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- PDB-9fdh: Closed Human phosphoglycerate kinase complex with BPG and ADP pro... -

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Basic information

Entry
Database: PDB / ID: 9fdh
TitleClosed Human phosphoglycerate kinase complex with BPG and ADP 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 / 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
ADENOSINE-5'-DIPHOSPHATE / DI(HYDROXYETHYL)ETHER / 1,3-BISPHOSPHOGLYCERIC ACID / Phosphoglycerate kinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.756 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

Downloads & links

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Assembly

Deposited unit
A: Phosphoglycerate kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,6618
Polymers44,6731
Non-polymers9887
Water4,432246
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NMR relaxation study
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1850 Å2
ΔGint-34 kcal/mol
Surface area17020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.845, 91.626, 108.734
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 , 7 types, 253 molecules

#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, 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-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Cl
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 246 / 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: 2.17 Å3/Da / Density % sol: 43.21 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Produced from MgF3 TSA crystals produced in 50 mM Tris (pH 7.5), 20 mM DTT, 25 mM MgCl2, 50 mM 3PG, and 10 mM ADP and supplemented with 20 mM NH4F and 1 mM deferoxamine. Cross-soaked with ...Details: Produced from MgF3 TSA crystals produced in 50 mM Tris (pH 7.5), 20 mM DTT, 25 mM MgCl2, 50 mM 3PG, and 10 mM ADP and supplemented with 20 mM NH4F and 1 mM deferoxamine. Cross-soaked with 35% PEG 2000 MME; 0.1 M Bis/Tris pH 6.5, 20 mM DTT, 25 mM MgCl2, 10mM ATP and 50 mM 3PG
Temp details: room temperature

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Data collection

DiffractionMean temperature: 83 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: May 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.756→70.12 Å / Num. obs: 39322 / % possible obs: 99.25 % / Redundancy: 1.9 % / Biso Wilson estimate: 25.68 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.029 / Rpim(I) all: 0.029 / Rrim(I) all: 0.041 / Net I/σ(I): 12.2
Reflection shellResolution: 1.76→1.82 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.385 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 3849 / CC1/2: 0.687 / Rpim(I) all: 0.385 / Rrim(I) all: 0.544 / % possible all: 99.3

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
xia2data scaling
xia2data reduction
PHENIX1.11.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.756→70.067 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1777 2000 5.09 %
Rwork0.1481 --
obs0.1496 39322 99.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.756→70.067 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3116 0 59 246 3421
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013260
X-RAY DIFFRACTIONf_angle_d1.0574400
X-RAY DIFFRACTIONf_dihedral_angle_d12.3151999
X-RAY DIFFRACTIONf_chiral_restr0.057499
X-RAY DIFFRACTIONf_plane_restr0.007562
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7562-1.80010.32831390.30092604X-RAY DIFFRACTION99
1.8001-1.84880.32581420.27312637X-RAY DIFFRACTION100
1.8488-1.90320.25961400.21572615X-RAY DIFFRACTION100
1.9032-1.96460.22231420.18692646X-RAY DIFFRACTION100
1.9646-2.03490.23291420.17262657X-RAY DIFFRACTION100
2.0349-2.11630.18881400.14712607X-RAY DIFFRACTION99
2.1163-2.21270.16521420.13452650X-RAY DIFFRACTION99
2.2127-2.32930.16951420.13492640X-RAY DIFFRACTION99
2.3293-2.47530.16951430.13722684X-RAY DIFFRACTION100
2.4753-2.66640.16091440.14392662X-RAY DIFFRACTION99
2.6664-2.93470.19531430.15292685X-RAY DIFFRACTION99
2.9347-3.35940.17651430.14952672X-RAY DIFFRACTION99
3.3594-4.23240.1561450.12242708X-RAY DIFFRACTION98
4.2324-70.0670.14841530.13632855X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.0168-0.91910.65663.4021-0.3782.87150.022-0.1874-0.06240.17870.10390.16980.1383-0.3376-0.09680.2023-0.03210.02120.23640.01650.1405-0.20120.5435-7.6894
22.0621-0.3542-0.08133.2342-0.1872.2642-0.0551-0.32080.27870.68990.1312-0.1755-0.5262-0.2217-0.03160.38930.0626-0.00260.304-0.05280.22892.550410.7609-0.615
31.2829-0.5875-0.09731.8570.08072.76390.0163-0.08470.04370.14630.0185-0.20.05490.207-0.07690.1614-0.0014-0.01470.1921-0.00040.201910.12762.903-12.4281
41.7721-0.2801-0.28141.9018-0.36421.5490.10680.16490.1109-0.2523-0.08440.1731-0.1136-0.1683-0.01060.2420.0586-0.03260.2434-0.00440.2048-7.713114.4394-34.5149
53.55960.1351.46951.72420.38012.6654-0.0113-0.01310.0667-0.0582-0.0190.04350.0914-0.03690.03630.20590.00530.01220.16790.0070.2133-0.4151.0381-24.7052
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 88 )
2X-RAY DIFFRACTION2chain 'A' and (resid 89 through 142 )
3X-RAY DIFFRACTION3chain 'A' and (resid 143 through 201 )
4X-RAY DIFFRACTION4chain 'A' and (resid 202 through 364 )
5X-RAY DIFFRACTION5chain 'A' and (resid 365 through 416 )

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