2kf3

Barnase, low pressure reference NMR structure

Method: SOLUTION NMR Dmax: 40.4 Å Quality: REASONABLE

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 48–157 Mutation:H102A No other associated polymer SOLUTION NMR NMR measurement conditions:pH 6.7;298 K;Pressure 3 NMR sample composition:1.1 mM [U-100% 13C; U-100% 15N] barnase, 30 mM sodium phosphate, 90% H2O/10% D2O | 90% H2O/10% D2O Resolution not provided

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 137 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

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 2kf3

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2kf3
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2kf3
Deposition date deposition_date2009-02-11
Structure title titleBarnase, low pressure reference NMR structure
Keywords keywordsbarnase, ribonuclease, pressure, Endonuclease, Hydrolase, Nuclease, Secreted; HYDROLASE
Experimental Method methodSOLUTION NMR

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

Radius of gyration Rg (Guinier) rg_guinier13.46
Radius of gyration Rg (electron density) rg_electron13.37
Forward intensity I(0) i0208084000.00
Molecular weight molecular_weight121200.0 kDa
Excluded volume excluded_volume151430 ų
Envelope volume envelope_volume16544 ų
Hydration-shell volume shell_volume10781 ų
Envelope diameter envelope_diameter46.5
Shell Rg shell_rg18.80
Envelope Rg envelope_rg13.65
Shape Rg shape_rg13.35
Total Rg total_rg13.61
Total atoms total_atoms16910
Residues n_residues1080
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 dmax40.4
Rg (real space) rg_real13.39
Rg uncertainty (real space) rg_real_error0.24
I(0) (real space) i0_real2.0810e+08
I(0) uncertainty (real space) i0_real_error2.3230e+06
Rg (reciprocal space) rg_reciprocal13.39
I(0) (reciprocal space) i0_reciprocal208100000.0000
Solution quality estimate total_estimate0.6569
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary15.8
Skewness Skewness skewness0.106
Kurtosis Kurtosis kurtosis-0.426
Angular range angular_range— – 0.5000 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha162500.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.929; Stabil: 0.997; Sysdev: 0.256; Positv: 1.000; Valcen: 0.988; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (1)

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd2kf3a_
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 (1 domains)

Domain ID domain_id2kf3A00
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)