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- PDB-16pk: PHOSPHOGLYCERATE KINASE FROM TRYPANOSOMA BRUCEI BISUBSTRATE ANALOG -

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Basic information

Entry
Database: PDB / ID: 16pk
TitlePHOSPHOGLYCERATE KINASE FROM TRYPANOSOMA BRUCEI BISUBSTRATE ANALOG
Components3-PHOSPHOGLYCERATE KINASE
KeywordsKINASE / PHOSPHOGLYCERATE / TERNARY COMPLEX / GLYCOLYSIS / TRANSFERASE / BISUBSTRATE / ANALOG
Function / homology
Function and homology information


phosphoglycerate kinase / phosphoglycerate kinase activity / glycosome / gluconeogenesis / glycolytic process / ADP binding / phosphorylation / ATP binding / cytosol
Similarity search - Function
Phosphoglycerate kinase, euglenozoa / 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
Chem-BIS / Phosphoglycerate kinase, glycosomal
Similarity search - Component
Biological speciesTrypanosoma brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsBernstein, B.E. / Bressi, J. / Blackburn, M. / Gelb, M. / Hol, W.G.J.
CitationJournal: J.Mol.Biol. / Year: 1998
Title: A bisubstrate analog induces unexpected conformational changes in phosphoglycerate kinase from Trypanosoma brucei.
Authors: Bernstein, B.E. / Williams, D.M. / Bressi, J.C. / Kuhn, P. / Gelb, M.H. / Blackburn, G.M. / Hol, W.G.
History
DepositionMay 18, 1998Processing site: BNL
Revision 1.0Nov 25, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2023Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_initial_refinement_model / 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 / _pdbx_database_status.process_site / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 3-PHOSPHOGLYCERATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,5723
Polymers44,7001
Non-polymers8722
Water10,449580
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.710, 79.760, 81.320
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
/ NCS ensembles :
ID
1
2

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Components

#1: Protein 3-PHOSPHOGLYCERATE KINASE / PGK


Mass: 44699.984 Da / Num. of mol.: 1
Mutation: TRUNCATION OF T. BRUCEI SPECIFIC C-TERMINAL SEQUENCE
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei (eukaryote) / Organelle: GLYCOSOME / Variant: GLYCOSOMAL VERSION / Plasmid: PET21A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P07378, phosphoglycerate kinase
#2: Chemical ChemComp-BIS / 1,1,5,5-TETRAFLUOROPHOSPHOPENTYLPHOSPHONIC ACID ADENYLATE ESTER


Mass: 633.276 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22F4N5O12P3
#3: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 580 / 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: 2.64 Å3/Da / Density % sol: 53 % / Description: MR SOLUTION USED INDIVIDUAL DOMAINS SEPARATELY
Crystal growMethod: vapor diffusion / pH: 7.7 / Details: VAPOR DIFFUSION BY MIXING, pH 7.7, vapor diffusion
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
16 mg/mlprotein1drop
210 mMadenyl 1,1,5,5-tetrafluoropentane-1,5-bisphosphonate1drop
325 mMTris-HCl1drop
450 mM1dropNaCl
55 mMdithiothreitol1drop
614 %PEG80001reservoir
750 mMHEPES1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 1
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 1, 1997
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.58→21 Å / Num. obs: 60549 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Rsym value: 0.052
Reflection
*PLUS
Rmerge(I) obs: 0.052

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Processing

Software
NameVersionClassification
X-PLOR3.8model building
X-PLOR3.8refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.8phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 13PK

13pk


Resolution: 1.6→8 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.235 4593 7 %RANDOM
Rwork0.188 ---
obs0.188 65142 97.3 %-
Displacement parametersBiso mean: 16.5 Å2
Refinement stepCycle: LAST / Resolution: 1.6→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3206 0 54 580 3840
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.41
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.5
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scbond_it2
X-RAY DIFFRACTIONx_scangle_it2.5
Refine LS restraints NCS
Ens-IDDom-IDNCS model detailsRefine-IDRms dev position (Å)
11RESTRAINTSX-RAY DIFFRACTION100
22X-RAY DIFFRACTION50
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM19X.PROTOPH19X.PRO
X-RAY DIFFRACTION2

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