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- PDB-1ky2: GPPNHP-BOUND YPT7P AT 1.6 A RESOLUTION -

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Basic information

Entry
Database: PDB / ID: 1ky2
TitleGPPNHP-BOUND YPT7P AT 1.6 A RESOLUTION
ComponentsGTP-BINDING PROTEIN YPT7P
KeywordsENDOCYTOSIS/EXOCYTOSIS / G PROTEIN / VESICULAR TRAFFIC / GTP HYDROLYSIS / YPT/RAB PROTEIN / ENDOCYTOSIS / HYDROLASE / ENDOCYTOSIS-EXOCYTOSIS COMPLEX
Function / homology
Function and homology information


RHOD GTPase cycle / TBC/RABGAPs / RAB geranylgeranylation / RHOQ GTPase cycle / regulation of vacuole fusion, non-autophagic / vacuole-mitochondrion membrane contact site / RAB GEFs exchange GTP for GDP on RABs / vacuole inheritance / protein localization to vacuole / cytoplasm to vacuole targeting by the Cvt pathway ...RHOD GTPase cycle / TBC/RABGAPs / RAB geranylgeranylation / RHOQ GTPase cycle / regulation of vacuole fusion, non-autophagic / vacuole-mitochondrion membrane contact site / RAB GEFs exchange GTP for GDP on RABs / vacuole inheritance / protein localization to vacuole / cytoplasm to vacuole targeting by the Cvt pathway / piecemeal microautophagy of the nucleus / fungal-type vacuole / vacuole / fungal-type vacuole membrane / retrograde transport, endosome to Golgi / regulation of protein-containing complex assembly / vesicle-mediated transport / multivesicular body / Neutrophil degranulation / macroautophagy / endocytosis / late endosome / mitochondrial outer membrane / GTPase activity / GTP binding / protein-containing complex binding / mitochondrion / cytosol
Similarity search - Function
Small GTPase Rab 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 ...Small GTPase Rab 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
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / Ypt/Rab-type GTPase YPT7
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsConstantinescu, A.-T. / Rak, A. / Scheidig, A.J.
CitationJournal: Structure / Year: 2002
Title: Rab-subfamily-specific regions of Ypt7p are structurally different from other RabGTPases.
Authors: Constantinescu, A.T. / Rak, A. / Alexandrov, K. / Esters, H. / Goody, R.S. / Scheidig, A.J.
History
DepositionFeb 2, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Aug 16, 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 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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_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: GTP-BINDING PROTEIN YPT7P
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7063
Polymers20,1601
Non-polymers5472
Water4,324240
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.137, 60.667, 73.537
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein GTP-BINDING PROTEIN YPT7P / GTP-BINDING PROTEIN YPT7


Mass: 20159.760 Da / Num. of mol.: 1 / Fragment: GTPASE DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: YPT7 / Plasmid: PET11 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21/DE3 / References: UniProt: P32939
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 522.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 240 / 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: 1.9 Å3/Da / Density % sol: 44.6 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG, TRIS, GppNHp, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Temperature: 20 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
17-9 mg/mlprotein1drop
21 M1reservoirLiCl
320-30 %PEG60001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 / Wavelength: 0.934 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 10, 2000 / Details: MIRROR
RadiationMonochromator: MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.6→25 Å / Num. all: 23450 / Num. obs: 23450 / % possible obs: 96.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.15 % / Biso Wilson estimate: 20.3 Å2 / Rsym value: 0.103 / Net I/σ(I): 8.1
Reflection shellResolution: 1.6→1.7 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 2.7 / Num. unique all: 3770 / Rsym value: 0.18 / % possible all: 95.7
Reflection
*PLUS
Num. measured all: 124357 / Rmerge(I) obs: 0.103
Reflection shell
*PLUS
Highest resolution: 1.57 Å / Lowest resolution: 1.6 Å / Rmerge(I) obs: 0.181

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Processing

Software
NameClassification
AMoREphasing
SHELXL-97refinement
MAR345data collection
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EK0

1ek0


Resolution: 1.6→25 Å / Isotropic thermal model: isotropic / Cross valid method: FREE R / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.2492 1876 8.7 %RANDOM
Rwork0.1832 ---
all0.1926 23450 --
obs0.1926 23450 96.2 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-22
Displacement parametersBiso mean: 22.4 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a0.13 Å0.11 Å
Refinement stepCycle: LAST / Resolution: 1.6→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1430 0 33 240 1703
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.007
X-RAY DIFFRACTIONs_angle_d0.023
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.025
X-RAY DIFFRACTIONs_zero_chiral_vol0.039
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.056
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.023
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.07
X-RAY DIFFRACTIONs_approx_iso_adps0
LS refinement shellResolution: 1.6→1.7 Å / Rfactor Rfree error: 0.017
RfactorNum. reflection% reflection
Rfree0.294 304 -
Rwork0.271 --
obs-3504 95.7 %
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.6 Å / % reflection Rfree: 8 % / Rfactor all: 0.1926 / Rfactor obs: 0.183 / Rfactor Rfree: 0.239 / Rfactor Rwork: 0.183
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.008
X-RAY DIFFRACTIONs_angle_d
X-RAY DIFFRACTIONs_angle_deg1.824
X-RAY DIFFRACTIONs_plane_restr0.039
X-RAY DIFFRACTIONs_chiral_restr0.056
LS refinement shell
*PLUS
Rfactor Rfree: 0.294 / Rfactor Rwork: 0.271

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