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- PDB-1odf: Structure of YGR205w protein. -

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Basic information

Entry
Database: PDB / ID: 1odf
TitleStructure of YGR205w protein.
ComponentsHYPOTHETICAL 33.3 KDA PROTEIN IN ADE3-SER2 INTERGENIC REGION
KeywordsYEAST PROTEIN / ATP BINDING PROTEIN
Function / homology
Function and homology information


Transferases; Transferring phosphorus-containing groups / kinase activity / ATP binding / nucleus / cytoplasm
Similarity search - Function
P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Probable ATP-dependent kinase TDA10
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.25 Å
AuthorsLi De La Sierra-Gallay, I. / Van Tilbeurgh, H.
CitationJournal: Proteins: Struct.,Funct., Genet. / Year: 2004
Title: Crystal Structure of the Ygr205W Protein from Saccharomyces Cerevisiae: Close Structural Resemblance to E.Coli Pantothenate Kinase
Authors: Li De La Sierra-Gallay, I. / Collinet, B. / Graille, M. / Quevillon-Cheruel, S. / Liger, D. / Minard, P. / Blondeau, K. / Henckes, G. / Aufrere, R. / Leulliot, N. / Zhou, C.Z. / Sorrel, I. / ...Authors: Li De La Sierra-Gallay, I. / Collinet, B. / Graille, M. / Quevillon-Cheruel, S. / Liger, D. / Minard, P. / Blondeau, K. / Henckes, G. / Aufrere, R. / Leulliot, N. / Zhou, C.Z. / Sorrel, I. / Ferrer, J.L. / Poupon, A. / Janin, J. / Van Tilbeurgh, H.
History
DepositionFeb 19, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 12, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HYPOTHETICAL 33.3 KDA PROTEIN IN ADE3-SER2 INTERGENIC REGION
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8416
Polymers33,3731
Non-polymers4685
Water1,33374
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)64.850, 64.850, 140.130
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein HYPOTHETICAL 33.3 KDA PROTEIN IN ADE3-SER2 INTERGENIC REGION / YGR205W


Mass: 33372.738 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Strain: S288C / Description: CLONED GENE / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P42938
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / Source method: isolated from a natural source / Formula: H2O
Compound detailsNUCLEOTIDE BINDING DOMAIN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.8 Å3/Da / Density % sol: 50 %
Crystal growpH: 6
Details: 2.4M AMMONIUM SULFATE, 0.1M NA CITRATE PH5.6, pH 6.00
Crystal grow
*PLUS
Temperature: 18 ℃ / pH: 8 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
14 mg/mlprotein1drop
225 mMTris-HCl1droppH8
31.9 Mammonium sulfate1reservoir
40.1 Msodium acetate1reservoirpH4.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9719
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 15, 2001
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9719 Å / Relative weight: 1
ReflectionResolution: 2.25→30 Å / Num. obs: 14707 / % possible obs: 98.9 % / Redundancy: 6.45 % / Biso Wilson estimate: 27.2 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 33.2
Reflection shellResolution: 2.25→2.32 Å / Rmerge(I) obs: 0.499 / Mean I/σ(I) obs: 3.9 / % possible all: 98.4
Reflection
*PLUS
Highest resolution: 2.25 Å / Lowest resolution: 30 Å / Redundancy: 6.4 % / Num. measured all: 94854 / Rmerge(I) obs: 0.055

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVE/RESOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.25→20 Å / Data cutoff high absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0 / Details: REGIONS A1-A4 AND A117-A122 DISORDERED
RfactorNum. reflection% reflectionSelection details
Rfree0.2597 700 4.7 %RANDOM
Rwork0.2063 ---
obs0.2063 13955 94 %-
Displacement parametersBiso mean: 47 Å2
Baniso -1Baniso -2Baniso -3
1-7.698 Å20 Å20 Å2
2--7.698 Å20 Å2
3----15.395 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.36 Å0.3 Å
Refinement stepCycle: LAST / Resolution: 2.25→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2270 0 28 74 2372
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.74
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.25→2.31 Å / Rfactor Rfree error: 0.037 / Total num. of bins used: 14
RfactorNum. reflection% reflection
Rfree0.3755 39 4.6 %
Rwork0.2983 786 -
obs--83.3 %
Refinement
*PLUS
% reflection Rfree: 4.8 % / Rfactor Rfree: 0.26 / Rfactor Rwork: 0.206
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.195
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.74

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