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- PDB-1ky3: GDP-BOUND YPT7P AT 1.35 A RESOLUTION -

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Basic information

Entry
Database: PDB / ID: 1ky3
TitleGDP-BOUND YPT7P AT 1.35 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
GUANOSINE-5'-DIPHOSPHATE / Ypt/Rab-type GTPase YPT7
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 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: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.classification / _software.name
Revision 1.4Feb 14, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / 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
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GTP-BINDING PROTEIN YPT7P
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,6273
Polymers20,1601
Non-polymers4682
Water3,099172
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.535, 55.430, 60.177
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-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 172 / 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: 1.98 Å3/Da / Density % sol: 39.96 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG, HEPES, GDP, pH 7.0, 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
220 %PEG33501reservoir
3200 mM1reservoirNaCl

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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: 1.35→25 Å / Num. all: 36543 / Num. obs: 36543 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Biso Wilson estimate: 14.7 Å2 / Rsym value: 0.081 / Net I/σ(I): 15.77
Reflection shellResolution: 1.35→1.45 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.308 / Mean I/σ(I) obs: 4.33 / Num. unique all: 6841 / % possible all: 97.3
Reflection
*PLUS
Num. measured all: 263110 / Rmerge(I) obs: 0.081
Reflection shell
*PLUS
Highest resolution: 1.3 Å / Lowest resolution: 1.4 Å / Rmerge(I) obs: 0.308

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Processing

Software
NameClassification
AMoREphasing
SHELXL-97refinement
MAR345data collection
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: YPT7-GPPNHP

Resolution: 1.35→22.61 Å / Data cutoff high absF: 1065395.08 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.227 2413 6.6 %RANDOM
Rwork0.161 ---
all0.191 36545 --
obs0.191 36545 98.4 %-
Displacement parametersBiso mean: 20.1 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å20 Å20 Å2
2--2.01 Å20 Å2
3----1.92 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.19 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a0.14 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 1.35→22.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1271 0 29 172 1472
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.012
X-RAY DIFFRACTIONs_angle_d0.029
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0282
X-RAY DIFFRACTIONs_zero_chiral_vol0.053
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.069
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.014
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.005
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.062
X-RAY DIFFRACTIONs_approx_iso_adps0.083
LS refinement shellResolution: 1.35→1.45 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.365 342 5.8 %
Rwork0.323 5543 -
obs--97.1 %
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
Num. reflection Rfree: 2636 / % reflection Rfree: 6.5 % / Rfactor all: 0.166 / Rfactor obs: 0.201 / Rfactor Rfree: 0.253 / Rfactor Rwork: 0.201
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.014
X-RAY DIFFRACTIONs_angle_d
X-RAY DIFFRACTIONs_angle_deg2.13
X-RAY DIFFRACTIONs_plane_restr0.028
X-RAY DIFFRACTIONs_chiral_restr0.053
LS refinement shell
*PLUS
Highest resolution: 1.3 Å / Lowest resolution: 1.4 Å / Rfactor Rfree: 0.365 / Rfactor Rwork: 0.323

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