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- PDB-2xe7: The complete reaction cycle of human phosphoglycerate kinase: The... -

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Basic information

Entry
Database: PDB / ID: 2xe7
TitleThe complete reaction cycle of human phosphoglycerate kinase: The open ternary complex with 3PG and ADP
ComponentsPHOSPHOGLYCERATE KINASE 1
KeywordsTRANSFERASE / TRANSITION STATE ANALOGUE / HEREDITARY HEMOLYTIC ANEMIA / PHOSPHOPROTEIN / GLYCOLYSIS / PHOSPHORYL TRANSFER / NUCLEOTIDE-BINDING / DOMAIN MOTIONS
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, 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
3-PHOSPHOGLYCERIC ACID / ADENOSINE-5'-DIPHOSPHATE / Phosphoglycerate kinase 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsCliff, M.J. / Baxter, N.J. / Blackburn, G.M. / Merli, A. / Vas, M. / Waltho, J.P. / Bowler, M.W.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: A Spring Loaded Release Mechanism Regulates Domain Movement and Catalysis in Phosphoglycerate Kinase.
Authors: Zerrad, L. / Merli, A. / Schroder, G.F. / Varga, A. / Graczer, E. / Pernot, P. / Round, A. / Vas, M. / Bowler, M.W.
History
DepositionMay 11, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 19, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 26, 2011Group: Database references / Version format compliance
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)45,2863
Polymers44,6731
Non-polymers6132
Water1,15364
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.620, 73.450, 93.440
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein PHOSPHOGLYCERATE KINASE 1 / PRIMER RECOGNITION PROTEIN 2 / PRP 2 / CELL MIGRATION-INDUCING GENE 10 PROTEIN


Mass: 44672.621 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET22A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P00558, phosphoglycerate kinase
#2: Chemical ChemComp-3PG / 3-PHOSPHOGLYCERIC ACID


Mass: 186.057 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7O7P
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / 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: 2.15 Å3/Da / Density % sol: 42.8 % / Description: NONE
Crystal growpH: 8 / Details: 30% PEG4000, 100MM TRIS PH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Jun 26, 2009 / Details: GE 221
RadiationMonochromator: DIAMOND 110 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. obs: 20841 / % possible obs: 99.1 % / Observed criterion σ(I): 3 / Redundancy: 3.9 % / Biso Wilson estimate: 32.8 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 12.8
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 4 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 4 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3C39

3c39


Resolution: 2.2→20 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.886 / SU B: 10.949 / SU ML: 0.231 / Cross valid method: THROUGHOUT / ESU R: 0.347 / ESU R Free: 0.262 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS
RfactorNum. reflection% reflectionSelection details
Rfree0.28829 1050 5 %RANDOM
Rwork0.22439 ---
obs0.22757 19766 98.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.974 Å2
Baniso -1Baniso -2Baniso -3
1-1.51 Å20 Å20 Å2
2--0.99 Å20 Å2
3----2.51 Å2
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3096 0 38 64 3198
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0223216
X-RAY DIFFRACTIONr_bond_other_d0.0010.022190
X-RAY DIFFRACTIONr_angle_refined_deg1.6211.9924337
X-RAY DIFFRACTIONr_angle_other_deg0.91535405
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.695415
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.56525.785121
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.9415586
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3931511
X-RAY DIFFRACTIONr_chiral_restr0.0820.2495
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213525
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02573
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6731.52060
X-RAY DIFFRACTIONr_mcbond_other0.1621.5857
X-RAY DIFFRACTIONr_mcangle_it1.21723293
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.08131156
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.2594.51043
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.256 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.375 88 -
Rwork0.302 1441 -
obs--99.87 %
Refinement TLS params.Method: refined / Origin x: 13.588 Å / Origin y: -20.151 Å / Origin z: -33.613 Å
111213212223313233
T0.0925 Å2-0.1807 Å2-0.0301 Å2-0.3252 Å20.0462 Å2--0.0029 Å2
L3.1756 °20.373 °20.9744 °2-3.3453 °20.1785 °2--4.711 °2
S-0.0825 Å °0.6285 Å °0.1308 Å °-0.096 Å °0.1399 Å °0.0098 Å °-0.5616 Å °0.6635 Å °-0.0574 Å °

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