1tkw

The transient complex of poplar plastocyanin with turnip cytochrome f determined with paramagnetic NMR

Method: SOLUTION NMR Dmax: 78.8 Å Quality: GOOD

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

Plastocyanin A

Populus nigra

UniProt P00299

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 × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 70–168 Not recorded Cytochrome f × 1 (P36438) CU COPPER (II) ION × 1 HEC HEME C × 1 SOLUTION NMR NMR measurement conditions:pH 6;303 K;Ionic strength (raw mmCIF value) 10 mM;Pressure 1 NMR measurement conditions:pH 6;303 K;Ionic strength (raw mmCIF value) 11 mM;Pressure 1 NMR sample composition:0.5 mM Cd-substituted poplar plastocyanin + 0.35 mM soluble fragment of turnip cytochrome f in oxidized state in 10 mM sodium phosphate pH 6.0 | 94% H2O, 6% D2O NMR sample composition:0.5 mM Cd-substituted poplar plastocyanin + 0.35 mM soluble fragment of turnip cytochrome f in reduced state in 10 mM sodium phosphate pH 6.0 + 1 mM sodium ascorbate | 94% H2O, 6% D2O Resolution not provided

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.

15 other PDB entries and 16 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name PLAS1_POPNI
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–99; UniProt 70–168

Cytochrome f

Brassica rapa subsp. rapa

UniProt P36438

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 × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain B; UniProt 36–287 Not recorded Plastocyanin A × 1 (P00299) CU COPPER (II) ION × 1 HEC HEME C × 1 SOLUTION NMR NMR measurement conditions:pH 6;303 K;Ionic strength (raw mmCIF value) 10 mM;Pressure 1 NMR measurement conditions:pH 6;303 K;Ionic strength (raw mmCIF value) 11 mM;Pressure 1 NMR sample composition:0.5 mM Cd-substituted poplar plastocyanin + 0.35 mM soluble fragment of turnip cytochrome f in oxidized state in 10 mM sodium phosphate pH 6.0 | 94% H2O, 6% D2O NMR sample composition:0.5 mM Cd-substituted poplar plastocyanin + 0.35 mM soluble fragment of turnip cytochrome f in reduced state in 10 mM sodium phosphate pH 6.0 + 1 mM sodium ascorbate | 94% H2O, 6% D2O Resolution not provided

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.

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CYF_BRARA
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 1–252; UniProt 36–287

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 1tkw

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id1tkw
Deposition date deposition_date2004-06-09
Structure title titleThe transient complex of poplar plastocyanin with turnip cytochrome f determined with paramagnetic NMR
Keywords keywordsElectron transfer, photosynthesis, paramagnetic, rigid body calculations; PHOTOSYNTHESIS
Experimental Method methodSOLUTION NMR

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

Radius of gyration Rg (Guinier) rg_guinier23.72
Radius of gyration Rg (electron density) rg_electron23.97
Forward intensity I(0) i01970730000.00
Molecular weight molecular_weight384300.0 kDa
Excluded volume excluded_volume483680 ų
Envelope volume envelope_volume68247 ų
Hydration-shell volume shell_volume24258 ų
Envelope diameter envelope_diameter90.1
Shell Rg shell_rg30.79
Envelope Rg envelope_rg24.96
Shape Rg shape_rg23.96
Total Rg total_rg24.13
Total atoms total_atoms53960
Residues n_residues3490
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 dmax78.8
Rg (real space) rg_real23.87
Rg uncertainty (real space) rg_real_error0.72
I(0) (real space) i0_real1.9710e+09
I(0) uncertainty (real space) i0_real_error2.7150e+07
Rg (reciprocal space) rg_reciprocal23.83
I(0) (reciprocal space) i0_reciprocal1971000000.0000
Solution quality estimate total_estimate0.8761
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary25.9
Skewness Skewness skewness0.509
Kurtosis Kurtosis kurtosis-0.161
Angular range angular_range— – 0.3350 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha3310000.0000
Real-space data points n_real_points65
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.852; Stabil: 0.997; Sysdev: 1.000; Positv: 1.000; Valcen: 0.892; Smooth: 0.946

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd1tkwa_
Class classb — All beta proteins
Fold Fold foldb.6 — Cupredoxin-like
Superfamily Superfamily superfamilyb.6.1 — Cupredoxins
Family Family familyb.6.1.1 — Plastocyanin/azurin-like

CATH v4.4 (3 domains)

Domain ID domain_id1tkwA00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily420 — Cupredoxins - blue copper proteins
Domain ID domain_id1tkwB01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily830 — Cytochrome f large domain
Domain ID domain_id1tkwB02
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily100 — RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain

8. Citations (1)

9. Files and Curves (10)