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Open data
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Basic information
Entry | Database: PDB / ID: 2ca6 | ||||||
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Title | MIRAS structure determination from hemihedrally twinned crystals | ||||||
![]() | RAN GTPASE-ACTIVATING PROTEIN 1 | ||||||
![]() | SIGNALING REGULATOR / GAP / GTPASE ACTIVATION / GTPASE-ACTIVATING PROTEIN / HEMIHEDRAL TWINNING / LEUCINE-RICH REPEAT PROTEIN / LRR / MEROHEDRAL TWINNING / MEROHEDRY / RANGAP / RNA1P / SIGNALING PROTEIN / SIGNALING ACTIVATOR / NUCLEAR TRANSPORT | ||||||
Function / homology | ![]() SUMOylation of nuclear envelope proteins / Postmitotic nuclear pore complex (NPC) reformation / nucleocytoplasmic transport / protein export from nucleus / nuclear periphery / GTPase activator activity / small GTPase binding / perinuclear region of cytoplasm / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Hillig, R.C. / Renault, L. | ||||||
![]() | ![]() Title: Detecting and Overcoming Hemihedral Twinning During the Mir Structure Determination of RNA1P. Authors: Hillig, R.C. / Renault, L. #1: ![]() Title: The Crystal Structure of RNA1P: A New Fold for a Gtpase-Activating Protein Authors: Hillig, R.C. / Renault, L. / Vetter, I.R. / Drell, T. / Wittinghofer, A. / Becker, J. #2: ![]() Title: Rangap Mediates GTP Hydrolysis without an Arginine Finger Authors: Seewald, M.J. / Korner, C. / Wittinghofer, A. / Vetter, I.R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 149.3 KB | Display | ![]() |
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PDB format | ![]() | 119.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 453.4 KB | Display | ![]() |
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Full document | ![]() | 469.2 KB | Display | |
Data in XML | ![]() | 29.5 KB | Display | |
Data in CIF | ![]() | 41.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.99729, 0.07335, 0.00611), Vector: |
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Components
#1: Protein | Mass: 43272.652 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: C-TERMINI OF BOTH COPIES OF RNA1P (RESIDUES 345-386) ARE DISORDERED AND WERE OMITTED FROM THE MODEL Source: (gene. exp.) ![]() ![]() Production host: ![]() ![]() #2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | Compound details | GTPASE ACTIVATOR FOR THE NUCLEAR RAS-RELATED REGULATORY PROTEIN SPI1 (RAN), CONVERTING IT TO THE ...GTPASE ACTIVATOR FOR THE NUCLEAR RAS-RELATED REGULATORY | Sequence details | THE CONFLICT SHOWN IN THE SEQADV RECORDS BELOW SER2ALA IS A CLONING ARTEFACT DUE TO EXPRESSION ...THE CONFLICT SHOWN IN THE SEQADV RECORDS BELOW SER2ALA IS A CLONING ARTEFACT DUE TO EXPRESSION | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.48 Å3/Da / Density % sol: 55.4 % |
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Crystal grow | pH: 8.5 Details: 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 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 2, 1996 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0093 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→31 Å / Num. obs: 42106 / % possible obs: 97.3 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 14.4 Å2 / Rsym value: 0.14 / Net I/σ(I): 8 |
Reflection shell | Resolution: 2.2→2.25 Å / Redundancy: 2 % / Mean I/σ(I) obs: 2.1 / Rsym value: 0.37 / % possible all: 87.4 |
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Processing
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Refinement | Method to determine structure: ![]() Details: THE DATA SET SHOWS HEMIHEDRAL TWINNING WITH A HIGH TWIN FRACTION OF 0.39. THE MODEL WAS REFINED AGAINST THIS ORIGINAL DATA SET, I.E. REFLECTIONS NOT TWIN CORRECTED, BY USING CNX IN TWIN MODE. ...Details: THE DATA SET SHOWS HEMIHEDRAL TWINNING WITH A HIGH TWIN FRACTION OF 0.39. THE MODEL WAS REFINED AGAINST THIS ORIGINAL DATA SET, I.E. REFLECTIONS NOT TWIN CORRECTED, BY USING CNX IN TWIN MODE. ALL R FACTORS ARE SO CALLED TWINNED R FACTORS, CALCULATED FROM THE DIFFERENCES BETWEEN THE ORIGINAL TWINNED REFLECTIONS AND THE ARTIFICIALLY TWINNED REFLECTIONS CALCULATED FROM THE MODEL.
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Solvent computation | Solvent model: MASK AROUND THE MOLECULE, DETERMINED AUTOMATICALLY BY CNX Bsol: 38.2404 Å2 / ksol: 0.352164 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→31 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.24 Å / Total num. of bins used: 20 /
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Xplor file | Serial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: ION.TOP |