1b3s

STRUCTURAL RESPONSE TO MUTATION AT A PROTEIN-PROTEIN INTERFACE

Method: X-RAY DIFFRACTION Dmax: 99.9 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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 48–157 Mutation:H102A PROTEIN (BARSTAR) × 1 (P11540) X-RAY DIFFRACTION X-ray crystallization conditions:pH 8;0.2M (NH4)2SO4; 0.1M TRIS/HCL PH 8.0: 22% PEG-8000 Resolution 2.39 Å R-free 0.324
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain B; UniProt 48–157 Mutation:H102A PROTEIN (BARSTAR) × 1 (P11540) X-RAY DIFFRACTION X-ray crystallization conditions:pH 8;0.2M (NH4)2SO4; 0.1M TRIS/HCL PH 8.0: 22% PEG-8000 Resolution 2.39 Å R-free 0.324
3 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain C; UniProt 50–157 Mutation:H102A PROTEIN (BARSTAR) × 1 (P11540) X-RAY DIFFRACTION X-ray crystallization conditions:pH 8;0.2M (NH4)2SO4; 0.1M TRIS/HCL PH 8.0: 22% PEG-8000 Resolution 2.39 Å R-free 0.324

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 50–157

PROTEIN (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 1–89 Mutation:Y30F PROTEIN (BARNASE) × 1 (P00648) X-RAY DIFFRACTION X-ray crystallization conditions:pH 8;0.2M (NH4)2SO4; 0.1M TRIS/HCL PH 8.0: 22% PEG-8000 Resolution 2.39 Å R-free 0.324
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain E; UniProt 1–89 Mutation:Y30F PROTEIN (BARNASE) × 1 (P00648) X-RAY DIFFRACTION X-ray crystallization conditions:pH 8;0.2M (NH4)2SO4; 0.1M TRIS/HCL PH 8.0: 22% PEG-8000 Resolution 2.39 Å R-free 0.324
3 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain F; UniProt 1–89 Mutation:Y30F PROTEIN (BARNASE) × 1 (P00648) X-RAY DIFFRACTION X-ray crystallization conditions:pH 8;0.2M (NH4)2SO4; 0.1M TRIS/HCL PH 8.0: 22% PEG-8000 Resolution 2.39 Å R-free 0.324

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 D; PDBConstruct 2–90; UniProt 1–89 Author chain E; PDBConstruct 2–90; UniProt 1–89 Author chain F; PDBConstruct 2–90; UniProt 1–89

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 1b3s

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1b3s
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1b3s
Deposition date deposition_date1998-12-01
Structure title titleSTRUCTURAL RESPONSE TO MUTATION AT A PROTEIN-PROTEIN INTERFACE
Keywords keywordsRNASE-INHIBITOR COMPLEX, INTERFACIAL DOUBLE MUTANT, HYDROLASE-HYDROLASE INHIBITOR COMPLEX; HYDROLASE/HYDROLASE INHIBITOR
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier30.24
Radius of gyration Rg (electron density) rg_electron29.73
Forward intensity I(0) i069901000.00
Molecular weight molecular_weight66265.0 kDa
Excluded volume excluded_volume83138 ų
Envelope volume envelope_volume106190 ų
Hydration-shell volume shell_volume30760 ų
Envelope diameter envelope_diameter102.7
Shell Rg shell_rg35.52
Envelope Rg envelope_rg29.75
Shape Rg shape_rg29.67
Total Rg total_rg30.49
Total atoms total_atoms4686
Residues n_residues587
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 dmax99.9
Rg (real space) rg_real30.23
Rg uncertainty (real space) rg_real_error0.55
I(0) (real space) i0_real6.9900e+07
I(0) uncertainty (real space) i0_real_error1.0280e+06
Rg (reciprocal space) rg_reciprocal30.23
I(0) (reciprocal space) i0_reciprocal69900000.0000
Solution quality estimate total_estimate0.8916
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary38.4
Skewness Skewness skewness0.251
Kurtosis Kurtosis kurtosis-0.530
Angular range angular_range— – 0.2600 −1
Current regularization parameter α current_alpha0.0001
Highest regularization parameter α highest_alpha19480000.0000
Real-space data points n_real_points53
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.907; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.948; Smooth: 0.919

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_idd1b3sa_
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_idd1b3sb_
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_idd1b3sc_
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_idd1b3sd_
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_idd1b3se_
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_idd1b3sf_
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 (6 domains)

Domain ID domain_id1b3sA00
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily30 — Microbial ribonucleases
Domain ID domain_id1b3sB00
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily30 — Microbial ribonucleases
Domain ID domain_id1b3sC00
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily30 — Microbial ribonucleases
Domain ID domain_id1b3sD00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology370 — Barnase; Chain D
Homologous superfamily homologous superfamily10 — Barstar-like
Domain ID domain_id1b3sE00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology370 — Barnase; Chain D
Homologous superfamily homologous superfamily10 — Barstar-like
Domain ID domain_id1b3sF00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology370 — Barnase; Chain D
Homologous superfamily homologous superfamily10 — Barstar-like

8. Citations (6)

9. Files and Curves (10)