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2ca6

MIRAS structure determination from hemihedrally twinned crystals

Method: X-RAY DIFFRACTION Dmax: 86.1 Å Quality: EXCELLENT
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1. Protein Identity and Related Structures Protein Identity & Related Structures

RAN GTPASE-ACTIVATING PROTEIN 1

SCHIZOSACCHAROMYCES POMBE

UniProt P41391

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 1–386 Not recorded No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions：pH 8.5；2 MICROLITER PROTEIN (25MG/ML IN 20MM TRIS-HCL PH7.5, 2MMDTE) AND 2 MICROLITER RESERVOIR (24% PEG2000MME, 100MM TRIS PH8.5, 200MM LI2SO4, 20MM MGCL2)., pH 8.50 Resolution 2.20 Å R-free 0.218
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain B； UniProt 1–386 Not recorded SO4 SULFATE ION × 4 X-RAY DIFFRACTION X-ray crystallization conditions：pH 8.5；2 MICROLITER PROTEIN (25MG/ML IN 20MM TRIS-HCL PH7.5, 2MMDTE) AND 2 MICROLITER RESERVOIR (24% PEG2000MME, 100MM TRIS PH8.5, 200MM LI2SO4, 20MM MGCL2)., pH 8.50 Resolution 2.20 Å R-free 0.218

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 2CA6 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1K5D Crystal structure of Ran-GPPNHP-RanBP1-RanGAP complex Deposited 2001-10-10 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 1–386（386 aa）
Not recorded MG MAGNESIUM ION × 1 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；PEG4000, POTASSIUM ACETATE, TRIS-HCL, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.70 Å R-free 0.267
1K5D Crystal structure of Ran-GPPNHP-RanBP1-RanGAP complex Deposited 2001-10-10 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain F 1–386（386 aa）
Not recorded MG MAGNESIUM ION × 1 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；PEG4000, POTASSIUM ACETATE, TRIS-HCL, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.70 Å R-free 0.267
1K5D Crystal structure of Ran-GPPNHP-RanBP1-RanGAP complex Deposited 2001-10-10 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain I 1–386（386 aa）
Not recorded MG MAGNESIUM ION × 1 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；PEG4000, POTASSIUM ACETATE, TRIS-HCL, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.70 Å R-free 0.267
1K5D Crystal structure of Ran-GPPNHP-RanBP1-RanGAP complex Deposited 2001-10-10 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain L 1–386（386 aa）
Not recorded MG MAGNESIUM ION × 1 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；PEG4000, POTASSIUM ACETATE, TRIS-HCL, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.70 Å R-free 0.267
1K5G Crystal structure of Ran-GDP-AlFx-RanBP1-RanGAP complex Deposited 2001-10-10 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 1–386（386 aa）
Not recorded MG MAGNESIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 AF3 ALUMINUM FLUORIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；PEG4000, TRIS-HCL, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 3.10 Å R-free 0.269
1K5G Crystal structure of Ran-GDP-AlFx-RanBP1-RanGAP complex Deposited 2001-10-10 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain F 1–386（386 aa）
Not recorded MG MAGNESIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 AF3 ALUMINUM FLUORIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；PEG4000, TRIS-HCL, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 3.10 Å R-free 0.269
1K5G Crystal structure of Ran-GDP-AlFx-RanBP1-RanGAP complex Deposited 2001-10-10 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain I 1–386（386 aa）
Not recorded MG MAGNESIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 AF3 ALUMINUM FLUORIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；PEG4000, TRIS-HCL, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 3.10 Å R-free 0.269
1K5G Crystal structure of Ran-GDP-AlFx-RanBP1-RanGAP complex Deposited 2001-10-10 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain L 1–386（386 aa）
Not recorded MG MAGNESIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 AF3 ALUMINUM FLUORIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；PEG4000, TRIS-HCL, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 3.10 Å R-free 0.269
1YRG THE CRYSTAL STRUCTURE OF RNA1P: A NEW FOLD FOR A GTPASE-ACTIVATING PROTEIN Deposited 1999-03-29 Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–386（385 aa）
Mutation：SER2ALA No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；HANGING DROPS MADE FROM 2-4 MICROLITER OF PROTEIN SOLUTION (25 MG/ML RNA1P IN 0.02 M TRIS-HCL, 0.002 M DTE, PH 7.5) AND THE SAME VOLUME OF RESERVOIR SOLUTION (21-24% PEG 2000 MME, 0.1 M TRIS-HCL, 0.2 M LI2SO4, 0.02 M MGCL2, PH 8.5), VAPOR DIFFUSION, HANGING DROP
Resolution 2.66 Å R-free 0.277
1YRG THE CRYSTAL STRUCTURE OF RNA1P: A NEW FOLD FOR A GTPASE-ACTIVATING PROTEIN Deposited 1999-03-29 Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 2–386（385 aa）
Mutation：SER2ALA No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；HANGING DROPS MADE FROM 2-4 MICROLITER OF PROTEIN SOLUTION (25 MG/ML RNA1P IN 0.02 M TRIS-HCL, 0.002 M DTE, PH 7.5) AND THE SAME VOLUME OF RESERVOIR SOLUTION (21-24% PEG 2000 MME, 0.1 M TRIS-HCL, 0.2 M LI2SO4, 0.02 M MGCL2, PH 8.5), VAPOR DIFFUSION, HANGING DROP
Resolution 2.66 Å R-free 0.277

3 other PDB entries and 10 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RNA1_SCHPO
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–386； UniProt 1–386 Author chain B； PDBConstruct 1–386； UniProt 1–386

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 2ca6

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2ca6
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2ca6
Deposition date deposition_date2005-12-17
Structure title titleMIRAS structure determination from hemihedrally twinned crystals
Keywords keywords;GAP, GTPASE ACTIVATION, GTPASE-ACTIVATING PROTEIN, HEMIHEDRAL TWINNING, LEUCINE-RICH REPEAT PROTEIN, LRR, MEROHEDRAL TWINNING, MEROHEDRY, RANGAP, RNA1P, SIGNALING PROTEIN, SIGNALING ACTIVATOR, NUCLEAR TRANSPORT, SIGNALING REGULATOR ;; SIGNALING REGULATOR
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier30.52 Å
Radius of gyration Rg (electron density) rg_electron29.51 Å
Forward intensity I(0) i095693100.00
Molecular weight molecular_weight76840.0 kDa
Excluded volume excluded_volume96246 ų
Envelope volume envelope_volume123870 ų
Hydration-shell volume shell_volume34061 ų
Envelope diameter envelope_diameter93.7 Å
Shell Rg shell_rg37.95 Å
Envelope Rg envelope_rg28.74 Å
Shape Rg shape_rg29.49 Å
Total Rg total_rg30.36 Å
Total atoms total_atoms5400
Residues n_residues688
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 dmax86.1 Å
Rg (real space) rg_real30.31 Å
Rg uncertainty (real space) rg_real_error0.50 Å
I(0) (real space) i0_real9.5690e+07
I(0) uncertainty (real space) i0_real_error1.4140e+06
Rg (reciprocal space) rg_reciprocal30.40 Å
I(0) (reciprocal space) i0_reciprocal95700000.0000
Solution quality estimate total_estimate0.9087
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary44.7 Å
Skewness Skewness skewness-0.041
Kurtosis Kurtosis kurtosis-0.731
Angular range angular_range— – 0.2600 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha38770000.0000
Real-space data points n_real_points53
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.976; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.883
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd2ca6a_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.10 — Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
Superfamily Superfamily superfamilyc.10.1 — RNI-like
Family Family familyc.10.1.2 — Rna1p (RanGAP1), N-terminal domain
Domain ID domain_idd2ca6b_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.10 — Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
Superfamily Superfamily superfamilyc.10.1 — RNI-like
Family Family familyc.10.1.2 — Rna1p (RanGAP1), N-terminal domain

CATH v4.4 (2 domains)

Domain ID domain_id2ca6A00
Class class3 — Alpha Beta
Architecture architecture80 — Alpha-Beta Horseshoe
Topology topology10 — Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
Homologous superfamily homologous superfamily10 — Ribonuclease Inhibitor
Domain ID domain_id2ca6B00
Class class3 — Alpha Beta
Architecture architecture80 — Alpha-Beta Horseshoe
Topology topology10 — Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
Homologous superfamily homologous superfamily10 — Ribonuclease Inhibitor
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8. Citations (3)

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9. Files and Curves (10)