9zdp

Crystal structure of rubredoxin from psychrophilic bacterium Polaromonas glacialis

Method: X-RAY DIFFRACTION Dmax: 79.7 Å Quality: REASONABLE

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

Rubredoxin

Polaromonas glacialis

UniProt A0AAU7LTP7

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 × 7 PDB declaration: heptameric(7) Consistent with protein copy count Chain A; UniProt 5–57 Chain B; UniProt 5–57 Chain C; UniProt 5–57 Chain D; UniProt 5–57 Chain E; UniProt 5–57 Chain F; UniProt 5–57 Chain G; UniProt 5–57 Not recorded FE FE (III) ION × 7 NA SODIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;298 K;VAPOR DIFFUSION AGAINST 1.5 M AMMONIUM SULFATE, pH 8.5 Resolution 1.83 Å R-free 0.201

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence
UniProt name A0AAU7LTP7_9BURK
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–53; UniProt 5–57 Author chain B; PDBConstruct 1–53; UniProt 5–57 Author chain C; PDBConstruct 1–53; UniProt 5–57 Author chain D; PDBConstruct 1–53; UniProt 5–57 Author chain E; PDBConstruct 1–53; UniProt 5–57 Author chain F; PDBConstruct 1–53; UniProt 5–57 Author chain G; PDBConstruct 1–53; UniProt 5–57

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 9zdp

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id9zdp
Deposition date deposition_date2025-11-26
Structure title titleCrystal structure of rubredoxin from psychrophilic bacterium Polaromonas glacialis
Keywords keywordsrubredoxin, electron transfer, psychrophilic, ELECTRON TRANSPORT; ELECTRON TRANSPORT
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier25.93
Radius of gyration Rg (electron density) rg_electron25.35
Forward intensity I(0) i033337700.00
Molecular weight molecular_weight42322.0 kDa
Excluded volume excluded_volume51817 ų
Envelope volume envelope_volume65905 ų
Hydration-shell volume shell_volume23086 ų
Envelope diameter envelope_diameter83.6
Shell Rg shell_rg30.84
Envelope Rg envelope_rg25.16
Shape Rg shape_rg25.37
Total Rg total_rg25.94
Total atoms total_atoms2913
Residues n_residues371
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 dmax79.7
Rg (real space) rg_real25.89
Rg uncertainty (real space) rg_real_error0.48
I(0) (real space) i0_real3.3340e+07
I(0) uncertainty (real space) i0_real_error4.7470e+05
Rg (reciprocal space) rg_reciprocal25.91
I(0) (reciprocal space) i0_reciprocal33340000.0000
Solution quality estimate total_estimate0.7041
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary32.6
Skewness Skewness skewness0.205
Kurtosis Kurtosis kurtosis-0.542
Angular range angular_range— – 0.3050 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha2443000.0000
Real-space data points n_real_points62
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.976; Stabil: 1.000; Sysdev: 0.105; Positv: 1.000; Valcen: 0.994; Smooth: 0.915

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

8. Citations (1)

9. Files and Curves (10)