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- PDB-5o7d: The X-ray structure of human R38M phosphoglycerate kinase 1 mutant -

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Basic information

Entry
Database: PDB / ID: 5o7d
TitleThe X-ray structure of human R38M phosphoglycerate kinase 1 mutant
ComponentsPhosphoglycerate kinase 1
KeywordsTRANSFERASE
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
ADENOSINE-5'-DIPHOSPHATE / Phosphoglycerate kinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 Å
AuthorsIlari, A. / Fiorillo, A. / Cipollone, A. / Petrosino, M.
CitationJournal: PLoS ONE / Year: 2018
Title: The phosphoglycerate kinase 1 variants found in carcinoma cells display different catalytic activity and conformational stability compared to the native enzyme.
Authors: Fiorillo, A. / Petrosino, M. / Ilari, A. / Pasquo, A. / Cipollone, A. / Maggi, M. / Chiaraluce, R. / Consalvi, V.
History
DepositionJun 8, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 20, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 12, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)45,0742
Polymers44,6471
Non-polymers4271
Water1,09961
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: already characterized
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area740 Å2
ΔGint-3 kcal/mol
Surface area18030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.050, 106.680, 50.690
Angle α, β, γ (deg.)90.00, 97.32, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 44646.621 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 (E. coli) / References: UniProt: P00558, phosphoglycerate kinase
#2: 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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 61 / 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: 2.18 Å3/Da / Density % sol: 43.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG2K-MME 28-34%, bis-tris 0.1M pH 7 / PH range: 6.5-7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 29, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 1.84→50 Å / Num. obs: 31685 / % possible obs: 96.1 % / Redundancy: 6.9 % / CC1/2: 0.996 / Rmerge(I) obs: 0.155 / Rpim(I) all: 0.097 / Net I/σ(I): 10.5
Reflection shellResolution: 1.84→1.871 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.8 / Num. unique obs: 1650 / CC1/2: 0.367 / Rpim(I) all: 0.501 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2x13

2x13


Resolution: 1.84→50 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.903 / SU B: 5.038 / SU ML: 0.145 / Cross valid method: THROUGHOUT / ESU R: 0.183 / ESU R Free: 0.164 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26684 1480 4.7 %RANDOM
Rwork0.22573 ---
obs0.22765 30205 96.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 21.544 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å2-0 Å2-0.62 Å2
2---1.16 Å2-0 Å2
3---1.29 Å2
Refinement stepCycle: 1 / Resolution: 1.84→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3107 0 27 61 3195
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0193185
X-RAY DIFFRACTIONr_bond_other_d0.0020.023154
X-RAY DIFFRACTIONr_angle_refined_deg1.4721.9884298
X-RAY DIFFRACTIONr_angle_other_deg0.92537296
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9635414
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.24125.847118
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.10815581
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5321510
X-RAY DIFFRACTIONr_chiral_restr0.0780.2492
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213562
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02641
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_it1.2092.0421659
X-RAY DIFFRACTIONr_mcbond_other1.2082.0411658
X-RAY DIFFRACTIONr_mcangle_it1.9593.0562072
X-RAY DIFFRACTIONr_mcangle_other1.9593.0572073
X-RAY DIFFRACTIONr_scbond_it1.5242.2471526
X-RAY DIFFRACTIONr_scbond_other1.5242.2471527
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.4693.2872227
X-RAY DIFFRACTIONr_long_range_B_refined3.54815.9343453
X-RAY DIFFRACTIONr_long_range_B_other3.54315.9373442
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.839→1.887 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.366 120 -
Rwork0.363 2297 -
obs--99.83 %

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