2jzh

structure of IIB domain of the mannose transporter of E. coli

Method: SOLUTION NMR Dmax: 53.6 Å Quality: GOOD

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

PTS system mannose-specific EIIAB component

Escherichia coli

UniProt P69797

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 154–323 Fragment:PTS EIIB type-4 domain No other associated polymer SOLUTION NMR NMR measurement conditions:pH 6.5;303 K;Ionic strength (raw mmCIF value) 20;Pressure ambient NMR sample composition:0.5-1 mM [U-100% 13C; U-100% 15N] protein, sodium phosphate, sodium azide, 100% D2O | 100% D2O NMR sample composition:0.5-1 mM [U-100% 15N] protein, sodium phosphate, sodium azide, 90% H2O/10% D2O | 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.

5 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name PTNAB_ECOLI
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 4–173; UniProt 154–323

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 2jzh

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id2jzh
Deposition date deposition_date2008-01-08
Structure title titlestructure of IIB domain of the mannose transporter of E. coli
Keywords keywords;Mannose specific PTS system IIAB, IIB domain, IIBMan phosphotransferase enzyme II, B component, Cytoplasm, Membrane, Phosphoprotein, Phosphotransferase system, Sugar transport, Transport, TRANSFERASE ;; TRANSFERASE
Experimental Method methodSOLUTION NMR

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

Radius of gyration Rg (Guinier) rg_guinier16.95
Radius of gyration Rg (electron density) rg_electron15.68
Forward intensity I(0) i06353480.00
Molecular weight molecular_weight18276.0 kDa
Excluded volume excluded_volume23052 ų
Envelope volume envelope_volume27812 ų
Hydration-shell volume shell_volume14954 ų
Envelope diameter envelope_diameter54.4
Shell Rg shell_rg21.55
Envelope Rg envelope_rg15.89
Shape Rg shape_rg15.68
Total Rg total_rg16.82
Total atoms total_atoms2623
Residues n_residues165
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 dmax53.6
Rg (real space) rg_real16.83
Rg uncertainty (real space) rg_real_error0.34
I(0) (real space) i0_real6.3530e+06
I(0) uncertainty (real space) i0_real_error7.5090e+04
Rg (reciprocal space) rg_reciprocal16.85
I(0) (reciprocal space) i0_reciprocal6354000.0000
Solution quality estimate total_estimate0.8078
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary22.6
Skewness Skewness skewness0.111
Kurtosis Kurtosis kurtosis-0.379
Angular range angular_range— – 0.4700 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha1764000.0000
Real-space data points n_real_points77
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.837; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.989; 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_idd2jzha_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.38 — PTS IIb component
Superfamily Superfamily superfamilyc.38.1 — PTS IIb component
Family Family familyc.38.1.0 — automated matches

CATH v4.4 (1 domains)

Domain ID domain_id2jzhA00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology35 — Fructose Permease
Homologous superfamily homologous superfamily10 — Phosphotransferase system, sorbose subfamily IIB component

8. Citations (1)

9. Files and Curves (10)