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- PDB-13pk: TERNARY COMPLEX OF PHOSPHOGLYCERATE KINASE FROM TRYPANOSOMA BRUCEI -

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Basic information

Entry
Database: PDB / ID: 13pk
TitleTERNARY COMPLEX OF PHOSPHOGLYCERATE KINASE FROM TRYPANOSOMA BRUCEI
Components3-PHOSPHOGLYCERATE KINASEPhosphoglycerate kinase
KeywordsKINASE / PHOSPHOGLYCERATE / TERNARY COMPLEX / GLYCOLYSIS / TRANSFERASE
Function / homologyPhosphoglycerate kinase, N-terminal / Phosphoglycerate kinase / Phosphoglycerate kinase, conserved site / Phosphoglycerate kinase, euglenozoa / Phosphoglycerate kinase superfamily / Phosphoglycerate kinase / Phosphoglycerate kinase signature. / phosphoglycerate kinase / phosphoglycerate kinase activity / glycosome ...Phosphoglycerate kinase, N-terminal / Phosphoglycerate kinase / Phosphoglycerate kinase, conserved site / Phosphoglycerate kinase, euglenozoa / Phosphoglycerate kinase superfamily / Phosphoglycerate kinase / Phosphoglycerate kinase signature. / phosphoglycerate kinase / phosphoglycerate kinase activity / glycosome / glycolytic process / ATP binding / Phosphoglycerate kinase, glycosomal
Function and homology information
Specimen sourceTrypanosoma brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / 2.5 Å resolution
AuthorsBernstein, B.E. / Michels, P.A.M. / Hol, W.G.J.
CitationJournal: Nature / Year: 1997
Title: Synergistic effects of substrate-induced conformational changes in phosphoglycerate kinase activation.
Authors: Bernstein, B.E. / Michels, P.A. / Hol, W.G.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Nov 23, 1996 / Release: Dec 24, 1997
RevisionDateData content typeGroupProviderType
1.0Dec 24, 1997Structure modelrepositoryInitial release
1.1Mar 24, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 3-PHOSPHOGLYCERATE KINASE
B: 3-PHOSPHOGLYCERATE KINASE
C: 3-PHOSPHOGLYCERATE KINASE
D: 3-PHOSPHOGLYCERATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)181,54820
Polyers178,8004
Non-polymers2,74816
Water10,791599
1
A: 3-PHOSPHOGLYCERATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,5276
Polyers44,7001
Non-polymers8285
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 3-PHOSPHOGLYCERATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3384
Polyers44,7001
Non-polymers6383
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: 3-PHOSPHOGLYCERATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4366
Polyers44,7001
Non-polymers7365
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: 3-PHOSPHOGLYCERATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2464
Polyers44,7001
Non-polymers5463
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)113.213, 115.959, 171.327
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP 21 21 21

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Components

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Protein/peptide , 1 types, 4 molecules ABCD

#1: Protein/peptide
3-PHOSPHOGLYCERATE KINASE / Phosphoglycerate kinase / PGK


Mass: 44699.984 Da / Num. of mol.: 4
Mutation: TRUNCATION OF T. BRUCEI SPECIFIC C-TERMINAL SEQUENCE
Source: (gene. exp.) Trypanosoma brucei (eukaryote) / Genus: Trypanosoma / Organelle: GLYCOSOME / Variant: GLYCOSOMAL VERSION / Plasmid name: PET21A / Genus (production host): Escherichia / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P07378, phosphoglycerate kinase

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Non-polymers , 5 types, 615 molecules

#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Formula: Mg / Magnesium
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 6 / Formula: PO4 / Phosphate
#4: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 4 / Formula: C10H15N5O10P2 / Adenosine diphosphate / Comment: ADP (energy-carrying molecule) *YM
#5: Chemical ChemComp-3PG / 3-PHOSPHOGLYCERIC ACID


Mass: 186.057 Da / Num. of mol.: 2 / Formula: C3H7O7P / 3-Phosphoglyceric acid
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 599 / Formula: H2O / Water

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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: 2.9 / Density percent sol: 60.87 % / Description: MR SOLUTION USED INDIVIDUAL DOMAINS SEPARATELY
Crystal growMethod: vapor diffusion / pH: 8
Details: VAPOR DIFFUSION BY MIXING EQUAL VOLUMES OF: PROTEIN: 6MG/ML PGK/25MM TRIS PH 7.5/10MM DTT/10MM MGADP/ 10MM 3- PGA WELL SOLUTION: 2.5 M SODIUM POTASSIUM PHOSPHATE PH 8.0, vapor diffusion
PH range: 7.5-8.0
Crystal grow
*PLUS
Temp: 10 ℃ / Method: vapor diffusion
Details: drop solution was mixed with an equal volume of reservoir solution
components of the solutions
*PLUS
IDConcCommon nameCrystal IDSol IDChemical formula
16 mg/mlprotein1drop
210 mM3-PGA1drop
310 mMMgADP1drop
425 mMTris-HCl1drop
550 mM1dropNaCl
610 mMdithiothreitol1drop
72.5 Mpotassium sodium phosphate1reservoir

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Data collection

DiffractionMean temperature: 100 kelvins
SourceSource: SYNCHROTRON / Type: SSRL BEAMLINE BL7-1 / Synchrotron site: SSRL / Beamline: BL7-1 / Wavelength: 1
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Collection date: Jun 1, 1996
RadiationMonochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionD resolution high: 2.5 Å / D resolution low: 3 Å / Number obs: 73223 / Observed criterion sigma I: 2 / Rsym value: 0.061 / Percent possible obs: 98.5
Reflection shellHighest resolution: 2.5 Å / Lowest resolution: 2.53 Å / Rsym value: 0.328
Reflection
*PLUS
Rmerge I obs: 0.061
Reflection shell
*PLUS
Rmerge I obs: 0.328

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Processing

Software
NameVersionClassification
X-PLOR3.8model building
X-PLOR3.8refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.8phasing
RefineMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PHP
R Free selection details: RANDOM / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / Sigma F: 2
Displacement parametersB iso mean: 47 Å2 / Aniso B11: 16.65 Å2 / Aniso B12: 0 Å2 / Aniso B13: 0 Å2 / Aniso B22: -5.29 Å2 / Aniso B23: 0 Å2 / Aniso B33: -11.36 Å2
Least-squares processR factor R free: 0.291 / R factor R work: 0.2206 / R factor obs: 0.2206 / Highest resolution: 2.5 Å / Lowest resolution: 8 Å / Number reflection R free: 2549 / Number reflection obs: 73223 / Percent reflection R free: 6.6 / Percent reflection obs: 98.5
Refine hist #LASTHighest resolution: 2.5 Å / Lowest resolution: 8 Å
Number of atoms included #LASTProtein: 12484 / Nucleic acid: 0 / Ligand: 168 / Solvent: 599 / Total: 13251
Refine LS restraints
Refine IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
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_deg1.6
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.3
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.55
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.5
X-RAY DIFFRACTIONx_mcangle_it2.0
X-RAY DIFFRACTIONx_scbond_it2.0
X-RAY DIFFRACTIONx_scangle_it2.5
Refine LS restraints ncs
Dom IDNcs model detailsEns IDRefine IDRms dev position
1RESTRAINTS1X-RAY DIFFRACTION100
22X-RAY DIFFRACTION50
Refine LS shellHighest resolution: 2.5 Å / R factor R free: 0.362 / R factor R work: 0.338 / Lowest resolution: 2.53 Å / Number reflection R free: 185 / Number reflection R work: 2497 / Total number of bins used: 25
Xplor file
Refine IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM19X.PROTOPH19X.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refine LS restraints
*PLUS
Refine IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.3
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.55
Refine LS shell
*PLUS
R factor obs: 0.338

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