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- PDB-1fw8: CIRCULARLY PERMUTED PHOSPHOGLYCERATE KINASE FROM YEAST: PGK P72 -

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Basic information

Entry
Database: PDB / ID: 1fw8
TitleCIRCULARLY PERMUTED PHOSPHOGLYCERATE KINASE FROM YEAST: PGK P72
ComponentsPhosphoglycerate kinase
KeywordsTRANSFERASE / phosphotransferase / kinase / phosphoglycerate kinase / glycolysis / mutant / permutation / permuted sequence / PGK / protein folding / two-domain protein
Function / homology
Function and homology information


Gluconeogenesis / Glycolysis / phosphoglycerate kinase / phosphoglycerate kinase activity / glycolytic process / gluconeogenesis / ADP binding / mitochondrion / ATP binding / metal ion binding ...Gluconeogenesis / Glycolysis / phosphoglycerate kinase / phosphoglycerate kinase activity / glycolytic process / gluconeogenesis / ADP binding / mitochondrion / ATP binding / metal ion binding / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Phosphoglycerate kinase, N-terminal domain / Phosphoglycerate kinase / Phosphoglycerate kinase, N-terminal / Phosphoglycerate kinase, conserved site / Phosphoglycerate kinase superfamily / Phosphoglycerate kinase / Phosphoglycerate kinase signature. / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Phosphoglycerate kinase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.3 Å
AuthorsTougard, P. / Bizebard, T. / Ritco-Vonsovici, M. / Minard, P. / Desmadril, M.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2002
Title: Structure of a circularly permuted phosphoglycerate kinase.
Authors: Tougard, P. / Bizebard, T. / Ritco-Vonsovici, M. / Minard, P. / Desmadril, M.
#1: Journal: Biochemistry / Year: 1995
Title: Is the continuity of the domains required for the correct folding of a two-domain protein?
Authors: Ritco-Vonsovici, M. / Minard, P. / Desmadril, M. / Yon, J.M.
History
DepositionSep 22, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 22, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Jun 28, 2017Group: Advisory / Database references ...Advisory / Database references / Refinement description / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / pdbx_distant_solvent_atoms / software / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_description
Revision 1.4Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / 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_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: Phosphoglycerate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,0225
Polymers44,6541
Non-polymers3684
Water3,261181
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.74, 104.77, 44.34
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Phosphoglycerate kinase


Mass: 44654.121 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast), (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: PGK1, YCR012W, YCR12W / Plasmid: PYE / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P00560, phosphoglycerate kinase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 181 / 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: 2.23 Å3/Da / Density % sol: 44.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.1
Details: ammonium sulfate, sodium pyrophosphate, dioxan, glycerol for cryogenic conditions, pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12.0-2.6 Mammonium sulfate1reservoir
27-10 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: LURE / Beamline: D41A / Wavelength: 1.375
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 10, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.375 Å / Relative weight: 1
ReflectionResolution: 2.3→14.99 Å / Num. all: 18305 / % possible obs: 99.8 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.079
Reflection shellResolution: 2.3→2.8 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.273 / Num. unique all: 1787 / % possible all: 99.4
Reflection
*PLUS
Num. obs: 18306 / Num. measured all: 64243
Reflection shell
*PLUS
% possible obs: 99.4 % / Rmerge(I) obs: 0.322 / Mean I/σ(I) obs: 3.5

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Processing

Software
NameVersionClassification
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementResolution: 2.3→7 Å
RfactorNum. reflectionSelection details
Rfree0.324 808 Random
Rwork0.211 --
obs-17625 -
Refinement stepCycle: LAST / Resolution: 2.3→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3148 0 24 181 3353
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_angle_deg1.7
X-RAY DIFFRACTIONx_torsion_deg24.1
X-RAY DIFFRACTIONx_torsion_impr_deg1.6
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
σ(I): 16817
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.1

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