8awp

Crystal structure of a manganese-containing cupin (tm1459) from Thermotoga maritima, variant 208 (V19I/R23H/M38I/I60F/C106Q)

Method: X-RAY DIFFRACTION Dmax: 60.6 Å Quality: GOOD

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

Cupin_2 domain-containing protein

Thermotoga maritima

UniProt Q9X1H0

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 × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 1–114 Chain B; UniProt 1–114 Mutation:V19I, R23H, M38I, I60F, C106Q No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 6.5;289 K;14.2 mg/ml protein concentration 1.6M Sodium citrate tribasic dihydrate pH 6.5 Resolution 1.59 Å R-free 0.208

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.

21 other PDB entries and 23 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name Q9X1H0_THEMA
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–114; UniProt 1–114 Author chain B; PDBConstruct 1–114; UniProt 1–114

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 8awp

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8awp
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2. Structure Basics 2. Structure Basics

Entry ID entry_id8awp
Deposition date deposition_date2022-08-30
Structure title titleCrystal structure of a manganese-containing cupin (tm1459) from Thermotoga maritima, variant 208 (V19I/R23H/M38I/I60F/C106Q)
Keywords keywordscupin, alkene cleavage, amino acid oxidation, 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_guinier19.03
Radius of gyration Rg (electron density) rg_electron17.45
Forward intensity I(0) i010499200.00
Molecular weight molecular_weight25067.0 kDa
Excluded volume excluded_volume31826 ų
Envelope volume envelope_volume36127 ų
Hydration-shell volume shell_volume17433 ų
Envelope diameter envelope_diameter60.5
Shell Rg shell_rg23.42
Envelope Rg envelope_rg17.63
Shape Rg shape_rg17.41
Total Rg total_rg18.56
Total atoms total_atoms1777
Residues n_residues215
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 dmax60.6
Rg (real space) rg_real18.94
Rg uncertainty (real space) rg_real_error0.30
I(0) (real space) i0_real1.0500e+07
I(0) uncertainty (real space) i0_real_error1.2440e+05
Rg (reciprocal space) rg_reciprocal18.96
I(0) (reciprocal space) i0_reciprocal10500000.0000
Solution quality estimate total_estimate0.8959
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary24.4
Skewness Skewness skewness0.214
Kurtosis Kurtosis kurtosis-0.388
Angular range angular_range— – 0.4200 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha1967000.0000
Real-space data points n_real_points73
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.887; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.981

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (2)

8. Citations (1)

9. Files and Curves (10)