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2dmo

Refined solution structure of the 1st SH3 domain from human Neutrophil cytosol factor 2 (NCF-2)

Method: SOLUTION NMR Dmax: 47.7 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Neutrophil cytosol factor 2

Homo sapiens

UniProt P19878

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 242–297 Fragment：SH3 domain No other associated polymer SOLUTION NMR NMR measurement conditions：pH 7；296 K；Ionic strength (raw mmCIF value) 120mM；Pressure ambient NMR sample composition：1.3mM SH3 domain U-15N,13C; 20mM d-Tris HCl; 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 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.

Other PDB Difference from Current Entry 2DMO Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1E96 Structure of the Rac/p67phox complex Deposited 2000-10-10 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–203（203 aa） Fragment：YES
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 10.5；0.1 M CAPS PH 10.5, 0.2 M LI ACETATE, 0.8 M NAH2PO4, 1.2 M K2HPO4
Resolution 2.40 Å R-free 0.284
1HH8 The active N-terminal region of p67phox: Structure at 1.8 Angstrom resolution and biochemical characterizations of the A128V mutant implicated in chronic granulomatous disease Deposited 2000-12-21 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–213（213 aa） Fragment：N-TERMINAL DOMAIN, RESIDUES 1-213
Not recorded FLC CITRATE ANION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 4.5；100 MM NA CITRATE PH 4.5, 17% PEG 2K MME, 10% GLYCEROL
Resolution 1.80 Å R-free 0.204
1K4U Solution structure of the C-terminal SH3 domain of p67phox complexed with the C-terminal tail region of p47phox Deposited 2001-10-08 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain S 455–516（62 aa） Fragment：C-TERMINAL SH3 DOMAIN (RESIDUES 455-516)
Mutation：C499S/C514S No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7.1；298 K；Ionic strength (raw mmCIF value) 100mM KCl；Pressure 1
NMR sample composition 0.7mM p67SH3(C) U-15N,13C; 0.77mM p47 tail peptide; 5mM MOPSO buffer; 30 mM d10-DTT; 100mM KCl | 90% H2O, 10% D2O; 100% D2O
NMR sample composition 0.5mM p47 tail peptide U-15N,13C; 0.55mM p67SH3(C); 5mM MOPSO buffer; 30mM d10-DTT; 100mM KCl | 90% H2O, 10% D2O; 100% D2O
Resolution not provided
1OEY Heterodimer of p40phox and p67phox PB1 domains from human NADPH oxidase Deposited 2003-04-02 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 352–429（78 aa） Fragment：PB1 DOMAIN, RESIDUES 352-429
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 9；18% PEG 3350, 17% PEG 400, 4.8% ISOPROPYL ALCOHOL, 0.1 M CAPSO PH 9.0
Resolution 2.00 Å R-free 0.252
1OEY Heterodimer of p40phox and p67phox PB1 domains from human NADPH oxidase Deposited 2003-04-02 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 352–429（78 aa） Fragment：PB1 DOMAIN, RESIDUES 352-429
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 9；18% PEG 3350, 17% PEG 400, 4.8% ISOPROPYL ALCOHOL, 0.1 M CAPSO PH 9.0
Resolution 2.00 Å R-free 0.252
1OEY Heterodimer of p40phox and p67phox PB1 domains from human NADPH oxidase Deposited 2003-04-02 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 352–429（78 aa） Fragment：PB1 DOMAIN, RESIDUES 352-429
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 9；18% PEG 3350, 17% PEG 400, 4.8% ISOPROPYL ALCOHOL, 0.1 M CAPSO PH 9.0
Resolution 2.00 Å R-free 0.252
1OEY Heterodimer of p40phox and p67phox PB1 domains from human NADPH oxidase Deposited 2003-04-02 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 352–429（78 aa） Fragment：PB1 DOMAIN, RESIDUES 352-429
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 9；18% PEG 3350, 17% PEG 400, 4.8% ISOPROPYL ALCOHOL, 0.1 M CAPSO PH 9.0
Resolution 2.00 Å R-free 0.252
1WM5 Crystal structure of the N-terminal TPR domain (1-203) of p67phox Deposited 2004-07-03 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–203（203 aa） Fragment：TPR domain
Not recorded SO4 SULFATE ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.9；277 K；ammonium sulfate, HEPES, pH 6.9, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 1.95 Å R-free 0.224

5 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name NCF2_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 8–62； UniProt 242–297

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 2dmo

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id2dmo
Deposition date deposition_date2006-04-22
Structure title titleRefined solution structure of the 1st SH3 domain from human Neutrophil cytosol factor 2 (NCF-2)
Keywords keywords;SH3 domain, Neutrophil Cytosol factor, Structural Genomics, NPPSFA, National Project on Protein Structural and Functional Analyses, RIKEN Structural Genomics/Proteomics Initiative, RSGI, SIGNALING PROTEIN ;; SIGNALING 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_guinier12.41 Å
Radius of gyration Rg (electron density) rg_electron11.87 Å
Forward intensity I(0) i0294475000.00
Molecular weight molecular_weight143580.0 kDa
Excluded volume excluded_volume179230 ų
Envelope volume envelope_volume26747 ų
Hydration-shell volume shell_volume14278 ų
Envelope diameter envelope_diameter51.6 Å
Shell Rg shell_rg21.83 Å
Envelope Rg envelope_rg16.60 Å
Shape Rg shape_rg11.85 Å
Total Rg total_rg12.28 Å
Total atoms total_atoms19940
Residues n_residues1360
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 dmax47.7 Å
Rg (real space) rg_real12.41 Å
Rg uncertainty (real space) rg_real_error0.42 Å
I(0) (real space) i0_real2.9450e+08
I(0) uncertainty (real space) i0_real_error3.8040e+06
Rg (reciprocal space) rg_reciprocal12.41 Å
I(0) (reciprocal space) i0_reciprocal294500000.0000
Solution quality estimate total_estimate0.7710
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary15.1 Å
Skewness Skewness skewness0.399
Kurtosis Kurtosis kurtosis0.187
Angular range angular_range— – 0.5000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha193200.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.369; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.911; Smooth: 1.000
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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) 4 domains

SCOP 2.08 (3 domains)

Domain ID domain_idd2dmoa1
Class classb — All beta proteins
Fold Fold foldb.34 — SH3-like barrel
Superfamily Superfamily superfamilyb.34.2 — SH3-domain
Family Family familyb.34.2.1 — SH3-domain
Domain ID domain_idd2dmoa2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd2dmoa3
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_id2dmoA00
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology30 — SH3 type barrels.
Homologous superfamily homologous superfamily40 — SH3 Domains
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8. Citations (1)

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9. Files and Curves (10)