- PDB-5ciq: Ran GDP wild type tetragonal crystal form -
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ID or keywords:
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Basic information
Entry
Database: PDB / ID: 5ciq
Title
Ran GDP wild type tetragonal crystal form
Components
GTP-binding nuclear protein Ran
Keywords
HYDROLASE / GTPase / nuclear transport / transport protein
Function / homology
Function and homology information
RNA nuclear export complex / pre-miRNA export from nucleus / snRNA import into nucleus / cellular response to mineralocorticoid stimulus / manchette / Regulation of cholesterol biosynthesis by SREBP (SREBF) / importin-alpha family protein binding / protein localization to nucleolus / Rev-mediated nuclear export of HIV RNA / Nuclear import of Rev protein ...RNA nuclear export complex / pre-miRNA export from nucleus / snRNA import into nucleus / cellular response to mineralocorticoid stimulus / manchette / Regulation of cholesterol biosynthesis by SREBP (SREBF) / importin-alpha family protein binding / protein localization to nucleolus / Rev-mediated nuclear export of HIV RNA / Nuclear import of Rev protein / GTP metabolic process / NEP/NS2 Interacts with the Cellular Export Machinery / tRNA processing in the nucleus / Postmitotic nuclear pore complex (NPC) reformation / MicroRNA (miRNA) biogenesis / DNA metabolic process / dynein intermediate chain binding / mitotic sister chromatid segregation / spermatid development / ribosomal large subunit export from nucleus / sperm flagellum / ribosomal small subunit export from nucleus / ribosomal subunit export from nucleus / nuclear pore / centriole / protein export from nucleus / viral process / mitotic spindle organization / G protein activity / male germ cell nucleus / hippocampus development / Transcriptional regulation by small RNAs / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / recycling endosome / positive regulation of protein import into nucleus / protein import into nucleus / GDP binding / melanosome / positive regulation of protein binding / nuclear envelope / mitotic cell cycle / midbody / actin cytoskeleton organization / cadherin binding / protein heterodimerization activity / protein domain specific binding / cell division / GTPase activity / chromatin binding / chromatin / nucleolus / GTP binding / magnesium ion binding / protein-containing complex / RNA binding / extracellular exosome / nucleoplasm / membrane / nucleus / cytoplasm / cytosol Similarity search - Function
small GTPase Ran family profile. / Ran GTPase / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases ...small GTPase Ran family profile. / Ran GTPase / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta Similarity search - Domain/homology
Monochromator: SI(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.984 Å / Relative weight: 1
Reflection
Resolution: 1.65→34.23 Å / Num. all: 52073 / Num. obs: 52073 / % possible obs: 98.2 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 18.11
Reflection shell
Resolution: 1.65→1.69 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.0585 / Mean I/σ(I) obs: 2.05 / % possible all: 85.7
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Processing
Software
Name
Version
Classification
REFMAC
5.8.0049
refinement
XDS
datareduction
XSCALE
datascaling
PHASER
phasing
Refinement
Method to determine structure: MOLECULAR REPLACEMENT Starting model: human Ran GDP Resolution: 1.65→34.23 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.933 / SU B: 2.218 / SU ML: 0.076 / Cross valid method: THROUGHOUT / ESU R: 0.103 / ESU R Free: 0.111 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.24938
2604
5 %
RANDOM
Rwork
0.19584
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obs
0.19844
49469
98.19 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK