2f56

Barnase cross-linked with glutaraldehyde soaked in 6M urea

Method: X-RAY DIFFRACTION Dmax: 81.2 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 monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain A; UniProt 50–157 Not recorded URE UREA × 3 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8;300 K;AMMONIUM SULFATE, HEPES BUFFER. PROTEIN 20 MG/ML, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 300K Resolution 1.96 Å
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 50–157 Not recorded URE UREA × 6 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8;300 K;AMMONIUM SULFATE, HEPES BUFFER. PROTEIN 20 MG/ML, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 300K Resolution 1.96 Å
3 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain C; UniProt 50–157 Not recorded URE UREA × 2 ZN ZINC ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8;300 K;AMMONIUM SULFATE, HEPES BUFFER. PROTEIN 20 MG/ML, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 300K Resolution 1.96 Å
4 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 50–157 Chain C; UniProt 50–157 Not recorded URE UREA × 5 ZN ZINC ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8;300 K;AMMONIUM SULFATE, HEPES BUFFER. PROTEIN 20 MG/ML, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 300K Resolution 1.96 Å

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 134 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 1–108; UniProt 50–157 Author chain B; PDBConstruct 1–108; UniProt 50–157 Author chain C; PDBConstruct 1–108; UniProt 50–157

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 2f56

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2f56
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2f56
Deposition date deposition_date2005-11-25
Structure title titleBarnase cross-linked with glutaraldehyde soaked in 6M urea
Keywords keywordsDENATURATION, LYSOZYME, BARNASE, CROSS-LINKED CRYSTALS, GLUTARALDEHYDE, UREA, THIOUREA, BROMOETHANOL, hydrolase; HYDROLASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier26.20
Radius of gyration Rg (electron density) rg_electron25.46
Forward intensity I(0) i024364000.00
Molecular weight molecular_weight37109.0 kDa
Excluded volume excluded_volume46015 ų
Envelope volume envelope_volume58426 ų
Hydration-shell volume shell_volume20098 ų
Envelope diameter envelope_diameter82.2
Shell Rg shell_rg30.95
Envelope Rg envelope_rg25.11
Shape Rg shape_rg25.44
Total Rg total_rg26.15
Total atoms total_atoms2625
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 dmax81.2
Rg (real space) rg_real26.22
Rg uncertainty (real space) rg_real_error0.52
I(0) (real space) i0_real2.4360e+07
I(0) uncertainty (real space) i0_real_error3.3140e+05
Rg (reciprocal space) rg_reciprocal26.22
I(0) (reciprocal space) i0_reciprocal24360000.0000
Solution quality estimate total_estimate0.9066
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary34.6
Skewness Skewness skewness0.229
Kurtosis Kurtosis kurtosis-0.697
Angular range angular_range— – 0.3050 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha4302000.0000
Real-space data points n_real_points62
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.967; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.917; Smooth: 0.965

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_idd2f56a_
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_idd2f56b_
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_idd2f56c_
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_id2f56A00
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily30 — Microbial ribonucleases
Domain ID domain_id2f56B00
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily30 — Microbial ribonucleases
Domain ID domain_id2f56C00
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily30 — Microbial ribonucleases

8. Citations (1)

9. Files and Curves (10)