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- PDB-9fdf: Human phosphoglycerate kinase in with mixture of products and sub... -

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Basic information

Entry
Database: PDB / ID: 9fdf
TitleHuman phosphoglycerate kinase in with mixture of products and substrates produced 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 / glycolytic process / gluconeogenesis / 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
ADENOSINE-5'-TRIPHOSPHATE / 1,3-BISPHOSPHOGLYCERIC ACID / Phosphoglycerate kinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.44 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
CitationJournal: 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.
History
DepositionMay 16, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 29, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phosphoglycerate kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,5045
Polymers44,6731
Non-polymers8324
Water9,350519
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NMR relaxation study
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1240 Å2
ΔGint-27 kcal/mol
Surface area17370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.430, 92.010, 108.610
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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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, 523 molecules

#2: 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
#3: Chemical ChemComp-X15 / 1,3-BISPHOSPHOGLYCERIC ACID


Mass: 266.037 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O10P2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 519 / 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: 2.21 Å3/Da / Density % sol: 44.22 % / Description: plates
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: crystals were initially produced 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. ...Details: crystals were initially produced 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 then cross-soaked with 35% PEG 2000 MME; 0.1 M Bis/Tris pH 6.5, 20 mM DTT, and 50 mM 3PG and 0.1mM deferoxamine
Temp details: "room temperature"

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.933 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Jul 23, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.44→37.06 Å / Num. obs: 71262 / % possible obs: 98.48 % / Redundancy: 1.9 % / Biso Wilson estimate: 15.43 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.03 / Rpim(I) all: 0.03 / Rrim(I) all: 0.042 / Net I/σ(I): 14.2
Reflection shellResolution: 1.44→1.49 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.353 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 6991 / CC1/2: 0.737 / Rpim(I) all: 0.353 / Rrim(I) all: 0.499 / % possible all: 97.8

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
xia2data reduction
xia2data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.44→37.06 Å / SU ML: 0.1353 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.6538
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1662 3604 5.06 %
Rwork0.1411 67650 -
obs0.1423 71254 98.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.82 Å2
Refinement stepCycle: LAST / Resolution: 1.44→37.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3116 0 48 519 3683
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00453260
X-RAY DIFFRACTIONf_angle_d0.87994410
X-RAY DIFFRACTIONf_chiral_restr0.0681501
X-RAY DIFFRACTIONf_plane_restr0.0057562
X-RAY DIFFRACTIONf_dihedral_angle_d13.06691257
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.44-1.460.29541370.22982578X-RAY DIFFRACTION97.21
1.46-1.480.26041180.20122516X-RAY DIFFRACTION97.95
1.48-1.50.21961260.18552602X-RAY DIFFRACTION98.91
1.5-1.520.23191360.16852594X-RAY DIFFRACTION99.42
1.52-1.550.22461550.16432542X-RAY DIFFRACTION99.34
1.55-1.570.19441350.14832616X-RAY DIFFRACTION99.24
1.57-1.60.19451470.14662559X-RAY DIFFRACTION98.9
1.6-1.630.20741450.14372578X-RAY DIFFRACTION99.02
1.63-1.660.20441550.14082538X-RAY DIFFRACTION96.63
1.66-1.690.16591240.13552555X-RAY DIFFRACTION98.53
1.69-1.730.2051420.13652629X-RAY DIFFRACTION99.71
1.73-1.770.18531430.1442568X-RAY DIFFRACTION99.52
1.77-1.820.17141350.14292634X-RAY DIFFRACTION99.68
1.82-1.860.18191300.13682628X-RAY DIFFRACTION99.39
1.86-1.920.161500.12792595X-RAY DIFFRACTION99.42
1.92-1.980.18761220.12192640X-RAY DIFFRACTION99.28
1.98-2.050.15381420.12942611X-RAY DIFFRACTION99.35
2.05-2.130.16611560.13442580X-RAY DIFFRACTION99.27
2.13-2.230.17581500.12692628X-RAY DIFFRACTION99.04
2.23-2.350.15351320.12342502X-RAY DIFFRACTION94.58
2.35-2.50.16851630.13252606X-RAY DIFFRACTION98.82
2.5-2.690.1591390.13812639X-RAY DIFFRACTION99
2.69-2.960.15271210.14842682X-RAY DIFFRACTION99.19
2.96-3.390.16881370.14552652X-RAY DIFFRACTION98.45
3.39-4.260.12031290.12992684X-RAY DIFFRACTION97.84
4.27-37.060.15041350.15462694X-RAY DIFFRACTION93.46

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