1rls

CRYSTAL STRUCTURE OF RNASE T1 COMPLEXED WITH THE PRODUCT NUCLEOTIDE 3'-GMP. STRUCTURAL EVIDENCE FOR DIRECT INTERACTION OF HISTIDINE 40 AND GLUTAMIC ACID 58 WITH THE 2'-HYDROXYL GROUP OF RIBOSE

Method: X-RAY DIFFRACTION Dmax: 41.8 Å Quality: GOOD

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

RIBONUCLEASE T1

Aspergillus oryzae

UniProt P00651

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 27–130 Not recorded CA CALCIUM ION × 1 3GP GUANOSINE-3'-MONOPHOSPHATE × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 1.90 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.

67 other PDB entries and 100 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RNT1_ASPOR
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–104; UniProt 27–130

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 1rls

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1rls
Download Download

2. Structure Basics 2. Structure Basics

Entry ID entry_id1rls
Deposition date deposition_date1994-03-29
Structure title titleCRYSTAL STRUCTURE OF RNASE T1 COMPLEXED WITH THE PRODUCT NUCLEOTIDE 3'-GMP. STRUCTURAL EVIDENCE FOR DIRECT INTERACTION OF HISTIDINE 40 AND GLUTAMIC ACID 58 WITH THE 2'-HYDROXYL GROUP OF RIBOSE
Keywords keywordsHYDROLASE(ENDORIBONUCLEASE); HYDROLASE(ENDORIBONUCLEASE)
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier13.81
Radius of gyration Rg (electron density) rg_electron12.34
Forward intensity I(0) i03297790.00
Molecular weight molecular_weight11437.0 kDa
Excluded volume excluded_volume13641 ų
Envelope volume envelope_volume15083 ų
Hydration-shell volume shell_volume10420 ų
Envelope diameter envelope_diameter40.8
Shell Rg shell_rg18.10
Envelope Rg envelope_rg12.62
Shape Rg shape_rg12.28
Total Rg total_rg13.65
Total atoms total_atoms803
Residues n_residues104
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 dmax41.8
Rg (real space) rg_real13.69
Rg uncertainty (real space) rg_real_error0.18
I(0) (real space) i0_real3.2980e+06
I(0) uncertainty (real space) i0_real_error3.5620e+04
Rg (reciprocal space) rg_reciprocal13.70
I(0) (reciprocal space) i0_reciprocal3298000.0000
Solution quality estimate total_estimate0.8976
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary19.6
Skewness Skewness skewness0.028
Kurtosis Kurtosis kurtosis-0.463
Angular range angular_range— – 0.5000 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha738500.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.908; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.982; Smooth: 0.961

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd1rlsa_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.1 — Microbial ribonucleases
Superfamily Superfamily superfamilyd.1.1 — Microbial ribonucleases
Family Family familyd.1.1.4 — Fungal ribonucleases

CATH v4.4 (1 domains)

Domain ID domain_id1rlsA00
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)