7am4

Crystal structure of Peptiligase mutant - L217H/M222P

Method: X-RAY DIFFRACTION Dmax: 52.5 Å Quality: EXCELLENT

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 monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain A; UniProt 108–382 Non-standard monomer:Yes (specific site not provided by mmCIF) GOL GLYCEROL × 3 SO4 SULFATE ION × 4 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 6.5;298 K;1.6 magnesium sulfate, 0.1 M MES Resolution 1.81 Å R-free 0.172

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 82 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 A; 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 7am4

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 7am4
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2. Structure Basics 2. Structure Basics

Entry ID entry_id7am4
Deposition date deposition_date2020-10-08
Structure title titleCrystal structure of Peptiligase mutant - L217H/M222P
Keywords keywordssubtilisin, peptide ligase, LIGASE; LIGASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier17.82
Radius of gyration Rg (electron density) rg_electron16.59
Forward intensity I(0) i014880000.00
Molecular weight molecular_weight27647.0 kDa
Excluded volume excluded_volume33970 ų
Envelope volume envelope_volume36881 ų
Hydration-shell volume shell_volume18122 ų
Envelope diameter envelope_diameter52.7
Shell Rg shell_rg23.24
Envelope Rg envelope_rg16.80
Shape Rg shape_rg16.59
Total Rg total_rg17.52
Total atoms total_atoms1938
Residues n_residues268
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 dmax52.5
Rg (real space) rg_real17.65
Rg uncertainty (real space) rg_real_error0.20
I(0) (real space) i0_real1.4880e+07
I(0) uncertainty (real space) i0_real_error1.4210e+05
Rg (reciprocal space) rg_reciprocal17.67
I(0) (reciprocal space) i0_reciprocal14880000.0000
Solution quality estimate total_estimate0.9066
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary23.4
Skewness Skewness skewness0.020
Kurtosis Kurtosis kurtosis-0.536
Angular range angular_range— – 0.4450 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha4787000.0000
Real-space data points n_real_points75
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.939; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.972; Smooth: 0.994

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd7am4a1
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_idd7am4a2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

8. Citations (1)

9. Files and Curves (10)