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1vsq

Solution NMR structure of the productive complex between IIAMannose and IIBMannose of the mannose transporter of the E. coli phosphotransferase system

Method: SOLUTION NMR Dmax: 83.5 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Mannose-specific phosphotransferase enzyme IIA 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 homooligomer Homooligomer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count Chain A； UniProt 2–134 Chain B； UniProt 2–134 Chain C； UniProt 159–323 Non-standard monomer：Yes (specific site not provided by mmCIF) No other associated polymer SOLUTION NMR NMR measurement conditions：pH 6.5；303 K；Ionic strength (raw mmCIF value) 20 mM phosphate；Pressure ambient NMR sample composition：0.5-1 mM IIAMan(H10E)+IIBMan, 90% H2O/10% D2O | 90% H2O/10% D2O NMR sample composition：0.5-1 mM IIAMan(H10E)+IIBMan, 100% D2O | 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.

Other PDB Difference from Current Entry 1VSQ Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1PDO PHOSPHOENOLPYRUVATE-DEPENDENT PHOSPHOTRANSFERASE SYSTEM Deposited 1996-03-08 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–132（132 aa） Fragment：IIA ==MAN== DOMAIN, RESIDUES 2 - 133, OF THE IIAB ==MAN== SUBUNIT PLUS PHE-ALA-GLY AT THE CARBOXY TERMINUS
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.8；pH 6.8
Resolution 1.70 Å R-free 0.244
1VRC Complex of enzyme IIAmannose and the histidine-containing phosphocarrier protein HPr from escherichia coli nmr, restrained regularized mean structure Deposited 2005-02-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–132（132 aa） Fragment：EIIA DOMAIN
Chain B 1–132（132 aa） Fragment：EIIA DOMAIN
Not recorded PO3 PHOSPHITE ION × 2 SOLUTION NMR
NMR measurement conditions pH 6.5；308 K；Ionic strength (raw mmCIF value) 40 mM SODIUM PHOSPHATE
Resolution not provided
2JZH structure of IIB domain of the mannose transporter of E. coli Deposited 2008-01-08 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 154–323（170 aa） Fragment：PTS EIIB type-4 domain
Not recorded No recorded non-water small molecule 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
2JZN Solution NMR structure of the productive complex between IIAMannose and IIBMannose of the mannose transporter of the E. coli phosphotransferase system Deposited 2008-01-10 Different mutation/modification Different experimental conditions Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 2–134（133 aa）
Chain B 2–134（133 aa）
Chain C 159–323（165 aa）
Mutation：H10E Mutation：H10E No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.5；303 K；Ionic strength (raw mmCIF value) 20 mM phosphate；Pressure ambient
NMR sample composition 0.5-1 mM see details IIAMan(H10E)+IIBMan, 100% D2O | 100% D2O
NMR sample composition 0.5-1 mM see details IIAMan(H10E)+IIBMan, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
2JZO Solution NMR structure of the non-productive complex between IIAMannose and IIBMannose of the mannose transporter of the E. coli phosphotransferase system Deposited 2008-01-10 Different construct Different mutation/modification Different experimental conditions Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 2–134（133 aa） Fragment：PTS EIIB type-4 domain
Chain B 2–134（133 aa） Fragment：PTS EIIB type-4 domain
Chain D 159–323（165 aa） Fragment：PTS EIIA type-4 domain
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.5；303 K；Ionic strength (raw mmCIF value) 20 mM phosphate；Pressure ambient
NMR sample composition 0.5-1 mM IIAMan+IIBMan, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 0.5-1 mM IIAMan+IIBMan, 100% D2O | 100% D2O
Resolution not provided

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, 2
Chains and sequence ranges Author chain A； PDBConstruct 1–133； UniProt 2–134 Author chain B； PDBConstruct 1–133； UniProt 2–134 Author chain C； PDBConstruct 1–165； UniProt 159–323

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 1vsq

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id1vsq
Deposition date deposition_date2008-01-10
Structure title titleSolution NMR structure of the productive complex between IIAMannose and IIBMannose of the mannose transporter of the E. coli phosphotransferase system
Keywords keywords;phosphotransferase, sugar transport, transferase, transferase-phosphocarrier complex, Membrane, Phosphoprotein, Phosphotransferase system ;; TRANSFERASE
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier23.78 Å
Radius of gyration Rg (electron density) rg_electron23.14 Å
Forward intensity I(0) i0129904000.00
Molecular weight molecular_weight94483.0 kDa
Excluded volume excluded_volume119320 ų
Envelope volume envelope_volume72883 ų
Hydration-shell volume shell_volume26306 ų
Envelope diameter envelope_diameter80.0 Å
Shell Rg shell_rg30.20 Å
Envelope Rg envelope_rg23.40 Å
Shape Rg shape_rg23.14 Å
Total Rg total_rg23.62 Å
Total atoms total_atoms13427
Residues n_residues858
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−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
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax83.5 Å
Rg (real space) rg_real23.73 Å
Rg uncertainty (real space) rg_real_error0.70 Å
I(0) (real space) i0_real1.2990e+08
I(0) uncertainty (real space) i0_real_error1.9680e+06
Rg (reciprocal space) rg_reciprocal23.75 Å
I(0) (reciprocal space) i0_reciprocal129900000.0000
Solution quality estimate total_estimate0.7823
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary26.1 Å
Skewness Skewness skewness0.292
Kurtosis Kurtosis kurtosis-0.455
Angular range angular_range— – 0.3350 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha13770000.0000
Real-space data points n_real_points65
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.744; Stabil: 0.996; Sysdev: 1.000; Positv: 1.000; Valcen: 0.947; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_idd1vsqa_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.54 — PTS system fructose IIA component-like
Superfamily Superfamily superfamilyc.54.1 — PTS system fructose IIA component-like
Family Family familyc.54.1.1 — EIIA-man component-like
Domain ID domain_idd1vsqb_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.54 — PTS system fructose IIA component-like
Superfamily Superfamily superfamilyc.54.1 — PTS system fructose IIA component-like
Family Family familyc.54.1.1 — EIIA-man component-like
Domain ID domain_idd1vsqc_
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 (3 domains)

Domain ID domain_id1vsqA00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily510 — Phosphotransferase system, mannose-type IIA component
Domain ID domain_id1vsqB00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily510 — Phosphotransferase system, mannose-type IIA component
Domain ID domain_id1vsqC00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology35 — Fructose Permease
Homologous superfamily homologous superfamily10 — Phosphotransferase system, sorbose subfamily IIB component
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8. Citations (1)

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9. Files and Curves (10)