7mrx

Cryogenic crystal structure of barnase A43C/S80C bound to barstar C40A/C82A

Method: X-RAY DIFFRACTION Dmax: 98.8 Å Quality: EXCELLENT

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

Ribonuclease

Bacillus amyloliquefaciens

UniProt P00648

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 48–157 Mutation:A43C, S80C Barstar × 1 (P11540) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;293 K;50mM NaPO4, 25% PEG 8K, 0.1M AmSO4 4uL protein at 10-15 mg/mL in H2O + 4uL motherliquor per hanging drop, over 1 mL motherliquor in well. cryoprotectant used before freezing was: 25% MPD Resolution 2.29 Å R-free 0.229
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain C; UniProt 48–157 Mutation:A43C, S80C Barstar × 1 (P11540) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;293 K;50mM NaPO4, 25% PEG 8K, 0.1M AmSO4 4uL protein at 10-15 mg/mL in H2O + 4uL motherliquor per hanging drop, over 1 mL motherliquor in well. cryoprotectant used before freezing was: 25% MPD Resolution 2.29 Å R-free 0.229
3 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain E; UniProt 48–157 Mutation:A43C, S80C Barstar × 1 (P11540) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;293 K;50mM NaPO4, 25% PEG 8K, 0.1M AmSO4 4uL protein at 10-15 mg/mL in H2O + 4uL motherliquor per hanging drop, over 1 mL motherliquor in well. cryoprotectant used before freezing was: 25% MPD Resolution 2.29 Å R-free 0.229

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.

51 other PDB entries and 135 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RNBR_BACAM
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 19–128; UniProt 48–157 Author chain C; PDBConstruct 19–128; UniProt 48–157 Author chain E; PDBConstruct 19–128; UniProt 48–157

Barstar

Bacillus amyloliquefaciens

UniProt P11540

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 1–90 Mutation:C41A, C83A Ribonuclease × 1 (P00648) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;293 K;50mM NaPO4, 25% PEG 8K, 0.1M AmSO4 4uL protein at 10-15 mg/mL in H2O + 4uL motherliquor per hanging drop, over 1 mL motherliquor in well. cryoprotectant used before freezing was: 25% MPD Resolution 2.29 Å R-free 0.229
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain D; UniProt 1–90 Mutation:C41A, C83A Ribonuclease × 1 (P00648) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;293 K;50mM NaPO4, 25% PEG 8K, 0.1M AmSO4 4uL protein at 10-15 mg/mL in H2O + 4uL motherliquor per hanging drop, over 1 mL motherliquor in well. cryoprotectant used before freezing was: 25% MPD Resolution 2.29 Å R-free 0.229
3 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain F; UniProt 1–90 Mutation:C41A, C83A Ribonuclease × 1 (P00648) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;293 K;50mM NaPO4, 25% PEG 8K, 0.1M AmSO4 4uL protein at 10-15 mg/mL in H2O + 4uL motherliquor per hanging drop, over 1 mL motherliquor in well. cryoprotectant used before freezing was: 25% MPD Resolution 2.29 Å R-free 0.229

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.

20 other PDB entries and 48 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name BARS_BACAM
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 1–90; UniProt 1–90 Author chain D; PDBConstruct 1–90; UniProt 1–90 Author chain F; PDBConstruct 1–90; UniProt 1–90

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 7mrx

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 7mrx
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2. Structure Basics 2. Structure Basics

Entry ID entry_id7mrx
Deposition date deposition_date2021-05-10
Structure title titleCryogenic crystal structure of barnase A43C/S80C bound to barstar C40A/C82A
Keywords keywordsDisulfides, Toxin, antitoxin, RNA BINDING PROTEIN-Inhibitor complex; RNA BINDING PROTEIN/Inhibitor
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier30.63
Radius of gyration Rg (electron density) rg_electron29.97
Forward intensity I(0) i071582900.00
Molecular weight molecular_weight67027.0 kDa
Excluded volume excluded_volume84036 ų
Envelope volume envelope_volume107570 ų
Hydration-shell volume shell_volume30444 ų
Envelope diameter envelope_diameter98.2
Shell Rg shell_rg36.51
Envelope Rg envelope_rg29.53
Shape Rg shape_rg29.94
Total Rg total_rg30.70
Total atoms total_atoms4741
Residues n_residues591
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 dmax98.8
Rg (real space) rg_real30.58
Rg uncertainty (real space) rg_real_error0.57
I(0) (real space) i0_real7.1580e+07
I(0) uncertainty (real space) i0_real_error1.0910e+06
Rg (reciprocal space) rg_reciprocal30.61
I(0) (reciprocal space) i0_reciprocal71580000.0000
Solution quality estimate total_estimate0.9012
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary41.8
Skewness Skewness skewness0.175
Kurtosis Kurtosis kurtosis-0.602
Angular range angular_range— – 0.2600 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha15050000.0000
Real-space data points n_real_points53
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.930; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.973; Smooth: 0.949

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

8. Citations (1)

9. Files and Curves (10)