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- PDB-1ek0: GPPNHP-BOUND YPT51 AT 1.48 A RESOLUTION -

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Basic information

Entry
Database: PDB / ID: 1ek0
TitleGPPNHP-BOUND YPT51 AT 1.48 A RESOLUTION
ComponentsPROTEIN (GTP-BINDING PROTEIN YPT51)
KeywordsENDOCYTOSIS/EXOCYTOSIS / G PROTEIN / VESICULAR TRAFFIC / GTP HYDROLYSIS / YPT/RAB PROTEIN / ENDOCYTOSIS / HYDROLASE / ENDOCYTOSIS-EXOCYTOSIS COMPLEX
Function / homology
Function and homology information


Factors involved in megakaryocyte development and platelet production / Clathrin-mediated endocytosis / RAB geranylgeranylation / RAB GEFs exchange GTP for GDP on RABs / vacuole inheritance / Golgi to endosome transport / protein localization to endosome / late endosome to vacuole transport via multivesicular body sorting pathway / protein targeting to vacuole / multivesicular body assembly ...Factors involved in megakaryocyte development and platelet production / Clathrin-mediated endocytosis / RAB geranylgeranylation / RAB GEFs exchange GTP for GDP on RABs / vacuole inheritance / Golgi to endosome transport / protein localization to endosome / late endosome to vacuole transport via multivesicular body sorting pathway / protein targeting to vacuole / multivesicular body assembly / reticulophagy / endomembrane system / intracellular protein transport / endocytosis / late endosome / mitochondrial outer membrane / early endosome / endosome membrane / GTPase activity / GTP binding / mitochondrion / cytosol
Similarity search - Function
small GTPase Rab1 family profile. / 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
GUANOSINE-5'-DIPHOSPHATE / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / NICKEL (II) ION / Vacuolar protein sorting-associated protein 21
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.48 Å
AuthorsEsters, H. / Scheidig, A.J.
CitationJournal: J.Mol.Biol. / Year: 2000
Title: High-resolution crystal structure of S. cerevisiae Ypt51(DeltaC15)-GppNHp, a small GTP-binding protein involved in regulation of endocytosis.
Authors: Esters, H. / Alexandrov, K. / Constantinescu, A.T. / Goody, R.S. / Scheidig, A.J.
History
DepositionMar 6, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Aug 9, 2023Group: 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 / diffrn_source / pdbx_initial_refinement_model / 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 / _diffrn_source.pdbx_synchrotron_site / _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.pdbx_leaving_atom_flag / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (GTP-BINDING PROTEIN YPT51)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,0125
Polymers18,9641
Non-polymers1,0484
Water3,765209
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.326, 62.326, 91.221
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

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Protein , 1 types, 1 molecules A

#1: Protein PROTEIN (GTP-BINDING PROTEIN YPT51)


Mass: 18963.666 Da / Num. of mol.: 1 / Fragment: GTPASE DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Plasmid: PET19 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21/DE3 / References: UniProt: P36017

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Non-polymers , 5 types, 213 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#4: 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
#5: 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
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 209 / 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 Å3/Da / Density % sol: 54.38 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 10% PEG-3350, 100 MM HEPES, PH 7.5, 20 MM NICL2 , VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
Temperature: 18 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
113 mg/mlprotein1drop
225 mMHEPES-NaOH1drop
35 mM1dropMgCl2
450 mM1dropNaCl
52 mMbeta-mercaptoethanol1drop
610 %(v/v)PEG33501reservoir
7100 mMHEPES-NaOH1reservoir
820 mM1reservoirNiCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.903
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 1, 1999 / Details: MIRROR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.903 Å / Relative weight: 1
ReflectionResolution: 1.48→20 Å / Num. all: 146199 / Num. obs: 33345 / % possible obs: 93.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Biso Wilson estimate: 34 Å2 / Rmerge(I) obs: 0.026 / Net I/σ(I): 27.55
Reflection shellResolution: 1.47→1.55 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.214 / Mean I/σ(I) obs: 5.22 / Num. unique all: 5853 / % possible all: 90
Reflection
*PLUS
Num. measured all: 146199

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Processing

Software
NameClassification
AMoREphasing
SHELXL-97refinement
MAR345data collection
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5P21

5p21


Resolution: 1.48→31 Å / Num. parameters: 660 / Num. restraintsaints: 610 / Cross valid method: FREE R / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.228 1673 5 %RANDOM
Rwork0.178 ---
all0.179 33452 --
obs0.178 33452 94.2 %-
Refine analyzeNum. disordered residues: 1 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 1609
Refinement stepCycle: LAST / Resolution: 1.48→31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1391 0 62 209 1662
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.01
X-RAY DIFFRACTIONs_angle_d0.04
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.027
X-RAY DIFFRACTIONs_zero_chiral_vol0.04
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.06
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.01
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.06
X-RAY DIFFRACTIONs_approx_iso_adps0
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 31 Å / σ(F): 0 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.01
X-RAY DIFFRACTIONs_angle_d0.04

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