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- PDB-2ga8: Crystal structure of YFH7 from Saccharomyces cerevisiae: a putati... -

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Basic information

Entry
Database: PDB / ID: 2ga8
TitleCrystal structure of YFH7 from Saccharomyces cerevisiae: a putative P-loop containing kinase with a circular permutation.
ComponentsHypothetical 39.9 kDa protein
KeywordsUNKNOWN FUNCTION / YFR007w / YFH7
Function / homology
Function and homology information


Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor / kinase activity / phosphorylation / ATP hydrolysis activity / ATP binding / cytoplasm
Similarity search - Function
AAA domain (dynein-related subfamily) / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
BETA-MERCAPTOETHANOL / : / ATP-dependent kinase YFH7
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.775 Å
AuthorsChaptal, V. / Morera, S.
CitationJournal: Proteins / Year: 2007
Title: Crystal structure and functional analysis identify the P-loop containing protein YFH7 of Saccharomyces cerevisiae as an ATP-dependent kinase.
Authors: Gueguen-Chaignon, V. / Chaptal, V. / Lariviere, L. / Costa, N. / Lopes, P. / Morera, S. / Nessler, S.
History
DepositionMar 8, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2007Provider: repository / Type: Initial release
Revision 1.1Dec 12, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hypothetical 39.9 kDa protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,35711
Polymers40,9971
Non-polymers1,36110
Water4,666259
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)135.278, 135.278, 48.476
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein Hypothetical 39.9 kDa protein


Mass: 40996.633 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Production host: Escherichia coli (E. coli) / Strain (production host): BL21 star / References: UniProt: P43591
#2: Chemical
ChemComp-HG / MERCURY (II) ION / Mercury (element)


Mass: 200.590 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Hg
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL / 2-Mercaptoethanol


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 259 / 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: 2.08 Å3/Da / Density % sol: 40.91 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 30% PEG 5000MME 0.2M Ammonium sulfate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 23, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.775→20 Å / Num. all: 31961 / Num. obs: 31950 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 11.3 % / Rsym value: 0.081
Reflection shellResolution: 1.775→1.87 Å / Redundancy: 11.1 % / Mean I/σ(I) obs: 2 / Num. unique all: 4681 / Rsym value: 0.323 / % possible all: 100

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNS1refinement
RefinementMethod to determine structure: SAD / Resolution: 1.775→20 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.219 1588 random
Rwork0.194 --
all-31961 -
obs-31950 -
Refinement stepCycle: LAST / Resolution: 1.775→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2629 0 33 259 2921
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0046
X-RAY DIFFRACTIONc_angle_deg1.18

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