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2ma2

Solution structure of RasGRP2 EF hands bound to calcium

Method: SOLUTION NMR Dmax: 54.4 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

RAS guanyl-releasing protein 2

Homo sapiens

UniProt Q7LDG7

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 417–497 Not recorded No other associated polymer SOLUTION NMR NMR measurement conditions：pH 7；304 K；Ionic strength (raw mmCIF value) 0.125；Pressure ambient NMR sample composition：500 uM [U-99% 13C; U-99% 15N] RasGRP2, 25 mM HEPES, 100 mM sodium chloride, 1 mM TCEP, 7 % D2O, 93% H2O/7% D2O | 93% H2O/7% D2O NMR sample composition：500 uM [U-99% 13C; U-99% 15N] RasGRP2, 25 mM HEPES, 100 mM sodium chloride, 1 mM TCEP, 7 % D2O, 17 mg/mL Pf1 phage, 93% H2O/7% D2O | 93% H2O/7% 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 2MA2 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
6AXF Structure of RasGRP2 in complex with Rap1B Deposited 2017-09-06 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 63–456（394 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；293 K；17% PEG3350 and 10 mM sodium citrate (pH 5.6)
Resolution 3.10 Å R-free 0.258
6AXF Structure of RasGRP2 in complex with Rap1B Deposited 2017-09-06 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 C 63–456（394 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；293 K；17% PEG3350 and 10 mM sodium citrate (pH 5.6)
Resolution 3.10 Å R-free 0.258
6AXF Structure of RasGRP2 in complex with Rap1B Deposited 2017-09-06 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 E 63–456（394 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；293 K；17% PEG3350 and 10 mM sodium citrate (pH 5.6)
Resolution 3.10 Å R-free 0.258
6AXF Structure of RasGRP2 in complex with Rap1B Deposited 2017-09-06 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 G 63–456（394 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；293 K；17% PEG3350 and 10 mM sodium citrate (pH 5.6)
Resolution 3.10 Å R-free 0.258
6AXF Structure of RasGRP2 in complex with Rap1B Deposited 2017-09-06 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 5 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain I 63–456（394 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；293 K；17% PEG3350 and 10 mM sodium citrate (pH 5.6)
Resolution 3.10 Å R-free 0.258
6AXF Structure of RasGRP2 in complex with Rap1B Deposited 2017-09-06 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 6 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain K 63–456（394 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；293 K；17% PEG3350 and 10 mM sodium citrate (pH 5.6)
Resolution 3.10 Å R-free 0.258
6AXF Structure of RasGRP2 in complex with Rap1B Deposited 2017-09-06 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 7 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain M 63–456（394 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；293 K；17% PEG3350 and 10 mM sodium citrate (pH 5.6)
Resolution 3.10 Å R-free 0.258
6AXF Structure of RasGRP2 in complex with Rap1B Deposited 2017-09-06 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 8 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain O 63–456（394 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；293 K；17% PEG3350 and 10 mM sodium citrate (pH 5.6)
Resolution 3.10 Å R-free 0.258

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

View Construct and Data Evidence
UniProt name GRP2_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–81； UniProt 417–497

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 2ma2

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2ma2
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2ma2
Deposition date deposition_date2013-06-24
Structure title titleSolution structure of RasGRP2 EF hands bound to calcium
Keywords keywordsprotein, EF hand, CALCIUM-BINDING PROTEIN; CALCIUM-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_guinier14.54 Å
Radius of gyration Rg (electron density) rg_electron14.37 Å
Forward intensity I(0) i0132298000.00
Molecular weight molecular_weight91992.0 kDa
Excluded volume excluded_volume113460 ų
Envelope volume envelope_volume28105 ų
Hydration-shell volume shell_volume14426 ų
Envelope diameter envelope_diameter54.1 Å
Shell Rg shell_rg22.33 Å
Envelope Rg envelope_rg17.46 Å
Shape Rg shape_rg14.33 Å
Total Rg total_rg14.84 Å
Total atoms total_atoms12620
Residues n_residues810
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 dmax54.4 Å
Rg (real space) rg_real14.56 Å
Rg uncertainty (real space) rg_real_error0.45 Å
I(0) (real space) i0_real1.3230e+08
I(0) uncertainty (real space) i0_real_error1.8240e+06
Rg (reciprocal space) rg_reciprocal14.56 Å
I(0) (reciprocal space) i0_reciprocal132300000.0000
Solution quality estimate total_estimate0.7319
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary17.2 Å
Skewness Skewness skewness0.344
Kurtosis Kurtosis kurtosis-0.131
Angular range angular_range— – 0.5000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha112300.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.545; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.875; 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_id2ma2A00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology238 — Recoverin; domain 1
Homologous superfamily homologous superfamily10 — EF-hand
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8. Citations (1)

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9. Files and Curves (10)