2qca

A New Crystal Form of Bovine Pancreatic RNase A in Complex with 2'-Deoxyguanosine-5'-monophosphate

Method: X-RAY DIFFRACTION Dmax: 52.1 Å Quality: GOOD

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

Ribonuclease pancreatic

OrganismNot specified

UniProt P61823

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 27–150 Not recorded DGP 2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE × 2 X-RAY DIFFRACTION X-ray crystallization conditions:pH 7;295 K;Reservoir: 0.6 ml of 30% PEG 3350 in 0.1 M HEPES at pH 7.0. Sample: 2 ul 10-40 mg/ml Protein in 0.1 M HEPES at pH 7.0 and 2 ul of 0.1 M DGP, cholesterol, thymine and oxamic acid in 15% PEG 3350 and 9.1 M HEPES at pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K, pH 7.00 Resolution 1.33 Å R-free 0.177

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.

333 other PDB entries and 495 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RNAS1_BOVIN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–124; UniProt 27–150

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 2qca

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id2qca
Deposition date deposition_date2007-06-19
Structure title titleA New Crystal Form of Bovine Pancreatic RNase A in Complex with 2'-Deoxyguanosine-5'-monophosphate
Keywords keywords;Ribonuclease, Protein-Nucleotide Complex, Structural Genomics, PSI-2, Protein Structure Initiative, Center for High-Throughput Structural Biology, CHTSB, HYDROLASE ;; HYDROLASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier14.94
Radius of gyration Rg (electron density) rg_electron14.07
Forward intensity I(0) i05092570.00
Molecular weight molecular_weight14389.0 kDa
Excluded volume excluded_volume17225 ų
Envelope volume envelope_volume19533 ų
Hydration-shell volume shell_volume11947 ų
Envelope diameter envelope_diameter50.0
Shell Rg shell_rg19.69
Envelope Rg envelope_rg14.40
Shape Rg shape_rg14.07
Total Rg total_rg15.10
Total atoms total_atoms997
Residues n_residues124
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 dmax52.1
Rg (real space) rg_real14.88
Rg uncertainty (real space) rg_real_error0.36
I(0) (real space) i0_real5.0930e+06
I(0) uncertainty (real space) i0_real_error6.3810e+04
Rg (reciprocal space) rg_reciprocal14.88
I(0) (reciprocal space) i0_reciprocal5093000.0000
Solution quality estimate total_estimate0.8597
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary17.8
Skewness Skewness skewness0.237
Kurtosis Kurtosis kurtosis-0.326
Angular range angular_range— – 0.5000 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha1126000.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.731; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.980; Smooth: 1.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd2qcaa_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.5 — RNase A-like
Superfamily Superfamily superfamilyd.5.1 — RNase A-like
Family Family familyd.5.1.1 — Ribonuclease A-like

CATH v4.4 (1 domains)

Domain ID domain_id2qcaA00
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology130 — P-30 Protein
Homologous superfamily homologous superfamily10 — Ribonuclease A-like domain

8. Citations (2)

9. Files and Curves (10)