6pqk

Cryogenic crystal structure of barnase A43C/S80C bound to barstar C40A/S59C/A67C/C82A

Method: X-RAY DIFFRACTION Dmax: 81.8 Å Quality: GOOD

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) PO4 PHOSPHATE ION × 3 EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.5;298 K;50mM NaPO4 pH 6.5, 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: 12.5% glycerol + 12.5% ethylene glycol Resolution 1.20 Å R-free 0.160
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) PO4 PHOSPHATE ION × 1 EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.5;298 K;50mM NaPO4 pH 6.5, 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: 12.5% glycerol + 12.5% ethylene glycol Resolution 1.20 Å R-free 0.160

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 136 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

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 D; UniProt 1–90 Mutation:C40A, S59C, A67C, C82A Ribonuclease × 1 (P00648) PO4 PHOSPHATE ION × 3 EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.5;298 K;50mM NaPO4 pH 6.5, 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: 12.5% glycerol + 12.5% ethylene glycol Resolution 1.20 Å R-free 0.160
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain B; UniProt 1–90 Mutation:C40A, S59C, A67C, C82A Ribonuclease × 1 (P00648) PO4 PHOSPHATE ION × 1 EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.5;298 K;50mM NaPO4 pH 6.5, 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: 12.5% glycerol + 12.5% ethylene glycol Resolution 1.20 Å R-free 0.160

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 49 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

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 6pqk

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6pqk
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6pqk
Deposition date deposition_date2019-07-09
Structure title titleCryogenic crystal structure of barnase A43C/S80C bound to barstar C40A/S59C/A67C/C82A
Keywords keywordsdisulfide, Toxin-Antitoxin, complex, nuclease, RNA BINDING PROTEIN; RNA BINDING PROTEIN
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier25.36
Radius of gyration Rg (electron density) rg_electron24.76
Forward intensity I(0) i035707300.00
Molecular weight molecular_weight45477.0 kDa
Excluded volume excluded_volume56642 ų
Envelope volume envelope_volume67749 ų
Hydration-shell volume shell_volume23631 ų
Envelope diameter envelope_diameter84.0
Shell Rg shell_rg30.95
Envelope Rg envelope_rg24.85
Shape Rg shape_rg24.75
Total Rg total_rg25.52
Total atoms total_atoms3203
Residues n_residues394
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 dmax81.8
Rg (real space) rg_real25.42
Rg uncertainty (real space) rg_real_error0.54
I(0) (real space) i0_real3.5710e+07
I(0) uncertainty (real space) i0_real_error4.7550e+05
Rg (reciprocal space) rg_reciprocal25.40
I(0) (reciprocal space) i0_reciprocal35710000.0000
Solution quality estimate total_estimate0.8913
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary26.0
Skewness Skewness skewness0.385
Kurtosis Kurtosis kurtosis-0.397
Angular range angular_range— – 0.3150 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha9384000.0000
Real-space data points n_real_points64
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.913; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.930; Smooth: 0.915

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd6pqka_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.1 — Microbial ribonucleases
Superfamily Superfamily superfamilyd.1.1 — Microbial ribonucleases
Family Family familyd.1.1.2 — Bacterial ribonucleases
Domain ID domain_idd6pqkb_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.9 — Barstar-like
Superfamily Superfamily superfamilyc.9.1 — Barstar-related
Family Family familyc.9.1.1 — Barstar-related
Domain ID domain_idd6pqkc_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.1 — Microbial ribonucleases
Superfamily Superfamily superfamilyd.1.1 — Microbial ribonucleases
Family Family familyd.1.1.2 — Bacterial ribonucleases
Domain ID domain_idd6pqkd_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.9 — Barstar-like
Superfamily Superfamily superfamilyc.9.1 — Barstar-related
Family Family familyc.9.1.1 — Barstar-related

CATH v4.4 (4 domains)

Domain ID domain_id6pqkA00
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily30 — Microbial ribonucleases
Domain ID domain_id6pqkB00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology370 — Barnase; Chain D
Homologous superfamily homologous superfamily10 — Barstar-like
Domain ID domain_id6pqkC00
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily30 — Microbial ribonucleases
Domain ID domain_id6pqkD00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology370 — Barnase; Chain D
Homologous superfamily homologous superfamily10 — Barstar-like

8. Citations (1)

9. Files and Curves (10)