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- PDB-4rke: Drosophila melanogaster Rab2 bound to GMPPNP -

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Basic information

Entry
Database: PDB / ID: 4rke
TitleDrosophila melanogaster Rab2 bound to GMPPNP
ComponentsGH01619p
KeywordsHYDROLASE / GTP hydrolysis
Function / homology
Function and homology information


type II terminal bouton / regulation of glutamate receptor clustering / Golgi Cisternae Pericentriolar Stack Reorganization / RAB geranylgeranylation / postsynapse of neuromuscular junction / Rab protein signal transduction / regulation of postsynapse organization / protein secretion / endoplasmic reticulum to Golgi vesicle-mediated transport / endoplasmic reticulum exit site ...type II terminal bouton / regulation of glutamate receptor clustering / Golgi Cisternae Pericentriolar Stack Reorganization / RAB geranylgeranylation / postsynapse of neuromuscular junction / Rab protein signal transduction / regulation of postsynapse organization / protein secretion / endoplasmic reticulum to Golgi vesicle-mediated transport / endoplasmic reticulum exit site / vesicle-mediated transport / vesicle / Golgi membrane / GTPase activity / neuronal cell body / GTP binding / Golgi apparatus / metal ion binding / plasma membrane
Similarity search - Function
Small GTPase / Ras family / 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
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / GH01619p
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.0006 Å
AuthorsLardong, J.A. / Driller, J.H. / Depner, H. / Weise, C. / Petzoldt, A. / Wahl, M.C. / Sigrist, S.J. / Loll, B.
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2015
Title: Structures of Drosophila melanogaster Rab2 and Rab3 bound to GMPPNP.
Authors: Lardong, J.A. / Driller, J.H. / Depner, H. / Weise, C. / Petzoldt, A. / Wahl, M.C. / Sigrist, S.J. / Loll, B.
History
DepositionOct 13, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 10, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 7, 2015Group: Database references
Revision 1.2Feb 4, 2015Group: Database references
Revision 1.3Feb 28, 2024Group: 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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GH01619p
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,0045
Polymers19,9811
Non-polymers1,0234
Water2,036113
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)81.355, 81.355, 53.128
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-376-

HOH

21A-403-

HOH

31A-412-

HOH

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Components

#1: Protein GH01619p / Rab-protein 2 / Rab2


Mass: 19980.785 Da / Num. of mol.: 1 / Fragment: GTPase domain (UNP Residues 1-172) / Mutation: Q65L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Rab2, CG3269, Dmel_CG3269 / Plasmid: pET-MBP / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O18333
#2: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / 5'-Guanylyl imidodiphosphate


Mass: 522.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol


Mass: 238.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 113 / 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: 2.54 Å3/Da / Density % sol: 51.58 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 34% (v/v) polyethylene glycol 400; 200 mM Na acetate at pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.3 / Wavelength: 0.895 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Apr 24, 2014 / Details: MIRROR
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.895 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 13981 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 5 % / Biso Wilson estimate: 25.7 Å2
Reflection shellResolution: 2→2.12 Å / Redundancy: 5 % / Mean I/σ(I) obs: 1.8 / % possible all: 99.2

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
PHENIX(phenix.refine: 1.9_1692)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.0006→42.419 Å / SU ML: 0.19 / σ(F): 1.36 / Phase error: 22.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2244 699 5.01 %
Rwork0.1668 --
obs0.1697 13966 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.0006→42.419 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1404 0 50 113 1567
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081492
X-RAY DIFFRACTIONf_angle_d1.1032014
X-RAY DIFFRACTIONf_dihedral_angle_d16.941560
X-RAY DIFFRACTIONf_chiral_restr0.046221
X-RAY DIFFRACTIONf_plane_restr0.003250
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0006-2.15510.29391370.22072602X-RAY DIFFRACTION99
2.1551-2.37190.26131370.19932615X-RAY DIFFRACTION100
2.3719-2.71510.22371400.18152647X-RAY DIFFRACTION100
2.7151-3.42050.24141390.16342655X-RAY DIFFRACTION100
3.4205-42.4290.18181460.13732748X-RAY DIFFRACTION99

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