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- PDB-9fdn: Human phosphoglycerate kinase in complex with ATP and 3PG formed ... -

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Basic information

Entry
Database: PDB / ID: 9fdn
TitleHuman phosphoglycerate kinase in complex with ATP and 3PG formed by cross-soaking a TSA crystal
ComponentsPhosphoglycerate kinase 1
KeywordsTRANSFERASE / Phosphoryl transfer Glycolysis ATP binding Rossmann fold
Function / homology
Function and homology information


negative regulation of pyruvate decarboxylation to acetyl-CoA / Manipulation of host energy metabolism / phosphoglycerate kinase / phosphoglycerate kinase activity / protein-disulfide reductase [NAD(P)H] activity / Gluconeogenesis / canonical glycolysis / Glycolysis / plasminogen activation / epithelial cell differentiation ...negative regulation of pyruvate decarboxylation to acetyl-CoA / Manipulation of host energy metabolism / phosphoglycerate kinase / phosphoglycerate kinase activity / protein-disulfide reductase [NAD(P)H] activity / Gluconeogenesis / canonical glycolysis / Glycolysis / plasminogen activation / epithelial cell differentiation / negative regulation of angiogenesis / gluconeogenesis / glycolytic process / ADP binding / cellular response to hypoxia / transmembrane transporter binding / non-specific serine/threonine protein kinase / mitochondrial matrix / membrane raft / protein serine kinase activity / protein serine/threonine kinase activity / extracellular space / extracellular exosome / ATP binding / metal ion binding / membrane / cytosol
Similarity search - Function
Phosphoglycerate kinase / Phosphoglycerate kinase, N-terminal / Phosphoglycerate kinase, conserved site / Phosphoglycerate kinase superfamily / Phosphoglycerate kinase / Phosphoglycerate kinase signature.
Similarity search - Domain/homology
3-PHOSPHOGLYCERIC ACID / ADENOSINE-5'-TRIPHOSPHATE / Phosphoglycerate kinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 Å
AuthorsCliff, M.J. / Waltho, J.P. / Bowler, M.W. / Baxter, N.J. / Bisson, C. / Blackburn, G.M.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/M021637/1 United Kingdom
Citation
Journal: To be published
Title: The role of magnesium in catalysis by phosphoglycerate kinase
Authors: Cliff, M.J. / Serimbetov, Z. / Bisson, C. / Baxter, N.J. / Blackburn, G.M. / Hay, S. / Bowler, M.W. / Waltho, J.P.
#1: Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionMay 17, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 28, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phosphoglycerate kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,5835
Polymers44,6731
Non-polymers9104
Water7,170398
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NMR relaxation study
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2070 Å2
ΔGint-14 kcal/mol
Surface area16970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.040, 91.100, 108.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Phosphoglycerate kinase 1 / Cell migration-inducing gene 10 protein / Primer recognition protein 2 / PRP 2


Mass: 44672.621 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PGK1, PGKA, MIG10, OK/SW-cl.110 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P00558, phosphoglycerate kinase

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Non-polymers , 5 types, 402 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#4: Chemical ChemComp-3PG / 3-PHOSPHOGLYCERIC ACID


Mass: 186.057 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7O7P / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 398 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.15 Å3/Da / Density % sol: 42.88 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: MgF3 TSA complex crystals were formed from 50 mM Tris (pH 7.5), 20 mM DTT, 25 mM MgCl2, 50 mM 3PG, and 10 mM ADP supplemented with 20 mM NH4F and 1 mM deferoxamine, in 28-33% PEG 2000 MME ...Details: MgF3 TSA complex crystals were formed from 50 mM Tris (pH 7.5), 20 mM DTT, 25 mM MgCl2, 50 mM 3PG, and 10 mM ADP supplemented with 20 mM NH4F and 1 mM deferoxamine, in 28-33% PEG 2000 MME and 0.1 M Bis/Tris pH 6.5. These were cross-soaked in 35% PEG 2000 MME; 0.1 M Bis/Tris pH 6.5, 20 mM DTT, 2.5mM EDTA, 10mM ATP and 50 mM 3PG

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Data collection

DiffractionMean temperature: 83 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jul 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.58→54.1 Å / Num. obs: 53778 / % possible obs: 99.9 % / Redundancy: 2 % / Biso Wilson estimate: 20.1 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.033 / Rpim(I) all: 0.033 / Rrim(I) all: 0.047 / Net I/σ(I): 12
Reflection shellResolution: 1.58→1.64 Å / Rmerge(I) obs: 0.635 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 5282 / CC1/2: 0.483 / Rpim(I) all: 0.635 / Rrim(I) all: 0.898 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
xia2data scaling
DIALSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.58→54.1 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2045 2000 3.72 %
Rwork0.1785 --
obs0.1795 53773 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.58→54.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3116 0 56 398 3570
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013259
X-RAY DIFFRACTIONf_angle_d1.2424404
X-RAY DIFFRACTIONf_dihedral_angle_d17.221466
X-RAY DIFFRACTIONf_chiral_restr0.059500
X-RAY DIFFRACTIONf_plane_restr0.008562
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.58-1.620.35851410.31263649X-RAY DIFFRACTION100
1.62-1.660.31851400.30293642X-RAY DIFFRACTION100
1.66-1.710.32861420.27693656X-RAY DIFFRACTION100
1.71-1.770.27841410.24643668X-RAY DIFFRACTION100
1.77-1.830.2861400.21823623X-RAY DIFFRACTION100
1.83-1.90.28321430.20693668X-RAY DIFFRACTION100
1.9-1.990.23781400.2033646X-RAY DIFFRACTION100
1.99-2.10.20981420.18843669X-RAY DIFFRACTION100
2.1-2.230.23491420.18123687X-RAY DIFFRACTION100
2.23-2.40.21171440.1723710X-RAY DIFFRACTION100
2.4-2.640.19091420.17443700X-RAY DIFFRACTION100
2.64-3.020.19371450.17183745X-RAY DIFFRACTION100
3.02-3.810.17281450.15353768X-RAY DIFFRACTION100
3.81-54.10.16681530.15463942X-RAY DIFFRACTION100

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