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- PDB-4zkd: Crystal structure of the S. cerevisiae Ski7 GTPase-like domain, b... -

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Basic information

Entry
Database: PDB / ID: 4zkd
TitleCrystal structure of the S. cerevisiae Ski7 GTPase-like domain, bound to GDP and inorganic phosphate.
ComponentsSuperkiller protein 7
KeywordsGTP-BINDING PROTEIN / GTPase / translation / NGD / Ski / hydrolase
Function / homology
Function and homology information


nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay / nuclear-transcribed mRNA catabolic process, non-stop decay / nonfunctional rRNA decay / nuclear-transcribed mRNA catabolic process / translational elongation / translation elongation factor activity / protein catabolic process / protein-macromolecule adaptor activity / translation / GTPase activity ...nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay / nuclear-transcribed mRNA catabolic process, non-stop decay / nonfunctional rRNA decay / nuclear-transcribed mRNA catabolic process / translational elongation / translation elongation factor activity / protein catabolic process / protein-macromolecule adaptor activity / translation / GTPase activity / protein-containing complex binding / GTP binding / cytosol / cytoplasm
Similarity search - Function
: / : / Ski7 III domain / Ski7 domain II / : / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold ...: / : / Ski7 III domain / Ski7 domain II / : / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / 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 / PHOSPHATE ION / Superkiller protein 7
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.181 Å
AuthorsKowalinski, E. / Conti, E.
CitationJournal: Structure / Year: 2015
Title: Saccharomyces cerevisiae Ski7 Is a GTP-Binding Protein Adopting the Characteristic Conformation of Active Translational GTPases.
Authors: Kowalinski, E. / Schuller, A. / Green, R. / Conti, E.
History
DepositionApr 30, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 17, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 24, 2015Group: Database references
Revision 1.2Jul 15, 2015Group: Database references
Revision 1.3May 8, 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
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.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Superkiller protein 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,2214
Polymers56,6581
Non-polymers5623
Water18010
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1130 Å2
ΔGint-29 kcal/mol
Surface area22070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.136, 120.617, 105.269
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Superkiller protein 7 / Ski7


Mass: 56658.477 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SKI7, YOR076C, YOR29-27 / Production host: Escherichia coli (E. coli) / References: UniProt: Q08491
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#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: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 2.61 Å3/Da / Density % sol: 52.86 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 100 mM Hepes pH 7.0, 700mM NaH2PO4/K2HPO4, 3% ethylene glycol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 19, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.181→73.72 Å / Num. obs: 59361 / % possible obs: 99.71 % / Redundancy: 6.6 % / Net I/σ(I): 15.98
Reflection shellResolution: 2.181→2.259 Å / Redundancy: 6.1 % / Mean I/σ(I) obs: 0.86 / % possible all: 97.48

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
XDSdata reduction
XDSdata scaling
SHARPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.181→73.717 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.11 / Phase error: 34.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.246 3008 5.08 %
Rwork0.2172 --
obs0.2188 59167 99.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.181→73.717 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3765 0 34 10 3809
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033922
X-RAY DIFFRACTIONf_angle_d0.7015338
X-RAY DIFFRACTIONf_dihedral_angle_d14.2121459
X-RAY DIFFRACTIONf_chiral_restr0.028630
X-RAY DIFFRACTIONf_plane_restr0.003668
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.181-2.21670.41871180.4312443X-RAY DIFFRACTION91
2.2167-2.25490.40881460.40242687X-RAY DIFFRACTION99
2.2549-2.29590.36421770.39272604X-RAY DIFFRACTION99
2.2959-2.34010.44471440.38352700X-RAY DIFFRACTION99
2.3401-2.38790.36311690.37632662X-RAY DIFFRACTION99
2.3879-2.43980.36131400.36142653X-RAY DIFFRACTION99
2.4398-2.49660.44641260.34882714X-RAY DIFFRACTION100
2.4966-2.5590.38391750.32912675X-RAY DIFFRACTION99
2.559-2.62820.36681390.31612665X-RAY DIFFRACTION100
2.6282-2.70550.3061140.28562740X-RAY DIFFRACTION99
2.7055-2.79290.34331080.27752675X-RAY DIFFRACTION100
2.7929-2.89270.32061490.26362717X-RAY DIFFRACTION100
2.8927-3.00850.29541370.26162696X-RAY DIFFRACTION100
3.0085-3.14540.26291430.24832679X-RAY DIFFRACTION100
3.1454-3.31130.25651210.23522750X-RAY DIFFRACTION100
3.3113-3.51870.27591560.23052660X-RAY DIFFRACTION100
3.5187-3.79040.23641480.20912688X-RAY DIFFRACTION100
3.7904-4.17180.24211570.18422670X-RAY DIFFRACTION100
4.1718-4.77540.19231420.1562716X-RAY DIFFRACTION100
4.7754-6.0160.1791440.16952678X-RAY DIFFRACTION100
6.016-73.75930.19041550.17662687X-RAY DIFFRACTION100

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