1dcj

SOLUTION STRUCTURE OF YHHP, A NOVEL ESCHERICHIA COLI PROTEIN IMPLICATED IN THE CELL DIVISION

Method: SOLUTION NMR Dmax: 40.1 Å Quality: GOOD

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

YHHP PROTEIN

Escherichia coli

UniProt P0A890

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 1–81 Not recorded No other associated polymer SOLUTION NMR NMR measurement conditions:pH 7.1;298 K;Ionic strength (raw mmCIF value) 100mM NACL;Pressure AMBIENT NMR measurement conditions:pH 7.1;298 K;Ionic strength (raw mmCIF value) 100mM NACL;Pressure AMBIENT NMR measurement conditions:pH 7.1;298 K;Ionic strength (raw mmCIF value) 100mM NACL;Pressure AMBIENT NMR sample composition:1MM YHHP U-15N; 10MM PHOSPHATE BUFFER K; 100MM NACL; 2MM NAN3; 2MM DTT; 90% H20, 10% D2O NMR sample composition:1MM YHHP U-15N, 13C; 10MM PHOSPHATE BUFFER K; 100MM NACL; 2MM NAN3; 2MM DTT; 90% H20, 10% D2O NMR sample composition:1MM YHHP U-15N, 13C; 10MM PHOSPHATE BUFFER K; 100MM NACL; 2MM NAN3; 2MM DTT; 100% 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 SIRA_ECOLI
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–81; UniProt 1–81

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 1dcj

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id1dcj
Deposition date deposition_date1999-11-05
Structure title titleSOLUTION STRUCTURE OF YHHP, A NOVEL ESCHERICHIA COLI PROTEIN IMPLICATED IN THE CELL DIVISION
Keywords keywordsALPHA-BETA SANDWICH, STRUCTURAL GENOMICS, UNKNOWN FUNCTION; STRUCTURAL GENOMICS, UNKNOWN FUNCTION
Experimental Method methodSOLUTION NMR

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

Radius of gyration Rg (Guinier) rg_guinier11.99
Radius of gyration Rg (electron density) rg_electron11.63
Forward intensity I(0) i0469278000.00
Molecular weight molecular_weight181830.0 kDa
Excluded volume excluded_volume227000 ų
Envelope volume envelope_volume16964 ų
Hydration-shell volume shell_volume10905 ų
Envelope diameter envelope_diameter47.4
Shell Rg shell_rg19.02
Envelope Rg envelope_rg14.09
Shape Rg shape_rg11.58
Total Rg total_rg11.96
Total atoms total_atoms25420
Residues n_residues1620
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 dmax40.1
Rg (real space) rg_real11.93
Rg uncertainty (real space) rg_real_error0.34
I(0) (real space) i0_real4.6930e+08
I(0) uncertainty (real space) i0_real_error5.7170e+06
Rg (reciprocal space) rg_reciprocal11.93
I(0) (reciprocal space) i0_reciprocal469300000.0000
Solution quality estimate total_estimate0.7950
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary14.2
Skewness Skewness skewness0.126
Kurtosis Kurtosis kurtosis-0.338
Angular range angular_range— – 0.5000 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha118200.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.777; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; 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_idd1dcja_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.68 — IF3-like
Superfamily Superfamily superfamilyd.68.3 — SirA-like
Family Family familyd.68.3.3 — SirA-like

CATH v4.4 (1 domains)

Domain ID domain_id1dcjA00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology110 — Translation Initiation Factor IF3
Homologous superfamily homologous superfamily40 — TusA-like domain

8. Citations (3)

9. Files and Curves (10)