1l9b

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

Method: X-RAY DIFFRACTION Dmax: 104.0 Å Quality: EXCELLENT

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) NA SODIUM ION × 1 BCL BACTERIOCHLOROPHYLL A × 4 BPH BACTERIOPHEOPHYTIN A × 2 LDA LAURYL DIMETHYLAMINE-N-OXIDE × 9 HTO HEPTANE-1,2,3-TRIOL × 2 FE2 FE (II) ION × 1 CL CHLORIDE ION × 1 U10 UBIQUINONE-10 × 1 HEM PROTOPORPHYRIN IX CONTAINING FE × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 8.5;292 K;10% PEG 4000, 0.06%(w/v) lauryldimethylamine-N-oxide, 3.9%(w/v) heptane-1,2,3-triol, 15 mM Tricine, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K Resolution 2.40 Å R-free 0.264

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

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) NA SODIUM ION × 1 BCL BACTERIOCHLOROPHYLL A × 4 BPH BACTERIOPHEOPHYTIN A × 2 LDA LAURYL DIMETHYLAMINE-N-OXIDE × 9 HTO HEPTANE-1,2,3-TRIOL × 2 FE2 FE (II) ION × 1 CL CHLORIDE ION × 1 U10 UBIQUINONE-10 × 1 HEM PROTOPORPHYRIN IX CONTAINING FE × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 8.5;292 K;10% PEG 4000, 0.06%(w/v) lauryldimethylamine-N-oxide, 3.9%(w/v) heptane-1,2,3-triol, 15 mM Tricine, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K Resolution 2.40 Å R-free 0.264

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

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) NA SODIUM ION × 1 BCL BACTERIOCHLOROPHYLL A × 4 BPH BACTERIOPHEOPHYTIN A × 2 LDA LAURYL DIMETHYLAMINE-N-OXIDE × 9 HTO HEPTANE-1,2,3-TRIOL × 2 FE2 FE (II) ION × 1 CL CHLORIDE ION × 1 U10 UBIQUINONE-10 × 1 HEM PROTOPORPHYRIN IX CONTAINING FE × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 8.5;292 K;10% PEG 4000, 0.06%(w/v) lauryldimethylamine-N-oxide, 3.9%(w/v) heptane-1,2,3-triol, 15 mM Tricine, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K Resolution 2.40 Å R-free 0.264

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

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) NA SODIUM ION × 1 BCL BACTERIOCHLOROPHYLL A × 4 BPH BACTERIOPHEOPHYTIN A × 2 LDA LAURYL DIMETHYLAMINE-N-OXIDE × 9 HTO HEPTANE-1,2,3-TRIOL × 2 FE2 FE (II) ION × 1 CL CHLORIDE ION × 1 U10 UBIQUINONE-10 × 1 HEM PROTOPORPHYRIN IX CONTAINING FE × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 8.5;292 K;10% PEG 4000, 0.06%(w/v) lauryldimethylamine-N-oxide, 3.9%(w/v) heptane-1,2,3-triol, 15 mM Tricine, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K Resolution 2.40 Å R-free 0.264

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 6 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

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 1l9b

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1l9b
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1l9b
Deposition date deposition_date2002-03-22
Structure title titleX-Ray Structure of the Cytochrome-c(2)-Photosynthetic Reaction Center Electron Transfer Complex from Rhodobacter sphaeroides in Type II Co-Crystals
Keywords keywords;bacterial photosynthesis, protein-protein interaction, electron transfer proteins, 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_guinier32.71
Radius of gyration Rg (electron density) rg_electron31.13
Forward intensity I(0) i0150364000.00
Molecular weight molecular_weight110170.0 kDa
Excluded volume excluded_volume142690 ų
Envelope volume envelope_volume170390 ų
Hydration-shell volume shell_volume44593 ų
Envelope diameter envelope_diameter112.5
Shell Rg shell_rg39.10
Envelope Rg envelope_rg31.27
Shape Rg shape_rg31.11
Total Rg total_rg31.92
Total atoms total_atoms7817
Residues n_residues918
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 dmax104.0
Rg (real space) rg_real32.69
Rg uncertainty (real space) rg_real_error0.73
I(0) (real space) i0_real1.5040e+08
I(0) uncertainty (real space) i0_real_error2.3660e+06
Rg (reciprocal space) rg_reciprocal32.70
I(0) (reciprocal space) i0_reciprocal150400000.0000
Solution quality estimate total_estimate0.9018
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary34.6
Skewness Skewness skewness0.285
Kurtosis Kurtosis kurtosis-0.530
Angular range angular_range— – 0.2400 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha20570000.0000
Real-space data points n_real_points49
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.936; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.915

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (14)

7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (5 domains)

Domain ID domain_idd1l9bc_
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_idd1l9bh1
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_idd1l9bh2
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_idd1l9bl_
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_idd1l9bm_
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 (7 domains)

Domain ID domain_id1l9bC00
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_id1l9bH01
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_id1l9bH02
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_id1l9bL01
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_id1l9bL02
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_id1l9bM01
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_id1l9bM02
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 (1)

9. Files and Curves (10)