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2m6u

NMR Structure of CbpAN from Streptococcus pneumoniae

Method: SOLUTION NMR Dmax: 52.7 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Choline binding protein A

Streptococcus pneumoniae

UniProt G6W2B2

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 67–148 Fragment：UNP residues 67-148 No other associated polymer SOLUTION NMR NMR measurement conditions：pH 7；298 K；Ionic strength (raw mmCIF value) 100；Pressure ambient NMR sample composition：50 uM DSS, 100 uM sodium azide, 50 mM sodium phosphate, 50 mM sodium chloride, 95% H2O/5% D2O | 95% H2O/5% D2O NMR sample composition：50 uM DSS, 100 uM sodium azide, 50 mM sodium phosphate, 50 mM sodium chloride, 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 2M6U Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
4K12 Structural Basis for Host Specificity of Factor H Binding by Streptococcus pneumoniae Deposited 2013-04-04 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 68–148（81 aa） Fragment：UNP residues 68-148
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；20% PEG3500, 0.1 M sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；20% PEG3500, 0.1 M sodium acetate, soaked in 0.5 M sodium iodide, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 1.08 Å R-free 0.170

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name G6W2B2_STREE
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 4–85； UniProt 67–148

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 2m6u

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2m6u
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2m6u
Deposition date deposition_date2013-04-10
Structure title titleNMR Structure of CbpAN from Streptococcus pneumoniae
Keywords keywordsthree-helix bundle, CHOLINE BINDING PROTEIN, CHOLINE-BINDING PROTEIN; CHOLINE-BINDING PROTEIN
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier13.99 Å
Radius of gyration Rg (electron density) rg_electron14.14 Å
Forward intensity I(0) i0505964000.00
Molecular weight molecular_weight189800.0 kDa
Excluded volume excluded_volume237980 ų
Envelope volume envelope_volume20440 ų
Hydration-shell volume shell_volume11809 ų
Envelope diameter envelope_diameter57.0 Å
Shell Rg shell_rg20.69 Å
Envelope Rg envelope_rg16.24 Å
Shape Rg shape_rg14.10 Å
Total Rg total_rg14.41 Å
Total atoms total_atoms27060
Residues n_residues1640
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 dmax52.7 Å
Rg (real space) rg_real14.14 Å
Rg uncertainty (real space) rg_real_error0.52 Å
I(0) (real space) i0_real5.0600e+08
I(0) uncertainty (real space) i0_real_error5.8900e+06
Rg (reciprocal space) rg_reciprocal14.13 Å
I(0) (reciprocal space) i0_reciprocal506000000.0000
Solution quality estimate total_estimate0.5875
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary14.0 Å
Skewness Skewness skewness0.577
Kurtosis Kurtosis kurtosis-0.067
Angular range angular_range— – 0.5000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha229100.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.323; Stabil: 1.000; Sysdev: 0.368; Positv: 1.000; Valcen: 0.570; Smooth: 0.989
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id2m6uA00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology81 — Receptor-associated Protein
Homologous superfamily homologous superfamily20 —
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8. Citations (1)

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9. Files and Curves (10)