9ppn

Cu-bound structure of the H77C variant of TriCyt2

Method: X-RAY DIFFRACTION Dmax: 66.3 Å Quality: GOOD

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

Soluble cytochrome b562

Escherichia coli BL21(DE3)

UniProt P0ABE7

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 homooligomer Homooligomer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain A; UniProt 23–128 Chain B; UniProt 23–128 Chain C; UniProt 23–128 Not recorded CU COPPER (II) ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 5.5;298 K;21% PEG 1500, 200 mM CaCl2, 100 mM MES (pH 5.5) Resolution 1.87 Å R-free 0.220

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.

714 other PDB entries and 822 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name C562_ECOLX
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–106; UniProt 23–128 Author chain B; PDBConstruct 1–106; UniProt 23–128 Author chain C; PDBConstruct 1–106; UniProt 23–128

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 9ppn

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9ppn
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9ppn
Deposition date deposition_date2025-07-21
最后修订 last_revision2025-10-22
Structure title titleCu-bound structure of the H77C variant of TriCyt2
Keywords keywordsCu-binding protein, assembly, METAL BINDING PROTEIN; METAL BINDING PROTEIN
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier20.58
Radius of gyration Rg (electron density) rg_electron19.38
Forward intensity I(0) i022569000.00
Molecular weight molecular_weight35642.0 kDa
Excluded volume excluded_volume44418 ų
Envelope volume envelope_volume51286 ų
Hydration-shell volume shell_volume21693 ų
Envelope diameter envelope_diameter61.7
Shell Rg shell_rg26.13
Envelope Rg envelope_rg19.56
Shape Rg shape_rg19.37
Total Rg total_rg20.27
Total atoms total_atoms2500
Residues n_residues318
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 dmax66.3
Rg (real space) rg_real20.41
Rg uncertainty (real space) rg_real_error0.45
I(0) (real space) i0_real2.2570e+07
I(0) uncertainty (real space) i0_real_error3.0170e+05
Rg (reciprocal space) rg_reciprocal20.44
I(0) (reciprocal space) i0_reciprocal22570000.0000
Solution quality estimate total_estimate0.7984
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary27.9
Skewness Skewness skewness0.007
Kurtosis Kurtosis kurtosis-0.571
Angular range angular_range— – 0.3850 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha12030000.0000
Real-space data points n_real_points70
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.804; Stabil: 0.990; Sysdev: 1.000; Positv: 1.000; Valcen: 0.992; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

8. Citations (1)

9. Files and Curves (10)