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

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Basic information

Entry
Database: PDB / ID: 2gaa
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 / ATP hydrolysis activity / ATP binding / cytoplasm
Similarity search - Function
AAA domain (dynein-related subfamily) / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ATP-dependent kinase YFH7
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.95 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 27, 2007Provider: repository / Type: Initial release
Revision 1.1Dec 12, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 30, 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 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)41,0932
Polymers40,9971
Non-polymers961
Water3,243180
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)134.756, 134.756, 48.679
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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 180 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.07 Å3/Da / Density % sol: 40.7 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 5000MME ammonium sulfate, pH 6.5,VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.98 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 20, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.95→20 Å / Num. all: 23990 / Num. obs: 23765 / % possible obs: 99.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 2.8 % / Rsym value: 0.059
Reflection shellResolution: 1.95→2.06 Å / Redundancy: 2.5 % / Num. unique all: 3436 / Rsym value: 0.378 / % possible all: 99

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 2GA8

2ga8


Resolution: 1.95→20 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.232 1156 random
Rwork0.193 --
all-23990 -
obs-23765 -
Refinement stepCycle: LAST / Resolution: 1.95→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2625 0 5 180 2810
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0048
X-RAY DIFFRACTIONc_angle_deg1.19

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