1yf6

Structure of a quintuple mutant of photosynthetic reaction center from rhodobacter sphaeroides

Method: X-RAY DIFFRACTION Dmax: 91.0 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 L; UniProt 1–281 Mutation:L181Y Reaction center protein M chain × 1 (P02953) Reaction center protein H chain × 1 (P11846) BCL BACTERIOCHLOROPHYLL A × 5 BPH BACTERIOPHEOPHYTIN A × 1 U10 UBIQUINONE-10 × 3 HTO HEPTANE-1,2,3-TRIOL × 1 LDA LAURYL DIMETHYLAMINE-N-OXIDE × 3 GOL GLYCEROL × 1 FE2 FE (II) ION × 1 CL CHLORIDE ION × 1 PO4 PHOSPHATE ION × 2 SPO SPHEROIDENE × 1 CDL CARDIOLIPIN × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 8.5;292 K;POTASSIUM PHOSPHATE, SODIUM CHLORIDE, HAPTANETRIOL, DIOXANE, HAXANETRIOL, LDAO, pH 8.50, VAPOR DIFFUSION, SITTING DROP, temperature 292K Resolution 2.25 Å R-free 0.216

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

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:M203D, M210F, M214H, M260W Reaction center protein L chain × 1 (P02954) Reaction center protein H chain × 1 (P11846) BCL BACTERIOCHLOROPHYLL A × 5 BPH BACTERIOPHEOPHYTIN A × 1 U10 UBIQUINONE-10 × 3 HTO HEPTANE-1,2,3-TRIOL × 1 LDA LAURYL DIMETHYLAMINE-N-OXIDE × 3 GOL GLYCEROL × 1 FE2 FE (II) ION × 1 CL CHLORIDE ION × 1 PO4 PHOSPHATE ION × 2 SPO SPHEROIDENE × 1 CDL CARDIOLIPIN × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 8.5;292 K;POTASSIUM PHOSPHATE, SODIUM CHLORIDE, HAPTANETRIOL, DIOXANE, HAXANETRIOL, LDAO, pH 8.50, VAPOR DIFFUSION, SITTING DROP, temperature 292K Resolution 2.25 Å R-free 0.216

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

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 Reaction center protein L chain × 1 (P02954) Reaction center protein M chain × 1 (P02953) BCL BACTERIOCHLOROPHYLL A × 5 BPH BACTERIOPHEOPHYTIN A × 1 U10 UBIQUINONE-10 × 3 HTO HEPTANE-1,2,3-TRIOL × 1 LDA LAURYL DIMETHYLAMINE-N-OXIDE × 3 GOL GLYCEROL × 1 FE2 FE (II) ION × 1 CL CHLORIDE ION × 1 PO4 PHOSPHATE ION × 2 SPO SPHEROIDENE × 1 CDL CARDIOLIPIN × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 8.5;292 K;POTASSIUM PHOSPHATE, SODIUM CHLORIDE, HAPTANETRIOL, DIOXANE, HAXANETRIOL, LDAO, pH 8.50, VAPOR DIFFUSION, SITTING DROP, temperature 292K Resolution 2.25 Å R-free 0.216

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 1yf6

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1yf6
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1yf6
Deposition date deposition_date2004-12-30
Structure title titleStructure of a quintuple mutant of photosynthetic reaction center from rhodobacter sphaeroides
Keywords keywords;BACTERIAL PHOTOSYNTHESIS, RHODOBACTER SPHAEROIDES, GATED ELECTRON TRANSFER, QUINONE MOVEMENT, 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_guinier29.61
Radius of gyration Rg (electron density) rg_electron28.41
Forward intensity I(0) i0124827000.00
Molecular weight molecular_weight99839.0 kDa
Excluded volume excluded_volume129300 ų
Envelope volume envelope_volume145700 ų
Hydration-shell volume shell_volume41157 ų
Envelope diameter envelope_diameter93.4
Shell Rg shell_rg37.04
Envelope Rg envelope_rg28.55
Shape Rg shape_rg28.40
Total Rg total_rg29.30
Total atoms total_atoms7086
Residues n_residues820
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 dmax91.0
Rg (real space) rg_real29.49
Rg uncertainty (real space) rg_real_error0.64
I(0) (real space) i0_real1.2480e+08
I(0) uncertainty (real space) i0_real_error1.8540e+06
Rg (reciprocal space) rg_reciprocal29.54
I(0) (reciprocal space) i0_reciprocal124800000.0000
Solution quality estimate total_estimate0.9080
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks0
Primary peak position r_peak_primary
Skewness Skewness skewness0.168
Kurtosis Kurtosis kurtosis-0.551
Angular range angular_range— – 0.2700 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha15650000.0000
Real-space data points n_real_points55
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.961; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.922

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (15)

7. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd1yf6h1
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_idd1yf6h2
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_idd1yf6l_
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_idd1yf6m_
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_id1yf6H01
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_id1yf6H02
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_id1yf6L01
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_id1yf6L02
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_id1yf6M01
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_id1yf6M02
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)