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- PDB-1qg4: CANINE GDP-RAN F72Y MUTANT -

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Basic information

Entry
Database: PDB / ID: 1qg4
TitleCANINE GDP-RAN F72Y MUTANT
ComponentsPROTEIN (RAN)
KeywordsGTPASE / NUCLEAR TRANSPORT
Function / homology
Function and homology information


RISC complex binding / pre-miRNA binding / pre-miRNA export from nucleus / snRNA import into nucleus / nuclear export signal receptor activity / RISC complex / GTP metabolic process / mitotic sister chromatid segregation / ribosomal subunit export from nucleus / protein export from nucleus ...RISC complex binding / pre-miRNA binding / pre-miRNA export from nucleus / snRNA import into nucleus / nuclear export signal receptor activity / RISC complex / GTP metabolic process / mitotic sister chromatid segregation / ribosomal subunit export from nucleus / protein export from nucleus / positive regulation of protein export from nucleus / protein import into nucleus / nuclear envelope / melanosome / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / cell division / GTPase activity / GTP binding / magnesium ion binding / protein-containing complex / nucleus / cytosol / cytoplasm
Similarity search - Function
Ran GTPase / Small GTPase Ran-type domain profile. / 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 ...Ran GTPase / Small GTPase Ran-type domain profile. / 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 / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 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 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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_asym_id / _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_asym_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 1.4Apr 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)
B: PROTEIN (RAN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,8796
Polymers48,9442
Non-polymers9354
Water3,333185
1
A: PROTEIN (RAN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9403
Polymers24,4721
Non-polymers4682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PROTEIN (RAN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9403
Polymers24,4721
Non-polymers4682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.520, 60.170, 61.440
Angle α, β, γ (deg.)90.00, 101.77, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.19623, 0.10066, 0.97538), (-0.08645, -0.99262, 0.08504), (0.97674, -0.06763, 0.20348)
Vector: 0.43123, 27.79929, -0.09516)

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Components

#1: Protein PROTEIN (RAN) / TC4


Mass: 24472.105 Da / Num. of mol.: 2 / Fragment: ALL / Mutation: F72Y
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.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 185 / 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: 2.24 Å3/Da / Density % sol: 35.5 %
Crystal growpH: 7.2 / Details: pH 7.20
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: ELETTRA / Beamline: 5.2R / Wavelength: 1.0378
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jan 29, 1998 / Details: MIRRORS
RadiationMonochromator: CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0378 Å / Relative weight: 1
ReflectionResolution: 2.5→19.174 Å / Num. obs: 14415 / % possible obs: 96 % / Redundancy: 2 % / Rmerge(I) obs: 0.052 / Rsym value: 0.052 / Net I/σ(I): 9.7
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 2 % / Rmerge(I) obs: 0.158 / Mean I/σ(I) obs: 4.7 / Rsym value: 0.158 / % possible all: 96.3
Reflection
*PLUS
% possible obs: 96 %
Reflection shell
*PLUS
% possible obs: 96.3 % / Redundancy: 2 % / Mean I/σ(I) obs: 4.7

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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. atoms3316 0 66 177 3559
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.174
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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