1d1r

NMR SOLUTION STRUCTURE OF THE PRODUCT OF THE E. COLI YCIH GENE.

Method: SOLUTION NMR Dmax: 59.5 Å Quality: REASONABLE

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

HYPOTHETICAL 11.4 KD PROTEIN YCIH IN PYRF-OSMB INTERGENIC REGION

Escherichia coli

UniProt P08245

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 1–108 Not recorded No other associated polymer SOLUTION NMR NMR measurement conditions:pH 7.4;298 K;Ionic strength (raw mmCIF value) 200 mM NACL, 50 mM SODIUM PHOSPHATE;Pressure 1 NMR sample composition:2-3 MM YCIH U-15N,13C; 50MM SODIUM PHOSPHATE PH 7.4; 200MM NACL; 10MM DITHIOTHREITOL; 90% H2O, 10% D2O NMR sample composition:2-3 MM YCIH U-15N; 50MM SODIUM PHOSPHATE PH 7.4; 200MM NACL; 10MM DITHIOTHREITOL; 90% H2O, 10% D2O NMR sample composition:2-3 MM YCIH U-15N,13C; 50MM SODIUM PHOSPHATE PH 7.4; 200MM NACL; 10MM DITHIOTHREITOL; 99% D2O NMR sample composition:2-3 MM YCIH U-15N; 50MM SODIUM PHOSPHATE PH 7.4; 200MM NACL; 10MM DITHIOTHREITOL; 99% D2O NMR sample composition:2-3 MM YCIH; 50MM SODIUM PHOSPHATE PH 7.4; 200MM NACL; 10MM DITHIOTHREITOL; 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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence
UniProt name YCIH_ECOLI
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–108; UniProt 1–108

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 1d1r

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1d1r
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1d1r
Deposition date deposition_date1999-09-20
Structure title titleNMR SOLUTION STRUCTURE OF THE PRODUCT OF THE E. COLI YCIH GENE.
Keywords keywordsALPHA-BETA PLAIT, OPEN-FACED BETA SANDWICH, FERREDOXIN-LIKE FOLD, STRUCTURAL GENOMICS; STRUCTURAL GENOMICS
Experimental Method methodSOLUTION NMR

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

Radius of gyration Rg (Guinier) rg_guinier13.57
Radius of gyration Rg (electron density) rg_electron13.11
Forward intensity I(0) i0422630000.00
Molecular weight molecular_weight173350.0 kDa
Excluded volume excluded_volume218630 ų
Envelope volume envelope_volume34822 ų
Hydration-shell volume shell_volume17030 ų
Envelope diameter envelope_diameter59.3
Shell Rg shell_rg23.57
Envelope Rg envelope_rg17.65
Shape Rg shape_rg13.09
Total Rg total_rg13.51
Total atoms total_atoms25200
Residues n_residues1660
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 dmax59.5
Rg (real space) rg_real13.56
Rg uncertainty (real space) rg_real_error0.69
I(0) (real space) i0_real4.2260e+08
I(0) uncertainty (real space) i0_real_error5.9190e+06
Rg (reciprocal space) rg_reciprocal13.56
I(0) (reciprocal space) i0_reciprocal422600000.0000
Solution quality estimate total_estimate0.7000
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary17.3
Skewness Skewness skewness0.391
Kurtosis Kurtosis kurtosis0.162
Angular range angular_range— – 0.5000 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha362100.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.192; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.519; Smooth: 1.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (1)

7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd1d1ra1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.64 — eIF1-like
Superfamily Superfamily superfamilyd.64.1 — eIF1-like
Family Family familyd.64.1.1 — eIF1-like
Domain ID domain_idd1d1ra2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (1 domains)

Domain ID domain_id1d1rA00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology780 — Translation Initiation Factor Eif1
Homologous superfamily homologous superfamily10 — SUI1-like domain

8. Citations (1)

9. Files and Curves (10)