1i4v

SOLUTION STRUCTURE OF THE UMUD' HOMODIMER

Method: SOLUTION NMR Dmax: 77.5 Å Quality: GOOD

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

;UMUD' PROTEIN ;

Escherichia coli

UniProt P04153

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 25–139 Chain B; UniProt 25–139 Mutation:G25A No other associated polymer SOLUTION NMR NMR measurement conditions:pH 6;303 K;Ionic strength (raw mmCIF value) 150 mM NaCl;Pressure ambient NMR sample composition:0.9 mM UmuD' U-15N; 150 mM NaCl, 10 mM phosphate, pH 6.0, 1mM DTT, 0.1 mM EDTA | 95% H2O/5% D2O NMR sample composition:1.3 mM UmuD' U-15N,13C; 150 mM NaCl, 20 mM phosphate, pH 6.0, 1 mM DTT, 0.1 mM EDTA | 95% H2O/5% D2O NMR sample composition:1.5 mM UmuD' unlabeled; 150 mM NaCl, 20 mM phosphate, pH 6.0, 1 mM DTT, 0.1 mM EDTA | 95% H20, 5% D2O NMR sample composition:1.4 mM UmuD' unlabeled; 150 mM NaCl, 20 mM phosphate, pH 6.0, 1 mM DTT, 0.1 mM EDTA | 100% D2O NMR sample composition:0.5 mM UmuD' U-10% 13C; 150 mM NaCl, 20 mM phosphate, pH 6.0, 1 mM DTT, 0.1 mM EDTA | 100% D2O NMR sample composition:2.7 mM UmuD' U-100% 2H,15N and 2.7 mM unlabeled UmuD'; 150 mM NaCl, 20 mM phosphate, pH 6.0, 1 mM DTT, 0.1 mM EDTA | 95% H20, 5% 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.

2 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name UMUD_ECOLI
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–115; UniProt 25–139 Author chain B; PDBConstruct 1–115; UniProt 25–139

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 1i4v

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1i4v
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1i4v
Deposition date deposition_date2001-02-23
Structure title titleSOLUTION STRUCTURE OF THE UMUD' HOMODIMER
Keywords keywords;SOS response, SOS mutagenesis, DNA repair, DNA polymerase V, DNA polymerase accessory protein, LexA repressor, lambda CI, signal peptidase, serine-lysine dyad, autocatalytic cleavage, serine protease, HYDROLASE ;; HYDROLASE
Experimental Method methodSOLUTION NMR

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

Radius of gyration Rg (Guinier) rg_guinier21.99
Radius of gyration Rg (electron density) rg_electron21.73
Forward intensity I(0) i03175560000.00
Molecular weight molecular_weight491680.0 kDa
Excluded volume excluded_volume620900 ų
Envelope volume envelope_volume106870 ų
Hydration-shell volume shell_volume32084 ų
Envelope diameter envelope_diameter87.3
Shell Rg shell_rg35.07
Envelope Rg envelope_rg28.30
Shape Rg shape_rg21.76
Total Rg total_rg21.85
Total atoms total_atoms69480
Residues n_residues4600
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 dmax77.5
Rg (real space) rg_real22.12
Rg uncertainty (real space) rg_real_error0.55
I(0) (real space) i0_real3.1760e+09
I(0) uncertainty (real space) i0_real_error3.7960e+07
Rg (reciprocal space) rg_reciprocal22.10
I(0) (reciprocal space) i0_reciprocal3176000000.0000
Solution quality estimate total_estimate0.8538
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary22.0
Skewness Skewness skewness0.449
Kurtosis Kurtosis kurtosis-0.277
Angular range angular_range— – 0.3600 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha1480000.0000
Real-space data points n_real_points68
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.795; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.725; Smooth: 0.984

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (1)

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd1i4va_
Class classb — All beta proteins
Fold Fold foldb.87 — LexA/Signal peptidase
Superfamily Superfamily superfamilyb.87.1 — LexA/Signal peptidase
Family Family familyb.87.1.1 — LexA-related
Domain ID domain_idd1i4vb_
Class classb — All beta proteins
Fold Fold foldb.87 — LexA/Signal peptidase
Superfamily Superfamily superfamilyb.87.1 — LexA/Signal peptidase
Family Family familyb.87.1.1 — LexA-related

CATH v4.4 (2 domains)

Domain ID domain_id1i4vA00
Class class2 — Mainly Beta
Architecture architecture10 — Ribbon
Topology topology109 — Umud Fragment, subunit A
Homologous superfamily homologous superfamily10 — Umud Fragment, subunit A
Domain ID domain_id1i4vB00
Class class2 — Mainly Beta
Architecture architecture10 — Ribbon
Topology topology109 — Umud Fragment, subunit A
Homologous superfamily homologous superfamily10 — Umud Fragment, subunit A

8. Citations (1)

9. Files and Curves (10)