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- PDB-5cit: Ran GDP wild type monoclinic crystal form -

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Basic information

Entry
Database: PDB / ID: 5cit
TitleRan GDP wild type monoclinic crystal form
ComponentsGTP-binding nuclear protein Ran
KeywordsHYDROLASE / GTPase / nuclear transport / transport protein
Function / homology
Function and homology information


pre-miRNA export from nucleus / RNA nuclear export complex / snRNA import into nucleus / Regulation of cholesterol biosynthesis by SREBP (SREBF) / protein localization to nucleolus / Rev-mediated nuclear export of HIV RNA / Nuclear import of Rev protein / NEP/NS2 Interacts with the Cellular Export Machinery / GTP metabolic process / tRNA processing in the nucleus ...pre-miRNA export from nucleus / RNA nuclear export complex / snRNA import into nucleus / Regulation of cholesterol biosynthesis by SREBP (SREBF) / protein localization to nucleolus / Rev-mediated nuclear export of HIV RNA / Nuclear import of Rev protein / NEP/NS2 Interacts with the Cellular Export Machinery / GTP metabolic process / tRNA processing in the nucleus / Postmitotic nuclear pore complex (NPC) reformation / MicroRNA (miRNA) biogenesis / DNA metabolic process / mitotic sister chromatid segregation / ribosomal large subunit export from nucleus / viral process / nuclear pore / ribosomal subunit export from nucleus / ribosomal small subunit export from nucleus / centriole / protein export from nucleus / mitotic spindle organization / Transcriptional regulation by small RNAs / recycling endosome / positive regulation of protein import into nucleus / protein import into nucleus / GDP binding / positive regulation of protein binding / nuclear envelope / melanosome / mitotic cell cycle / G protein activity / midbody / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / cadherin binding / protein heterodimerization activity / cell division / GTPase activity / chromatin binding / GTP binding / chromatin / nucleolus / magnesium ion binding / protein-containing complex / RNA binding / extracellular exosome / nucleoplasm / nucleus / membrane / 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 / 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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsVetter, I.R. / Brucker, S.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Catalysis of GTP Hydrolysis by Small GTPases at Atomic Detail by Integration of X-ray Crystallography, Experimental, and Theoretical IR Spectroscopy.
Authors: Rudack, T. / Jenrich, S. / Brucker, S. / Vetter, I.R. / Gerwert, K. / Kotting, C.
History
DepositionJul 13, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 9, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 14, 2015Group: Database references
Revision 1.2May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GTP-binding nuclear protein Ran
B: GTP-binding nuclear protein Ran
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,8476
Polymers48,9122
Non-polymers9354
Water1,54986
1
A: GTP-binding nuclear protein Ran
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9243
Polymers24,4561
Non-polymers4682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: GTP-binding nuclear protein Ran
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9243
Polymers24,4561
Non-polymers4682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.010, 59.230, 64.770
Angle α, β, γ (deg.)90.00, 96.95, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein GTP-binding nuclear protein Ran / Androgen receptor-associated protein 24 / GTPase Ran / Ras-like protein TC4 / Ras-related nuclear protein


Mass: 24456.105 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAN, ARA24, OK/SW-cl.81 / Plasmid: pET3d / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P62826
#2: 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
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.45 Å3/Da / Density % sol: 41.93 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 32 % PEG 1000, 50 mM HEPES pH 7.2, 20 mM MgCl2, 1mM BeF

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.984 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 4, 2009
RadiationMonochromator: SI(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.984 Å / Relative weight: 1
ReflectionResolution: 1.75→19.81 Å / Num. obs: 42451 / % possible obs: 96.2 % / Redundancy: 3.29 % / Rmerge(I) obs: 0.037 / Net I/σ(I): 17.86
Reflection shellResolution: 1.75→1.8 Å / Redundancy: 3.35 % / Rmerge(I) obs: 0.641 / Mean I/σ(I) obs: 2.13 / % possible all: 95.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: human Ran GDP

Resolution: 1.75→19.81 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.936 / SU B: 3.433 / SU ML: 0.107 / Cross valid method: THROUGHOUT / ESU R: 0.137 / ESU R Free: 0.136 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.26188 2123 5 %RANDOM
Rwork0.21635 ---
obs0.21863 40326 96.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.881 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å20 Å20.18 Å2
2---0.02 Å20 Å2
3----0.14 Å2
Refinement stepCycle: 1 / Resolution: 1.75→19.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3184 0 58 86 3328
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0193324
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.2381.974516
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6165394
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.49223.907151
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.04815565
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7881518
X-RAY DIFFRACTIONr_chiral_restr0.1970.2493
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0212492
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.7573.5681582
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.9555.3351974
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.5833.9021742
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined8.30630.6985160
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.396 155 -
Rwork0.329 2936 -
obs--95.79 %

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