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- PDB-1qg2: CANINE GDP-RAN R76E MUTANT -

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Basic information

Entry
Database: PDB / ID: 1qg2
TitleCANINE GDP-RAN R76E MUTANT
ComponentsPROTEIN (RAN)
KeywordsGTPASE / NUCLEAR TRANSPORT
Function / homology
Function and homology information


RISC complex binding / pre-miRNA binding / nuclear export signal receptor activity / pre-miRNA export from nucleus / snRNA import into nucleus / RISC complex / GTP metabolic process / ribosomal subunit export from nucleus / mitotic sister chromatid segregation / protein export from nucleus ...RISC complex binding / pre-miRNA binding / nuclear export signal receptor activity / pre-miRNA export from nucleus / snRNA import into nucleus / RISC complex / GTP metabolic process / ribosomal subunit export from nucleus / mitotic sister chromatid segregation / protein export from nucleus / positive regulation of protein export from nucleus / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / protein import into nucleus / melanosome / nuclear envelope / cell division / GTPase activity / GTP binding / magnesium ion binding / protein-containing complex / nucleus / cytosol / cytoplasm
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
GUANOSINE-5'-DIPHOSPHATE / GTP-binding nuclear protein Ran
Similarity search - Component
Biological speciesCanis lupus familiaris (dog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsKent, H.M. / Moore, M.S. / Quimby, B.B. / Baker, A.M.E. / McCoy, A.J. / Murphy, G.A. / Corbett, A.H. / Stewart, M.
CitationJournal: J.Mol.Biol. / Year: 1999
Title: Engineered mutants in the switch II loop of Ran define the contribution made by key residues to the interaction with nuclear transport factor 2 (NTF2) and the role of this interaction in nuclear protein import.
Authors: Kent, H.M. / Moore, M.S. / Quimby, B.B. / Baker, A.M. / McCoy, A.J. / Murphy, G.A. / Corbett, A.H. / Stewart, M.
History
DepositionApr 20, 1999Deposition site: PDBE / Processing site: RCSB
Revision 1.0Jun 11, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (RAN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8963
Polymers24,4281
Non-polymers4682
Water1,11762
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)102.320, 102.320, 42.080
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein PROTEIN (RAN) / TC4


Mass: 24428.023 Da / Num. of mol.: 1 / Fragment: ALL / Mutation: R76E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Canis lupus familiaris (dog) / Species: Canis lupus / Strain: familiaris
Description: CDNA OBTAINED BY SITE-SPECIFIC MUTAGENESIS OF WILD-TYPE CANINE RAN CDNA AS DESCRIBED IN PUBLIC
Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P62825
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 62 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.25 Å3/Da / Density % sol: 35.8 %
Crystal growpH: 7.2 / Details: SEE PUBLICATION, pH 7.20
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 18 ℃ / pH: 8 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
220-36 %(v/v)PEG10001reservoir
320 mM1reservoirMgCl2
450 mMTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1.033
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jun 21, 1998 / Details: MIRRORS
RadiationMonochromator: CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.3→24.112 Å / Num. obs: 9871 / % possible obs: 95.5 % / Redundancy: 8.4 % / Rmerge(I) obs: 0.066 / Rsym value: 0.066 / Net I/σ(I): 9.4
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.343 / Mean I/σ(I) obs: 2.1 / Rsym value: 0.343 / % possible all: 91.9
Reflection
*PLUS
Highest resolution: 2.3 Å / % possible obs: 95.5 % / Redundancy: 2.5 %
Reflection shell
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 2.42 Å / % possible obs: 91.9 % / Redundancy: 7.1 % / Mean I/σ(I) obs: 2.1

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Processing

Software
NameVersionClassification
AMoREphasing
REFMACrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: EBI-1279

Resolution: 2.5→6 Å / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.237 -5 %RANDOM
Rwork0.174 ---
obs-22660 94.7 %-
Refinement stepCycle: LAST / Resolution: 2.5→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1578 0 33 58 1669
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 6 Å / Num. reflection obs: 9825 / Rfactor obs: 0.198 / Rfactor Rfree: 0.246 / Rfactor Rwork: 0.198
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.011
X-RAY DIFFRACTIONp_angle_deg2

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