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4hx2

Crystal structure of Streptomyces caespitosus sermetstatin in complex with Bacillus licheniformis subtilisin

Method: X-RAY DIFFRACTION Dmax: 122.7 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

KerA

OrganismNot specified

UniProt Q9FDF2

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain A； UniProt 37–310 Chain C； UniProt 37–310 Fragment：Mature protease Neutral proteinase inhibitor ScNPI × 2 （Q9FDS0） CA CALCIUM ION × 4 ZN ZINC ION × 2 CL CHLORIDE ION × 1 1AX (2R,2'R)-3,3'-oxydipropane-1,2-diol × 1 PO4 PHOSPHATE ION × 1 GOL GLYCEROL × 2 IPA ISOPROPYL ALCOHOL × 3 K POTASSIUM ION × 2 CAC CACODYLATE ION × 1 ACT ACETATE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；0.1 M cacodylate, 0.2 M zinc acetate dihydrate, 10% (v/v) 2-propanol, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K Resolution 2.25 Å R-free 0.217

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.

Other PDB Difference from Current Entry 4HX2 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
4GI3 Crystal structure of Greglin in complex with subtilisin Deposited 2012-08-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 37–310（274 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；0.68M sodium citrate, 0.36M sodium formate, 0.066M Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 1.75 Å R-free 0.201
6DWQ Subtilisin serine protease modified with the protease inhibitor cyanobenzylsulfonylfluoride Deposited 2018-06-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 37–310（274 aa） Fragment：residues 37-310
Non-standard monomer：Yes (specific site not provided by mmCIF) EDO 1,2-ETHANEDIOL × 12 NO3 NITRATE ION × 2 CA CALCIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；26% PEG 3350, 0.350 M NH4NO3
Resolution 1.27 Å R-free 0.148

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name Q9FDF2_BACLI
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–274； UniProt 37–310 Author chain C； PDBConstruct 1–274； UniProt 37–310

Neutral proteinase inhibitor ScNPI

Streptomyces caespitosus

UniProt Q9FDS0

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain B； UniProt 29–141 Chain D； UniProt 29–141 Not recorded KerA × 2 （Q9FDF2） CA CALCIUM ION × 4 ZN ZINC ION × 2 CL CHLORIDE ION × 1 1AX (2R,2'R)-3,3'-oxydipropane-1,2-diol × 1 PO4 PHOSPHATE ION × 1 GOL GLYCEROL × 2 IPA ISOPROPYL ALCOHOL × 3 K POTASSIUM ION × 2 CAC CACODYLATE ION × 1 ACT ACETATE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；0.1 M cacodylate, 0.2 M zinc acetate dihydrate, 10% (v/v) 2-propanol, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K Resolution 2.25 Å R-free 0.217

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.

Other PDB Difference from Current Entry 4HX2 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
4HWX Crystal structure of Streptomyces caespitosus sermetstatin Deposited 2012-11-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 29–141（113 aa）
Not recorded GOL GLYCEROL × 2 ACT ACETATE ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；293 K；0.1 M sodium citrate dihydrate, 0.2 M ammonium acetate, 10% (w/v) PEG3350, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 1.90 Å R-free 0.214
4HWX Crystal structure of Streptomyces caespitosus sermetstatin Deposited 2012-11-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 29–141（113 aa）
Not recorded GOL GLYCEROL × 2 ACT ACETATE ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；293 K；0.1 M sodium citrate dihydrate, 0.2 M ammonium acetate, 10% (w/v) PEG3350, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 1.90 Å R-free 0.214
4HX3 Crystal structure of Streptomyces caespitosus sermetstatin in complex with S. caespitosus snapalysin Deposited 2012-11-09 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 29–141（113 aa）
Chain D 29–141（113 aa）
Not recorded ZN ZINC ION × 2 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.1 M HEPES, 0.2 M magnesium chloride, 15.0% (v/v) ethanol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.70 Å R-free 0.242
4HX3 Crystal structure of Streptomyces caespitosus sermetstatin in complex with S. caespitosus snapalysin Deposited 2012-11-09 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain F 29–141（113 aa）
Chain H 29–141（113 aa）
Not recorded ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.1 M HEPES, 0.2 M magnesium chloride, 15.0% (v/v) ethanol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.70 Å R-free 0.242
4HX3 Crystal structure of Streptomyces caespitosus sermetstatin in complex with S. caespitosus snapalysin Deposited 2012-11-09 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain J 29–141（113 aa）
Chain L 29–141（113 aa）
Not recorded ZN ZINC ION × 2 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.1 M HEPES, 0.2 M magnesium chloride, 15.0% (v/v) ethanol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.70 Å R-free 0.242

2 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name Q9FDS0_STRCS
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 2–114； UniProt 29–141 Author chain D； PDBConstruct 2–114； UniProt 29–141

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 4hx2

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4hx2
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4hx2
Deposition date deposition_date2012-11-09
Structure title titleCrystal structure of Streptomyces caespitosus sermetstatin in complex with Bacillus licheniformis subtilisin
Keywords keywordsStreptomyces subtilisin inhibitor fold, Subtilisin Carlsberg, Hydrolase-Hydrolase Inhibitor complex; Hydrolase/Hydrolase Inhibitor
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier37.65 Å
Radius of gyration Rg (electron density) rg_electron38.04 Å
Forward intensity I(0) i0102409000.00
Molecular weight molecular_weight79272.0 kDa
Excluded volume excluded_volume97997 ų
Envelope volume envelope_volume125580 ų
Hydration-shell volume shell_volume29750 ų
Envelope diameter envelope_diameter124.1 Å
Shell Rg shell_rg40.90 Å
Envelope Rg envelope_rg36.87 Å
Shape Rg shape_rg38.05 Å
Total Rg total_rg38.20 Å
Total atoms total_atoms5541
Residues n_residues772
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−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
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax122.7 Å
Rg (real space) rg_real38.13 Å
Rg uncertainty (real space) rg_real_error1.22 Å
I(0) (real space) i0_real1.0240e+08
I(0) uncertainty (real space) i0_real_error1.7770e+06
Rg (reciprocal space) rg_reciprocal37.84 Å
I(0) (reciprocal space) i0_reciprocal102400000.0000
Solution quality estimate total_estimate0.7277
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary26.3 Å
Skewness Skewness skewness0.420
Kurtosis Kurtosis kurtosis-0.823
Angular range angular_range— – 0.2100 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha30980000.0000
Real-space data points n_real_points43
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.532; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.447; Smooth: 0.413
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (13)

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7. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (5 domains)

Domain ID domain_idd4hx2a_
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_idd4hx2b1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.84 — Subtilisin inhibitor
Superfamily Superfamily superfamilyd.84.1 — Subtilisin inhibitor
Family Family familyd.84.1.0 — automated matches
Domain ID domain_idd4hx2b2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd4hx2c_
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_idd4hx2d_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.84 — Subtilisin inhibitor
Superfamily Superfamily superfamilyd.84.1 — Subtilisin inhibitor
Family Family familyd.84.1.0 — automated matches

CATH v4.4 (4 domains)

Domain ID domain_id4hx2A00
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_id4hx2B00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology350 — Subtilisin Inhibitor
Homologous superfamily homologous superfamily10 — Subtilisin inhibitor-like
Domain ID domain_id4hx2C00
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_id4hx2D00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology350 — Subtilisin Inhibitor
Homologous superfamily homologous superfamily10 — Subtilisin inhibitor-like
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8. Citations (1)

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9. Files and Curves (10)