1kby

Structure of Photosynthetic Reaction Center with bacteriochlorophyll-bacteriopheophytin heterodimer

Method: X-RAY DIFFRACTION Dmax: 92.5 Å Quality: EXCELLENT

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

PHOTOSYNTHETIC REACTION CENTER PROTEIN L CHAIN

Rhodobacter sphaeroides

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 Not recorded PHOTOSYNTHETIC REACTION CENTER PROTEIN M CHAIN × 1 (P02953) PHOTOSYNTHETIC REACTION CENTER PROTEIN H CHAIN × 1 (P11846) BCL BACTERIOCHLOROPHYLL A × 3 BPH BACTERIOPHEOPHYTIN A × 3 FE FE (III) ION × 1 CL CHLORIDE ION × 1 U10 UBIQUINONE-10 × 1 SPO SPHEROIDENE × 1 CDL CARDIOLIPIN × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7.4;298 K;LDAO, Potassium phosphate, heptano-1,2,3-triol, dioxane, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 25K Resolution 2.50 Å R-free 0.224

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 48 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

PHOTOSYNTHETIC REACTION CENTER PROTEIN M CHAIN

Rhodobacter sphaeroides

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 Mutation:H202L PHOTOSYNTHETIC REACTION CENTER PROTEIN L CHAIN × 1 (P02954) PHOTOSYNTHETIC REACTION CENTER PROTEIN H CHAIN × 1 (P11846) BCL BACTERIOCHLOROPHYLL A × 3 BPH BACTERIOPHEOPHYTIN A × 3 FE FE (III) ION × 1 CL CHLORIDE ION × 1 U10 UBIQUINONE-10 × 1 SPO SPHEROIDENE × 1 CDL CARDIOLIPIN × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7.4;298 K;LDAO, Potassium phosphate, heptano-1,2,3-triol, dioxane, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 25K Resolution 2.50 Å R-free 0.224

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 48 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

PHOTOSYNTHETIC REACTION CENTER PROTEIN H CHAIN

Rhodobacter sphaeroides

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 Not recorded PHOTOSYNTHETIC REACTION CENTER PROTEIN L CHAIN × 1 (P02954) PHOTOSYNTHETIC REACTION CENTER PROTEIN M CHAIN × 1 (P02953) BCL BACTERIOCHLOROPHYLL A × 3 BPH BACTERIOPHEOPHYTIN A × 3 FE FE (III) ION × 1 CL CHLORIDE ION × 1 U10 UBIQUINONE-10 × 1 SPO SPHEROIDENE × 1 CDL CARDIOLIPIN × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7.4;298 K;LDAO, Potassium phosphate, heptano-1,2,3-triol, dioxane, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 25K Resolution 2.50 Å R-free 0.224

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 48 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

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 1kby

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id1kby
Deposition date deposition_date2001-11-07
Structure title titleStructure of Photosynthetic Reaction Center with bacteriochlorophyll-bacteriopheophytin heterodimer
Keywords keywordstransmembrane alpha helix, PHOTOSYNTHESIS; PHOTOSYNTHESIS
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier29.84
Radius of gyration Rg (electron density) rg_electron28.53
Forward intensity I(0) i0119592000.00
Molecular weight molecular_weight98516.0 kDa
Excluded volume excluded_volume127920 ų
Envelope volume envelope_volume146420 ų
Hydration-shell volume shell_volume41281 ų
Envelope diameter envelope_diameter94.4
Shell Rg shell_rg37.17
Envelope Rg envelope_rg28.58
Shape Rg shape_rg28.53
Total Rg total_rg29.41
Total atoms total_atoms6998
Residues n_residues819
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 dmax92.5
Rg (real space) rg_real29.71
Rg uncertainty (real space) rg_real_error0.54
I(0) (real space) i0_real1.1960e+08
I(0) uncertainty (real space) i0_real_error1.7500e+06
Rg (reciprocal space) rg_reciprocal29.76
I(0) (reciprocal space) i0_reciprocal119600000.0000
Solution quality estimate total_estimate0.9091
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary36.7
Skewness Skewness skewness0.157
Kurtosis Kurtosis kurtosis-0.568
Angular range angular_range— – 0.2650 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha14470000.0000
Real-space data points n_real_points54
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.955; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.951

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (11)

7. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd1kbyh1
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_idd1kbyh2
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_idd1kbyl_
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_idd1kbym_
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

CATH v4.4 (6 domains)

Domain ID domain_id1kbyH01
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_id1kbyH02
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_id1kbyL01
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_id1kbyL02
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_id1kbyM01
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_id1kbyM02
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

8. Citations (2)

9. Files and Curves (10)