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- PDB-6y3a: Structure of Plasmodium vivax phosphoglycerate kinase -

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Basic information

Entry
Database: PDB / ID: 6y3a
TitleStructure of Plasmodium vivax phosphoglycerate kinase
ComponentsPhosphoglycerate kinase
KeywordsBIOSYNTHETIC PROTEIN / phosphoglycerate kinase / metabolic enzyme / kinase
Function / homology
Function and homology information


phosphoglycerate kinase / phosphoglycerate kinase activity / glycolytic process / ATP binding
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
BROMIDE ION / : / Phosphoglycerate kinase
Similarity search - Component
Biological speciesPlasmodium vivax (malaria parasite P. vivax)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 Å
AuthorsBlaszczyk, B.K. / Hyvonen, M.
CitationJournal: to be published
Title: Phosphoglycerate Kinase as a potential target for antimalarial therapy
Authors: Bilsland, E. / Costa, F. / Blaszczyk, B.K. / Hyvonen, M. / Sunnerhagen, P.
History
DepositionFeb 17, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 26, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phosphoglycerate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3653
Polymers46,2461
Non-polymers1192
Water8,485471
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area260 Å2
ΔGint0 kcal/mol
Surface area19100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.340, 84.120, 125.520
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Phosphoglycerate kinase


Mass: 46246.176 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium vivax (malaria parasite P. vivax)
Gene: PVX_099535 / Plasmid: pHAT2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A5K6T9, phosphoglycerate kinase
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Br
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 471 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.47 Å3/Da / Density % sol: 50.26 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 7.4 / Details: 20% PEG-MME 2K, 0.15 M KBr

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92818 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 20, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92818 Å / Relative weight: 1
ReflectionResolution: 1.49→69.88 Å / Num. obs: 74103 / % possible obs: 99.8 % / Redundancy: 5.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.027 / Rrim(I) all: 0.068 / Net I/σ(I): 14 / Num. measured all: 428316 / Scaling rejects: 5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.49-1.534.11.14153980.5080.6331.31199.5
6.66-69.885.50.0349570.9980.0150.03899.2

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
Aimless0.5.15data scaling
PDB_EXTRACT3.23data extraction
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ltk

1ltk


Resolution: 1.49→69.879 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.82
RfactorNum. reflection% reflection
Rfree0.1953 3657 4.94 %
Rwork0.1632 --
obs0.1648 74019 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 84.68 Å2 / Biso mean: 27.4428 Å2 / Biso min: 11.4 Å2
Refinement stepCycle: final / Resolution: 1.49→69.879 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3168 0 2 471 3641
Biso mean--42.21 36.78 -
Num. residues----416
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.49-1.50960.28321350.23962697100
1.5096-1.53030.34751610.2381262499
1.5303-1.55220.30061380.24262299
1.5522-1.57530.25041320.21762704100
1.5753-1.60.26691350.20822632100
1.6-1.62620.29071340.20272712100
1.6262-1.65420.25441200.19022684100
1.6542-1.68430.22511260.1762702100
1.6843-1.71670.2481540.16542670100
1.7167-1.75180.20241260.15272679100
1.7518-1.78980.22321390.15422681100
1.7898-1.83150.22191400.14422676100
1.8315-1.87730.19851300.15432695100
1.8773-1.9280.22961560.15672710100
1.928-1.98480.20291500.16142657100
1.9848-2.04890.20871380.16522697100
2.0489-2.12210.20431390.16082719100
2.1221-2.20710.17861370.15452709100
2.2071-2.30750.19691450.15412697100
2.3075-2.42920.21611190.16182721100
2.4292-2.58140.19621500.16782724100
2.5814-2.78070.20981380.17182746100
2.7807-3.06050.15971360.17282762100
3.0605-3.50340.18451530.1642756100
3.5034-4.41380.1641610.14482763100
4.4138-69.8790.17711650.15572923100

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