 — Photosystem II reaction centre subunit H, transmembrane region
Family Family familyf.23.10.1 — Photosystem II reaction centre subunit H, transmembrane region

CATH v4.4 (12 domains)

Domain ID domain_id1dv3H01
Class class4 — Few Secondary Structures
Architecture architecture10 — Irregular
Topology topology540 — Photosynthetic Reaction Center; Chain H, domain 1
Homologous superfamily homologous superfamily10 — Photosynthetic reaction centre, H subunit, N-terminal domain
Domain ID domain_id1dv3H02
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology50 — Photosynthetic Reaction Center; Chain H, domain 2
Homologous superfamily homologous superfamily10 — Photosynthetic Reaction Center, subunit H, domain 2
Domain ID domain_id1dv3L01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology85 — Photosynthetic Reaction Center, subunit M; domain 1
Homologous superfamily homologous superfamily10 — Photosystem II protein D1-like
Domain ID domain_id1dv3L02
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology85 — Photosynthetic Reaction Center, subunit M; domain 1
Homologous superfamily homologous superfamily10 — Photosystem II protein D1-like
Domain ID domain_id1dv3M01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology85 — Photosynthetic Reaction Center, subunit M; domain 1
Homologous superfamily homologous superfamily10 — Photosystem II protein D1-like
Domain ID domain_id1dv3M02
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology85 — Photosynthetic Reaction Center, subunit M; domain 1
Homologous superfamily homologous superfamily10 — Photosystem II protein D1-like
Domain ID domain_id1dv3R01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology85 — Photosynthetic Reaction Center, subunit M; domain 1
Homologous superfamily homologous superfamily10 — Photosystem II protein D1-like
Domain ID domain_id1dv3R02
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology85 — Photosynthetic Reaction Center, subunit M; domain 1
Homologous superfamily homologous superfamily10 — Photosystem II protein D1-like
Domain ID domain_id1dv3S01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology85 — Photosynthetic Reaction Center, subunit M; domain 1
Homologous superfamily homologous superfamily10 — Photosystem II protein D1-like
Domain ID domain_id1dv3S02
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology85 — Photosynthetic Reaction Center, subunit M; domain 1
Homologous superfamily homologous superfamily10 — Photosystem II protein D1-like
Domain ID domain_id1dv3T01
Class class4 — Few Secondary Structures
Architecture architecture10 — Irregular
Topology topology540 — Photosynthetic Reaction Center; Chain H, domain 1
Homologous superfamily homologous superfamily10 — Photosynthetic reaction centre, H subunit, N-terminal domain
Domain ID domain_id1dv3T02
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology50 — Photosynthetic Reaction Center; Chain H, domain 2
Homologous superfamily homologous superfamily10 — Photosynthetic Reaction Center, subunit H, domain 2

8. Citations (4)

9. Files and Curves (10)