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2d93

Solution structure of the cNMP_binding domain of human Rap guanine nucleotide exchange factor 6

Method: SOLUTION NMR Dmax: 52.9 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Rap guanine nucleotide exchange factor 6

Homo sapiens

UniProt Q8TEU7

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 265–385 Fragment：cNMP_binding domain No other associated polymer SOLUTION NMR NMR measurement conditions：pH 7；298 K；Ionic strength (raw mmCIF value) 120mM；Pressure ambient NMR sample composition：1.06mM U-15N, 13C-labeled protein; 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 2D93 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3LNY Second PDZ domain from human PTP1E in complex with RA-GEF2 peptide Deposited 2010-02-03 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain B 1596–1601（6 aa） Fragment：C-terminal residues 1596-1601
Not recorded SCN THIOCYANATE ION × 6 SO4 SULFATE ION × 12 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；277 K；20% PEG 3350, 0.8 M (NH4)2SO4, 0.2 M NaSCN, 0.1 M Na citrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 1.30 Å R-free 0.189

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

View Construct and Data Evidence
UniProt name RPGF6_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 8–128； UniProt 265–385

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 2d93

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2d93
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2d93
Deposition date deposition_date2005-12-08
Structure title titleSolution structure of the cNMP_binding domain of human Rap guanine nucleotide exchange factor 6
Keywords keywords;cNMP_binding domain, Rap guanine nucleotide exchange factor 6, PDZ domain containing guanine nucleotide exchange factor 2, PDZ-GEF2, RA-GEF-2, RAPGEF6, 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_guinier16.17 Å
Radius of gyration Rg (electron density) rg_electron15.46 Å
Forward intensity I(0) i01301800000.00
Molecular weight molecular_weight297730.0 kDa
Excluded volume excluded_volume368350 ų
Envelope volume envelope_volume38205 ų
Hydration-shell volume shell_volume17585 ų
Envelope diameter envelope_diameter60.0 Å
Shell Rg shell_rg24.51 Å
Envelope Rg envelope_rg18.77 Å
Shape Rg shape_rg15.47 Å
Total Rg total_rg15.57 Å
Total atoms total_atoms40920
Residues n_residues2680
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 dmax52.9 Å
Rg (real space) rg_real16.11 Å
Rg uncertainty (real space) rg_real_error0.38 Å
I(0) (real space) i0_real1.3020e+09
I(0) uncertainty (real space) i0_real_error1.4280e+07
Rg (reciprocal space) rg_reciprocal16.12 Å
I(0) (reciprocal space) i0_reciprocal1302000000.0000
Solution quality estimate total_estimate0.8167
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary19.7 Å
Skewness Skewness skewness0.196
Kurtosis Kurtosis kurtosis-0.366
Angular range angular_range— – 0.4900 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha342000.0000
Real-space data points n_real_points79
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.872; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.000
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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) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id2d93A00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily10 — Jelly Rolls
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8. Citations (1)

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9. Files and Curves (10)