3bgo

Azide complex of Engineered Subtilisin SUBT_BACAM

Method: X-RAY DIFFRACTION Dmax: 69.5 Å Quality: GOOD

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain P; UniProt 32–106 Chain S; UniProt 108–382 Fragment:Prodomain Mutation:K27E, V37L, Q40C, K57E, H72K, V73L, A74Y, H75R, Y77L Fragment:Enzyme domain Mutation:;Q2K, S3C, P5S, S9A, I31L, D32A, K43N, M50F, A73L, Y104A, G128S, E156S, G166S, G169A, S188P, Q206C, N212G, K217L, N218S, S221A, T254A, Q271E ; AZI AZIDE ION × 1 ZN ZINC ION × 4 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.5;298 K;l8% PEG 8K, 0.2 M ZnAc, 0.1 M Na Cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 1.80 Å R-free 0.262
2 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain P; UniProt 32–106 Chain S; UniProt 108–382 Fragment:Prodomain Mutation:K27E, V37L, Q40C, K57E, H72K, V73L, A74Y, H75R, Y77L Fragment:Enzyme domain Mutation:;Q2K, S3C, P5S, S9A, I31L, D32A, K43N, M50F, A73L, Y104A, G128S, E156S, G166S, G169A, S188P, Q206C, N212G, K217L, N218S, S221A, T254A, Q271E ; AZI AZIDE ION × 1 ZN ZINC ION × 4 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.5;298 K;l8% PEG 8K, 0.2 M ZnAc, 0.1 M Na Cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 1.80 Å R-free 0.262

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, 2
Chains and sequence ranges Author chain P; PDBConstruct 3–75; UniProt 32–106 Author chain S; PDBConstruct 1–266; UniProt 108–382

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 3bgo

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3bgo
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3bgo
Deposition date deposition_date2007-11-27
Structure title titleAzide complex of Engineered Subtilisin SUBT_BACAM
Keywords keywordsazide switch, anion sensor, Hydrolase, Metal-binding, Protease, Secreted, Serine protease, Sporulation, Zymogen; HYDROLASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier20.65
Radius of gyration Rg (electron density) rg_electron19.70
Forward intensity I(0) i021198200.00
Molecular weight molecular_weight34320.0 kDa
Excluded volume excluded_volume42666 ų
Envelope volume envelope_volume47842 ų
Hydration-shell volume shell_volume20468 ų
Envelope diameter envelope_diameter71.0
Shell Rg shell_rg26.26
Envelope Rg envelope_rg20.19
Shape Rg shape_rg19.68
Total Rg total_rg20.64
Total atoms total_atoms2401
Residues n_residues334
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 dmax69.5
Rg (real space) rg_real20.63
Rg uncertainty (real space) rg_real_error0.40
I(0) (real space) i0_real2.1200e+07
I(0) uncertainty (real space) i0_real_error2.4810e+05
Rg (reciprocal space) rg_reciprocal20.63
I(0) (reciprocal space) i0_reciprocal21200000.0000
Solution quality estimate total_estimate0.8757
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary24.2
Skewness Skewness skewness0.366
Kurtosis Kurtosis kurtosis-0.243
Angular range angular_range— – 0.3850 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha7939000.0000
Real-space data points n_real_points70
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.806; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.989; Smooth: 0.974

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

7. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (3 domains)

Domain ID domain_idd3bgop1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.58 — Ferredoxin-like
Superfamily Superfamily superfamilyd.58.3 — Protease propeptides/inhibitors
Family Family familyd.58.3.2 — Subtilase propeptides/inhibitors
Domain ID domain_idd3bgop2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd3bgos_
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

CATH v4.4 (2 domains)

Domain ID domain_id3bgoP00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily80 — Peptidase S8 propeptide/proteinase inhibitor I9
Domain ID domain_id3bgoS00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily200 — Peptidase S8/S53 domain

8. Citations (1)

9. Files and Curves (10)