3kch

Baranase crosslinked by glutaraldehyde

Method: X-RAY DIFFRACTION Dmax: 82.2 Å Quality: EXCELLENT

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

Ribonuclease

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 48–157 Not recorded PTD PENTANEDIAL × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.5;290 K;ammonium sulfate, PEG 1000, HEPES, glutaraldehyde, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K Resolution 1.94 Å R-free 0.185
2 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain B; UniProt 48–157 Not recorded PTD PENTANEDIAL × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.5;290 K;ammonium sulfate, PEG 1000, HEPES, glutaraldehyde, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K Resolution 1.94 Å R-free 0.185
3 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain C; UniProt 48–157 Not recorded PTD PENTANEDIAL × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.5;290 K;ammonium sulfate, PEG 1000, HEPES, glutaraldehyde, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K Resolution 1.94 Å R-free 0.185

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 48–157

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 3kch

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id3kch
Deposition date deposition_date2009-10-21
Structure title titleBaranase crosslinked by glutaraldehyde
Keywords keywordsribonuclease, microbial ribonuclease, glutaraldehyde, crosslink, Endonuclease, Hydrolase, Nuclease, Secreted; HYDROLASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier26.10
Radius of gyration Rg (electron density) rg_electron25.48
Forward intensity I(0) i022815700.00
Molecular weight molecular_weight36761.0 kDa
Excluded volume excluded_volume45991 ų
Envelope volume envelope_volume58771 ų
Hydration-shell volume shell_volume20135 ų
Envelope diameter envelope_diameter86.3
Shell Rg shell_rg31.00
Envelope Rg envelope_rg25.15
Shape Rg shape_rg25.46
Total Rg total_rg26.20
Total atoms total_atoms2607
Residues n_residues324
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 dmax82.2
Rg (real space) rg_real26.11
Rg uncertainty (real space) rg_real_error0.63
I(0) (real space) i0_real2.2820e+07
I(0) uncertainty (real space) i0_real_error3.3120e+05
Rg (reciprocal space) rg_reciprocal26.11
I(0) (reciprocal space) i0_reciprocal22820000.0000
Solution quality estimate total_estimate0.9063
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary22.9
Skewness Skewness skewness0.218
Kurtosis Kurtosis kurtosis-0.674
Angular range angular_range— – 0.3050 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha4042000.0000
Real-space data points n_real_points62
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.953; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.923; Smooth: 0.996

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_idd3kcha_
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_idd3kchb_
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_idd3kchc_
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

CATH v4.4 (3 domains)

Domain ID domain_id3kchA00
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily30 — Microbial ribonucleases
Domain ID domain_id3kchB00
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily30 — Microbial ribonucleases
Domain ID domain_id3kchC00
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily30 — Microbial ribonucleases

8. Citations (2)

9. Files and Curves (10)