1z9k

Photosynthetic Reaction Center from Rhodobacter sphaeroides

Method: X-RAY DIFFRACTION Dmax: 92.9 Å Quality: EXCELLENT

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

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 A; UniProt 1–281 Not recorded Reaction center protein M chain × 1 (P02953) Reaction center protein H chain × 1 (P11846) BCL BACTERIOCHLOROPHYLL A × 4 BPH BACTERIOPHEOPHYTIN A × 2 U10 UBIQUINONE-10 × 2 FE FE (III) ION × 1 MN MANGANESE (II) ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 8;298 K;PEG, NaCL, MnCl, LDAO, pH 8, VAPOR DIFFUSION, SITTING DROP, temperature 298K Resolution 4.60 Å R-free 0.330
2 Protein heterocomplex Heteromer Protein × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain A; UniProt 1–281 Not recorded Reaction center protein M chain × 2 (P02953) Reaction center protein H chain × 2 (P11846) BCL BACTERIOCHLOROPHYLL A × 8 BPH BACTERIOPHEOPHYTIN A × 4 U10 UBIQUINONE-10 × 4 FE FE (III) ION × 2 MN MANGANESE (II) ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 8;298 K;PEG, NaCL, MnCl, LDAO, pH 8, VAPOR DIFFUSION, SITTING DROP, temperature 298K Resolution 4.60 Å R-free 0.330

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 A; PDBConstruct 1–281; UniProt 1–281

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 B; UniProt 1–307 Not recorded Reaction center protein L chain × 1 (P02954) Reaction center protein H chain × 1 (P11846) BCL BACTERIOCHLOROPHYLL A × 4 BPH BACTERIOPHEOPHYTIN A × 2 U10 UBIQUINONE-10 × 2 FE FE (III) ION × 1 MN MANGANESE (II) ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 8;298 K;PEG, NaCL, MnCl, LDAO, pH 8, VAPOR DIFFUSION, SITTING DROP, temperature 298K Resolution 4.60 Å R-free 0.330
2 Protein heterocomplex Heteromer Protein × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain B; UniProt 1–307 Not recorded Reaction center protein L chain × 2 (P02954) Reaction center protein H chain × 2 (P11846) BCL BACTERIOCHLOROPHYLL A × 8 BPH BACTERIOPHEOPHYTIN A × 4 U10 UBIQUINONE-10 × 4 FE FE (III) ION × 2 MN MANGANESE (II) ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 8;298 K;PEG, NaCL, MnCl, LDAO, pH 8, VAPOR DIFFUSION, SITTING DROP, temperature 298K Resolution 4.60 Å R-free 0.330

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 B; PDBConstruct 1–307; UniProt 1–307

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 C; UniProt 1–260 Not recorded Reaction center protein L chain × 1 (P02954) Reaction center protein M chain × 1 (P02953) BCL BACTERIOCHLOROPHYLL A × 4 BPH BACTERIOPHEOPHYTIN A × 2 U10 UBIQUINONE-10 × 2 FE FE (III) ION × 1 MN MANGANESE (II) ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 8;298 K;PEG, NaCL, MnCl, LDAO, pH 8, VAPOR DIFFUSION, SITTING DROP, temperature 298K Resolution 4.60 Å R-free 0.330
2 Protein heterocomplex Heteromer Protein × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain C; UniProt 1–260 Not recorded Reaction center protein L chain × 2 (P02954) Reaction center protein M chain × 2 (P02953) BCL BACTERIOCHLOROPHYLL A × 8 BPH BACTERIOPHEOPHYTIN A × 4 U10 UBIQUINONE-10 × 4 FE FE (III) ION × 2 MN MANGANESE (II) ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 8;298 K;PEG, NaCL, MnCl, LDAO, pH 8, VAPOR DIFFUSION, SITTING DROP, temperature 298K Resolution 4.60 Å R-free 0.330

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 C; 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 1z9k

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1z9k
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1z9k
Deposition date deposition_date2005-04-02
Structure title titlePhotosynthetic Reaction Center from Rhodobacter sphaeroides
Keywords keywordsALPHA HELIX, 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_guinier29.97
Radius of gyration Rg (electron density) rg_electron28.63
Forward intensity I(0) i0120437000.00
Molecular weight molecular_weight97764.0 kDa
Excluded volume excluded_volume126630 ų
Envelope volume envelope_volume149890 ų
Hydration-shell volume shell_volume42021 ų
Envelope diameter envelope_diameter94.7
Shell Rg shell_rg37.19
Envelope Rg envelope_rg28.74
Shape Rg shape_rg28.62
Total Rg total_rg29.55
Total atoms total_atoms6946
Residues n_residues821
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 dmax92.9
Rg (real space) rg_real29.84
Rg uncertainty (real space) rg_real_error0.54
I(0) (real space) i0_real1.2040e+08
I(0) uncertainty (real space) i0_real_error1.9660e+06
Rg (reciprocal space) rg_reciprocal29.90
I(0) (reciprocal space) i0_reciprocal120400000.0000
Solution quality estimate total_estimate0.9082
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary36.8
Skewness Skewness skewness0.159
Kurtosis Kurtosis kurtosis-0.566
Angular range angular_range— – 0.2650 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha17030000.0000
Real-space data points n_real_points54
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.954; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.942

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (8)

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd1z9ka1
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_idd1z9kb1
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

8. Citations (1)

9. Files and Curves (10)