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- PDB-5m6z: The X-ray structure of human M189I PGK-1 mutant in partially clos... -

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Basic information

Entry
Database: PDB / ID: 5m6z
TitleThe X-ray structure of human M189I PGK-1 mutant in partially closed conformation
ComponentsPhosphoglycerate kinase 1
KeywordsTRANSFERASE / human phosphoglycerate kinase 1 / M189I SNP -derived mutant
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 / epithelial cell differentiation / negative regulation of angiogenesis ...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 / ADP binding / gluconeogenesis / glycolytic process / cellular response to hypoxia / membrane raft / phosphorylation / 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
3-PHOSPHOGLYCERIC ACID / ADENOSINE-5'-DIPHOSPHATE / PHOSPHATE ION / Phosphoglycerate kinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.67 Å
AuthorsIlari, A. / Fiorillo, A. / Petrosino, M. / Cipollone, A.
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 26, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 29, 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_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)45,2806
Polymers44,5231
Non-polymers7575
Water3,603200
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1670 Å2
ΔGint-34 kcal/mol
Surface area17650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.880, 106.121, 50.472
Angle α, β, γ (deg.)90.00, 98.13, 90.00
Int Tables number4
Space group name H-MP1211

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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: 44523.387 Da / Num. of mol.: 1 / Mutation: M189I
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

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Non-polymers , 5 types, 205 molecules

#2: Chemical ChemComp-3PG / 3-PHOSPHOGLYCERIC ACID / 3-Phosphoglyceric acid


Mass: 186.057 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7O7P
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#5: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 200 / 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: 2.02 Å3/Da / Density % sol: 38.51 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8.6 / Details: 2.5 M Na//KPO4, pH=8.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.872899 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: 0.872899 Å / Relative weight: 1
ReflectionResolution: 1.67→60 Å / Num. obs: 42601 / % possible obs: 97.5 % / Redundancy: 4.26 % / CC1/2: 0.99 / Rmerge(I) obs: 0.054 / Net I/σ(I): 15.08
Reflection shellResolution: 1.67→1.77 Å / Redundancy: 4.18 % / Rmerge(I) obs: 0.675 / Mean I/σ(I) obs: 1.89 / CC1/2: 0.59 / % possible all: 94.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ZGV
Resolution: 1.67→53.06 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.949 / SU B: 2.867 / SU ML: 0.092 / Cross valid method: THROUGHOUT / ESU R: 0.111 / ESU R Free: 0.11 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22295 2181 5.1 %RANDOM
Rwork0.18281 ---
obs0.18488 40389 97.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 27.804 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å2-0 Å2-0.02 Å2
2---1 Å2-0 Å2
3---1.07 Å2
Refinement stepCycle: 1 / Resolution: 1.67→53.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3116 0 45 200 3361
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0193218
X-RAY DIFFRACTIONr_bond_other_d0.0020.023173
X-RAY DIFFRACTIONr_angle_refined_deg1.5581.9924346
X-RAY DIFFRACTIONr_angle_other_deg0.95737341
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1535417
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.57525.75120
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.57315583
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9751511
X-RAY DIFFRACTIONr_chiral_restr0.0850.2496
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213596
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02648
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_it1.7942.5411668
X-RAY DIFFRACTIONr_mcbond_other1.7932.5391667
X-RAY DIFFRACTIONr_mcangle_it2.7273.8052085
X-RAY DIFFRACTIONr_mcangle_other2.7273.8072086
X-RAY DIFFRACTIONr_scbond_it2.6252.9161550
X-RAY DIFFRACTIONr_scbond_other2.6242.9151551
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.1294.2292262
X-RAY DIFFRACTIONr_long_range_B_refined5.60431.1013482
X-RAY DIFFRACTIONr_long_range_B_other5.60431.0963483
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.667→1.71 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 156 -
Rwork0.301 2841 -
obs--92.67 %

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