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

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Basic information

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


Eukaryotic Translation Elongation / nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay / : / nuclear-transcribed mRNA catabolic process, non-stop decay / HSF1 activation / nonfunctional rRNA decay / Protein methylation / translational elongation / translation elongation factor activity / Neutrophil degranulation ...Eukaryotic Translation Elongation / nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay / : / nuclear-transcribed mRNA catabolic process, non-stop decay / HSF1 activation / nonfunctional rRNA decay / Protein methylation / translational elongation / translation elongation factor activity / Neutrophil degranulation / protein catabolic process / protein-macromolecule adaptor activity / translation / GTPase activity / protein-containing complex binding / GTP binding / cytosol / cytoplasm
Similarity search - Function
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 / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / TRIETHYLENE GLYCOL / Superkiller protein 7
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.251 Å
AuthorsKowalinski, E. / Conti, E.
Funding support Germany, 4items
OrganizationGrant numberCountry
European CommissionERC Advanced Investigator Grant 294371, Marie Curie ITN RNPnet, FP7-PEOPLE-2012-IEF
German Research FoundationSFB646, SFB1035, GRK1721, FOR1680 and CIPSM Germany
European Molecular Biology OrganizationALTF 391-2012
Daimler Benz Foundation32-04/12 Germany
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 1.3Sep 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jan 10, 2024Group: 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
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.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.value / _struct_conn.pdbx_dist_value / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Superkiller protein 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,3795
Polymers56,6581
Non-polymers7214
Water1,72996
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1520 Å2
ΔGint-22 kcal/mol
Surface area22220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.150, 123.106, 104.967
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 1 types, 1 molecules A

#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

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Non-polymers , 5 types, 100 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / Guanosine triphosphate


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 96 / 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: 2.6 Å3/Da / Density % sol: 52.67 %
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: Dec 21, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.251→45.58 Å / Num. obs: 27933 / % possible obs: 98.47 % / Redundancy: 6.7 % / Net I/σ(I): 13.36
Reflection shellResolution: 2.251→2.331 Å / Redundancy: 6.8 % / Mean I/σ(I) obs: 1.25 / % possible all: 94.89

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZKD

4zkd


Resolution: 2.251→45.58 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / Phase error: 28.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2387 2674 5.02 %
Rwork0.2047 --
obs0.2065 188256 98.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.251→45.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3785 0 44 96 3925
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033968
X-RAY DIFFRACTIONf_angle_d0.7635400
X-RAY DIFFRACTIONf_dihedral_angle_d16.2091478
X-RAY DIFFRACTIONf_chiral_restr0.03635
X-RAY DIFFRACTIONf_plane_restr0.003677
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2505-2.29150.40571410.34652457X-RAY DIFFRACTION91
2.2915-2.33550.34081470.32922659X-RAY DIFFRACTION98
2.3355-2.38320.37361540.31452654X-RAY DIFFRACTION98
2.3832-2.4350.36611480.3132652X-RAY DIFFRACTION98
2.435-2.49170.30931330.30672655X-RAY DIFFRACTION98
2.4917-2.5540.3131130.28112707X-RAY DIFFRACTION98
2.554-2.6230.31791160.28082664X-RAY DIFFRACTION98
2.623-2.70020.29561420.26392639X-RAY DIFFRACTION98
2.7002-2.78730.27051440.24692644X-RAY DIFFRACTION98
2.7873-2.88690.25931310.23262691X-RAY DIFFRACTION99
2.8869-3.00250.27781360.23482668X-RAY DIFFRACTION98
3.0025-3.13910.28321260.22572699X-RAY DIFFRACTION99
3.1391-3.30460.26021420.21342675X-RAY DIFFRACTION99
3.3046-3.51150.26311600.20212683X-RAY DIFFRACTION99
3.5115-3.78260.2111410.18472644X-RAY DIFFRACTION99
3.7826-4.1630.22861470.16822712X-RAY DIFFRACTION99
4.163-4.76480.17191560.14662677X-RAY DIFFRACTION99
4.7648-6.0010.22011280.1692694X-RAY DIFFRACTION100
6.001-45.58430.18881690.18782667X-RAY DIFFRACTION99

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