1b21

DELETION OF A BURIED SALT BRIDGE IN BARNASE

Method: X-RAY DIFFRACTION Dmax: 83.4 Å Quality: GOOD

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

PROTEIN (BARNASE)

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 monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain A; UniProt 48–157 Mutation:R69S, D93N No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:pH 7.5;DROP: 8-12 MG/ML PROTEIN 6 MM ZNSO4 0.6 M (NH4)2SO4 WELL: 2.58-2.73 M AMMONIUM PHOSPHATE BUFFER, PH 7.5 1-2 MM ZNSO4 0.15-0.30 M (NH4)2SO4 5-10 MM NH4OH Resolution 2.00 Å R-free 0.268
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 48–157 Mutation:R69S, D93N No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:pH 7.5;DROP: 8-12 MG/ML PROTEIN 6 MM ZNSO4 0.6 M (NH4)2SO4 WELL: 2.58-2.73 M AMMONIUM PHOSPHATE BUFFER, PH 7.5 1-2 MM ZNSO4 0.15-0.30 M (NH4)2SO4 5-10 MM NH4OH Resolution 2.00 Å R-free 0.268
3 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain C; UniProt 48–157 Mutation:R69S, D93N ZN ZINC ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:pH 7.5;DROP: 8-12 MG/ML PROTEIN 6 MM ZNSO4 0.6 M (NH4)2SO4 WELL: 2.58-2.73 M AMMONIUM PHOSPHATE BUFFER, PH 7.5 1-2 MM ZNSO4 0.15-0.30 M (NH4)2SO4 5-10 MM NH4OH Resolution 2.00 Å R-free 0.268

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 1–110; UniProt 48–157 Author chain B; PDBConstruct 1–110; UniProt 48–157 Author chain C; PDBConstruct 1–110; UniProt 48–157

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 1b21

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1b21
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1b21
Deposition date deposition_date1998-12-03
Structure title titleDELETION OF A BURIED SALT BRIDGE IN BARNASE
Keywords keywordsMICROBIAL RIBONUCLEASE, ALPHA/BETA PROTEIN, HYDROLASE; HYDROLASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier25.47
Radius of gyration Rg (electron density) rg_electron24.83
Forward intensity I(0) i023114400.00
Molecular weight molecular_weight36552.0 kDa
Excluded volume excluded_volume45564 ų
Envelope volume envelope_volume57677 ų
Hydration-shell volume shell_volume20491 ų
Envelope diameter envelope_diameter86.7
Shell Rg shell_rg30.23
Envelope Rg envelope_rg24.54
Shape Rg shape_rg24.81
Total Rg total_rg25.54
Total atoms total_atoms2588
Residues n_residues326
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 dmax83.4
Rg (real space) rg_real25.50
Rg uncertainty (real space) rg_real_error0.95
I(0) (real space) i0_real2.3110e+07
I(0) uncertainty (real space) i0_real_error3.4260e+05
Rg (reciprocal space) rg_reciprocal25.49
I(0) (reciprocal space) i0_reciprocal23110000.0000
Solution quality estimate total_estimate0.8195
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary32.3
Skewness Skewness skewness0.269
Kurtosis Kurtosis kurtosis-0.600
Angular range angular_range— – 0.3100 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha4369000.0000
Real-space data points n_real_points63
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.910; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.922; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_idd1b21a_
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_idd1b21b_
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_idd1b21c_
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

CATH v4.4 (3 domains)

Domain ID domain_id1b21A00
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily30 — Microbial ribonucleases
Domain ID domain_id1b21B00
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily30 — Microbial ribonucleases
Domain ID domain_id1b21C00
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily30 — Microbial ribonucleases

8. Citations (2)

9. Files and Curves (10)