1l9j

X-Ray Structure of the Cytochrome-c(2)-Photosynthetic Reaction Center Electron Transfer Complex from Rhodobacter sphaeroides in Type I Co-Crystals

Method: X-RAY DIFFRACTION Dmax: 240.4 Å Quality: REASONABLE

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

REACTION CENTER PROTEIN L CHAIN

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 × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain L; UniProt 1–281 Not recorded REACTION CENTER PROTEIN M CHAIN × 1 (P02953) REACTION CENTER PROTEIN H CHAIN × 1 (P11846) cytochrome c-2 × 1 (P00095) BCL BACTERIOCHLOROPHYLL A × 4 BPH BACTERIOPHEOPHYTIN A × 2 FE2 FE (II) ION × 1 CL CHLORIDE ION × 1 U10 UBIQUINONE-10 × 1 LDA LAURYL DIMETHYLAMINE-N-OXIDE × 2 HEM PROTOPORPHYRIN IX CONTAINING FE × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 8.5;292 K;PEG 4000, lauryl-dimethylamine-N-oxide, heptane-1,2,3-triol, tricine buffer, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K Resolution 3.25 Å R-free 0.287
2 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain R; UniProt 1–281 Not recorded REACTION CENTER PROTEIN M CHAIN × 1 (P02953) REACTION CENTER PROTEIN H CHAIN × 1 (P11846) cytochrome c-2 × 1 (P00095) BCL BACTERIOCHLOROPHYLL A × 4 BPH BACTERIOPHEOPHYTIN A × 2 FE2 FE (II) ION × 1 CL CHLORIDE ION × 1 U10 UBIQUINONE-10 × 1 LDA LAURYL DIMETHYLAMINE-N-OXIDE × 2 HEM PROTOPORPHYRIN IX CONTAINING FE × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 8.5;292 K;PEG 4000, lauryl-dimethylamine-N-oxide, heptane-1,2,3-triol, tricine buffer, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K Resolution 3.25 Å R-free 0.287

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

REACTION CENTER PROTEIN M CHAIN

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 × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain M; UniProt 1–307 Not recorded REACTION CENTER PROTEIN L CHAIN × 1 (P02954) REACTION CENTER PROTEIN H CHAIN × 1 (P11846) cytochrome c-2 × 1 (P00095) BCL BACTERIOCHLOROPHYLL A × 4 BPH BACTERIOPHEOPHYTIN A × 2 FE2 FE (II) ION × 1 CL CHLORIDE ION × 1 U10 UBIQUINONE-10 × 1 LDA LAURYL DIMETHYLAMINE-N-OXIDE × 2 HEM PROTOPORPHYRIN IX CONTAINING FE × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 8.5;292 K;PEG 4000, lauryl-dimethylamine-N-oxide, heptane-1,2,3-triol, tricine buffer, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K Resolution 3.25 Å R-free 0.287
2 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain S; UniProt 1–307 Not recorded REACTION CENTER PROTEIN L CHAIN × 1 (P02954) REACTION CENTER PROTEIN H CHAIN × 1 (P11846) cytochrome c-2 × 1 (P00095) BCL BACTERIOCHLOROPHYLL A × 4 BPH BACTERIOPHEOPHYTIN A × 2 FE2 FE (II) ION × 1 CL CHLORIDE ION × 1 U10 UBIQUINONE-10 × 1 LDA LAURYL DIMETHYLAMINE-N-OXIDE × 2 HEM PROTOPORPHYRIN IX CONTAINING FE × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 8.5;292 K;PEG 4000, lauryl-dimethylamine-N-oxide, heptane-1,2,3-triol, tricine buffer, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K Resolution 3.25 Å R-free 0.287

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

REACTION CENTER PROTEIN H CHAIN

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 × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain H; UniProt 1–260 Not recorded REACTION CENTER PROTEIN L CHAIN × 1 (P02954) REACTION CENTER PROTEIN M CHAIN × 1 (P02953) cytochrome c-2 × 1 (P00095) BCL BACTERIOCHLOROPHYLL A × 4 BPH BACTERIOPHEOPHYTIN A × 2 FE2 FE (II) ION × 1 CL CHLORIDE ION × 1 U10 UBIQUINONE-10 × 1 LDA LAURYL DIMETHYLAMINE-N-OXIDE × 2 HEM PROTOPORPHYRIN IX CONTAINING FE × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 8.5;292 K;PEG 4000, lauryl-dimethylamine-N-oxide, heptane-1,2,3-triol, tricine buffer, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K Resolution 3.25 Å R-free 0.287
2 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain T; UniProt 1–260 Not recorded REACTION CENTER PROTEIN L CHAIN × 1 (P02954) REACTION CENTER PROTEIN M CHAIN × 1 (P02953) cytochrome c-2 × 1 (P00095) BCL BACTERIOCHLOROPHYLL A × 4 BPH BACTERIOPHEOPHYTIN A × 2 FE2 FE (II) ION × 1 CL CHLORIDE ION × 1 U10 UBIQUINONE-10 × 1 LDA LAURYL DIMETHYLAMINE-N-OXIDE × 2 HEM PROTOPORPHYRIN IX CONTAINING FE × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 8.5;292 K;PEG 4000, lauryl-dimethylamine-N-oxide, heptane-1,2,3-triol, tricine buffer, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K Resolution 3.25 Å R-free 0.287

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

cytochrome c-2

OrganismNot specified

UniProt P00095

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 × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain C; UniProt 22–145 Not recorded REACTION CENTER PROTEIN L CHAIN × 1 (P02954) REACTION CENTER PROTEIN M CHAIN × 1 (P02953) REACTION CENTER PROTEIN H CHAIN × 1 (P11846) BCL BACTERIOCHLOROPHYLL A × 4 BPH BACTERIOPHEOPHYTIN A × 2 FE2 FE (II) ION × 1 CL CHLORIDE ION × 1 U10 UBIQUINONE-10 × 1 LDA LAURYL DIMETHYLAMINE-N-OXIDE × 2 HEM PROTOPORPHYRIN IX CONTAINING FE × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 8.5;292 K;PEG 4000, lauryl-dimethylamine-N-oxide, heptane-1,2,3-triol, tricine buffer, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K Resolution 3.25 Å R-free 0.287
2 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain D; UniProt 22–145 Not recorded REACTION CENTER PROTEIN L CHAIN × 1 (P02954) REACTION CENTER PROTEIN M CHAIN × 1 (P02953) REACTION CENTER PROTEIN H CHAIN × 1 (P11846) BCL BACTERIOCHLOROPHYLL A × 4 BPH BACTERIOPHEOPHYTIN A × 2 FE2 FE (II) ION × 1 CL CHLORIDE ION × 1 U10 UBIQUINONE-10 × 1 LDA LAURYL DIMETHYLAMINE-N-OXIDE × 2 HEM PROTOPORPHYRIN IX CONTAINING FE × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 8.5;292 K;PEG 4000, lauryl-dimethylamine-N-oxide, heptane-1,2,3-triol, tricine buffer, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K Resolution 3.25 Å R-free 0.287

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.

4 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CYC2_RHOSH
Isoform
PDB entities 4
Chains and sequence ranges Author chain C; PDBConstruct 1–124; UniProt 22–145 Author chain D; PDBConstruct 1–124; UniProt 22–145

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 1l9j

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1l9j
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1l9j
Deposition date deposition_date2002-03-24
Structure title titleX-Ray Structure of the Cytochrome-c(2)-Photosynthetic Reaction Center Electron Transfer Complex from Rhodobacter sphaeroides in Type I Co-Crystals
Keywords keywords;bacterial photosynthesis, electron transfer proteins, protein-protein interactions, membrane proteins, protein complexes, PHOTOSYNTHESIS ;; PHOTOSYNTHESIS
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier71.04
Radius of gyration Rg (electron density) rg_electron70.84
Forward intensity I(0) i0523449000.00
Molecular weight molecular_weight216490.0 kDa
Excluded volume excluded_volume278800 ų
Envelope volume envelope_volume445780 ų
Hydration-shell volume shell_volume50881 ų
Envelope diameter envelope_diameter207.9
Shell Rg shell_rg80.13
Envelope Rg envelope_rg65.79
Shape Rg shape_rg70.83
Total Rg total_rg71.02
Total atoms total_atoms15368
Residues n_residues1836
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 dmax240.4
Rg (real space) rg_real71.32
Rg uncertainty (real space) rg_real_error3.14
I(0) (real space) i0_real5.2340e+08
I(0) uncertainty (real space) i0_real_error1.2830e+07
Rg (reciprocal space) rg_reciprocal69.51
I(0) (reciprocal space) i0_reciprocal521400000.0000
Solution quality estimate total_estimate0.5783
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary32.8
Skewness Skewness skewness0.054
Kurtosis Kurtosis kurtosis-1.477
Angular range angular_range— – 0.1100 −1
Current regularization parameter α current_alpha0.0007
Highest regularization parameter α highest_alpha13030000.0000
Real-space data points n_real_points23
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.002; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.509; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (12)

7. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (10 domains)

Domain ID domain_idd1l9jc_
Class classa — All alpha proteins
Fold Fold folda.3 — Cytochrome c
Superfamily Superfamily superfamilya.3.1 — Cytochrome c
Family Family familya.3.1.1 — monodomain cytochrome c
Domain ID domain_idd1l9jd_
Class classa — All alpha proteins
Fold Fold folda.3 — Cytochrome c
Superfamily Superfamily superfamilya.3.1 — Cytochrome c
Family Family familya.3.1.1 — monodomain cytochrome c
Domain ID domain_idd1l9jh1
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_idd1l9jh2
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_idd1l9jl_
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_idd1l9jm_
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_idd1l9jr_
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_idd1l9js_
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_idd1l9jt1
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_idd1l9jt2
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 (14 domains)

Domain ID domain_id1l9jC00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology760 — Cytochrome Bc1 Complex; Chain D, domain 2
Homologous superfamily homologous superfamily10 — Cytochrome c-like domain
Domain ID domain_id1l9jD00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology760 — Cytochrome Bc1 Complex; Chain D, domain 2
Homologous superfamily homologous superfamily10 — Cytochrome c-like domain
Domain ID domain_id1l9jH01
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_id1l9jH02
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_id1l9jL01
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_id1l9jL02
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_id1l9jM01
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_id1l9jM02
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_id1l9jR01
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_id1l9jR02
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_id1l9jS01
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_id1l9jS02
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_id1l9jT01
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_id1l9jT02
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 (1)

9. Files and Curves (10)