1y3f

Crystal structure of the complex of subtilisin BPN' with chymotrypsin inhibitor 2 F69A mutant

Method: X-RAY DIFFRACTION Dmax: 68.4 Å Quality: REASONABLE

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

;subtilisin BPN' ;

Bacillus amyloliquefaciens

UniProt P00782

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 E; UniProt 108–382 Mutation:C-terminal 6-His tag chymotrypsin inhibitor 2 × 1 (Q40059) CA CALCIUM ION × 1 NA SODIUM ION × 1 CIT CITRIC ACID × 3 15P POLYETHYLENE GLYCOL (N=34) × 3 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 4.6;277 K;sodium citrate, isopropanol, PEG 4000, 3% xylitol, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K Resolution 1.72 Å R-free 0.190
2 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain E; UniProt 108–382 Mutation:C-terminal 6-His tag chymotrypsin inhibitor 2 × 2 (Q40059) CA CALCIUM ION × 2 NA SODIUM ION × 2 CIT CITRIC ACID × 6 15P POLYETHYLENE GLYCOL (N=34) × 6 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 4.6;277 K;sodium citrate, isopropanol, PEG 4000, 3% xylitol, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K Resolution 1.72 Å R-free 0.190

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.

62 other PDB entries and 81 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name SUBT_BACAM
Isoform
PDB entities 1
Chains and sequence ranges Author chain E; PDBConstruct 1–275; UniProt 108–382

chymotrypsin inhibitor 2

Hordeum vulgare

UniProt Q40059

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 I; UniProt 22–84 Mutation:initiating Met, F69A ;subtilisin BPN' ; × 1 (P00782) CA CALCIUM ION × 1 NA SODIUM ION × 1 CIT CITRIC ACID × 3 15P POLYETHYLENE GLYCOL (N=34) × 3 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 4.6;277 K;sodium citrate, isopropanol, PEG 4000, 3% xylitol, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K Resolution 1.72 Å R-free 0.190
2 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain I; UniProt 22–84 Mutation:initiating Met, F69A ;subtilisin BPN' ; × 2 (P00782) CA CALCIUM ION × 2 NA SODIUM ION × 2 CIT CITRIC ACID × 6 15P POLYETHYLENE GLYCOL (N=34) × 6 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 4.6;277 K;sodium citrate, isopropanol, PEG 4000, 3% xylitol, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K Resolution 1.72 Å R-free 0.190

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.

16 other PDB entries and 26 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name Q40059_HORVU
Isoform
PDB entities 2
Chains and sequence ranges Author chain I; PDBConstruct 2–64; UniProt 22–84

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 1y3f

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1y3f
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1y3f
Deposition date deposition_date2004-11-24
Structure title titleCrystal structure of the complex of subtilisin BPN' with chymotrypsin inhibitor 2 F69A mutant
Keywords keywordsserine protease; inhibitor, 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_guinier20.28
Radius of gyration Rg (electron density) rg_electron19.34
Forward intensity I(0) i023884900.00
Molecular weight molecular_weight36681.0 kDa
Excluded volume excluded_volume45633 ų
Envelope volume envelope_volume51185 ų
Hydration-shell volume shell_volume21807 ų
Envelope diameter envelope_diameter70.6
Shell Rg shell_rg26.30
Envelope Rg envelope_rg19.77
Shape Rg shape_rg19.34
Total Rg total_rg20.22
Total atoms total_atoms2578
Residues n_residues345
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 dmax68.4
Rg (real space) rg_real20.21
Rg uncertainty (real space) rg_real_error0.41
I(0) (real space) i0_real2.3880e+07
I(0) uncertainty (real space) i0_real_error3.3900e+05
Rg (reciprocal space) rg_reciprocal20.22
I(0) (reciprocal space) i0_reciprocal23890000.0000
Solution quality estimate total_estimate0.6801
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary25.4
Skewness Skewness skewness0.313
Kurtosis Kurtosis kurtosis-0.134
Angular range angular_range— – 0.3900 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha7314000.0000
Real-space data points n_real_points71
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.760; Stabil: 1.000; Sysdev: 0.193; Positv: 1.000; Valcen: 1.000; Smooth: 0.978

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (7)

7. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (3 domains)

Domain ID domain_idd1y3fe2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.41 — Subtilisin-like
Superfamily Superfamily superfamilyc.41.1 — Subtilisin-like
Family Family familyc.41.1.1 — Subtilases
Domain ID domain_idd1y3fe3
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd1y3fi1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.40 — CI-2 family of serine protease inhibitors
Superfamily Superfamily superfamilyd.40.1 — CI-2 family of serine protease inhibitors
Family Family familyd.40.1.1 — CI-2 family of serine protease inhibitors

CATH v4.4 (2 domains)

Domain ID domain_id1y3fE00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily200 — Peptidase S8/S53 domain
Domain ID domain_id1y3fI00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology10 — Trypsin Inhibitor V; Chain A
Homologous superfamily homologous superfamily10 — Trypsin Inhibitor V, subunit A

8. Citations (1)

9. Files and Curves (10)