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- PDB-5m1r: X-ray structure of human G166D PGK-1 mutant -

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Basic information

Entry
Database: PDB / ID: 5m1r
TitleX-ray structure of human G166D PGK-1 mutant
ComponentsPhosphoglycerate kinase 1
KeywordsTRANSFERASE / Phosphoglycerate kinase / Single Nucleotide Polymorphism derived mutant G166D
Function / homology
Function and homology information


Manipulation of host energy metabolism / phosphoglycerate kinase / phosphoglycerate kinase activity / protein-disulfide reductase (NAD(P)H) activity / Gluconeogenesis / canonical glycolysis / Glycolysis / plasminogen activation / phosphorylation / epithelial cell differentiation ...Manipulation of host energy metabolism / phosphoglycerate kinase / phosphoglycerate kinase activity / protein-disulfide reductase (NAD(P)H) activity / Gluconeogenesis / canonical glycolysis / Glycolysis / plasminogen activation / phosphorylation / epithelial cell differentiation / negative regulation of angiogenesis / gluconeogenesis / glycolytic process / ADP binding / cellular response to hypoxia / membrane raft / extracellular space / extracellular exosome / ATP 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: 1.64 Å
AuthorsIlari, A. / Cipollone, A. / Fiorillo, 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
DepositionOct 10, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 20, 2017Provider: 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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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)45,0754
Polymers44,5991
Non-polymers4763
Water4,306239
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1010 Å2
ΔGint-22 kcal/mol
Surface area17620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.721, 105.570, 50.002
Angle α, β, γ (deg.)90.00, 97.76, 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: 44599.461 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: G166D PGK-1 mutant / 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: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 239 / 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: 1.93 Å3/Da / Density % sol: 35.83 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: Sodium Citrate, 1.6 M / PH range: 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8729 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: May 13, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8729 Å / Relative weight: 1
ReflectionResolution: 1.64→60 Å / Num. obs: 44562 / % possible obs: 98.7 % / Redundancy: 3.7 % / Biso Wilson estimate: 27.4 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.097 / Net I/σ(I): 7.84
Reflection shellResolution: 1.64→1.74 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 1.82 / CC1/2: 0.688 / % possible all: 97.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ZGV

2zgv


Resolution: 1.64→52.78 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.957 / SU B: 2.174 / SU ML: 0.072 / Cross valid method: THROUGHOUT / ESU R: 0.096 / ESU R Free: 0.096 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20095 2196 4.9 %RANDOM
Rwork0.16425 ---
obs0.16601 42334 98.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 21.517 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å20 Å20.3 Å2
2---0.96 Å20 Å2
3---0.9 Å2
Refinement stepCycle: 1 / Resolution: 1.64→52.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3120 0 29 240 3389
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0193270
X-RAY DIFFRACTIONr_bond_other_d0.0020.023214
X-RAY DIFFRACTIONr_angle_refined_deg1.6671.9994430
X-RAY DIFFRACTIONr_angle_other_deg0.96837448
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.9495429
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.48925.887124
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.05815597
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4231511
X-RAY DIFFRACTIONr_chiral_restr0.0920.2505
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213662
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02661
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_it1.4791.9051677
X-RAY DIFFRACTIONr_mcbond_other1.4691.9031676
X-RAY DIFFRACTIONr_mcangle_it2.3512.8532098
X-RAY DIFFRACTIONr_mcangle_other2.3512.8542099
X-RAY DIFFRACTIONr_scbond_it2.2752.2311593
X-RAY DIFFRACTIONr_scbond_other2.2742.2311594
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.6743.2082326
X-RAY DIFFRACTIONr_long_range_B_refined5.53123.6823597
X-RAY DIFFRACTIONr_long_range_B_other5.47923.383551
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.637→1.68 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 169 -
Rwork0.259 3006 -
obs--95.83 %

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