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- PDB-7zzi: Plasmodium falciparum hexokinase complexed with glucose and citrate -

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Basic information

Entry
Database: PDB / ID: 7zzi
TitlePlasmodium falciparum hexokinase complexed with glucose and citrate
ComponentsPhosphotransferase
KeywordsTRANSFERASE / glycolysis / hexokinase / phosphotransferase / actin-like ATPase
Function / homology
Function and homology information


hexokinase activity / Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor / D-glucose binding / intracellular glucose homeostasis / glycolytic process / ATP binding
Similarity search - Function
Hexokinase / Hexokinase, binding site / Hexokinase, N-terminal / Hexokinase, C-terminal / Hexokinase / Hexokinase / Hexokinase domain signature. / Hexokinase domain profile. / ATPase, nucleotide binding domain
Similarity search - Domain/homology
CITRIC ACID / alpha-D-glucopyranose / TRIETHYLENE GLYCOL / Phosphotransferase
Similarity search - Component
Biological speciesPlasmodium (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsFritz-Wolf, K. / Dillenberger, M. / Rahlfs, S. / Becker, K.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)BE1540/23 2 Germany
CitationJournal: Int J Mol Sci / Year: 2023
Title: Structural Analysis of Plasmodium falciparum Hexokinase Provides Novel Information about Catalysis Due to a Plasmodium -Specific Insertion.
Authors: Dillenberger, M. / Werner, A.D. / Velten, A.S. / Rahlfs, S. / Becker, K. / Fritz-Wolf, K.
History
DepositionMay 25, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 30, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phosphotransferase
B: Phosphotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,80311
Polymers110,6602
Non-polymers1,1439
Water43224
1
A: Phosphotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,0196
Polymers55,3301
Non-polymers6895
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Phosphotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,7855
Polymers55,3301
Non-polymers4544
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)125.240, 125.240, 120.930
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11A-503-

EDO

21A-503-

EDO

31B-503-

EDO

41B-503-

EDO

51B-608-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 24 through 486 or resid 701))
d_2ens_1(chain "B" and (resid 24 through 486 or resid 1301))

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11PROPROASNASNAA24 - 48624 - 486
d_12EDOEDOEDOEDOAE503
d_21PROPROASNASNBB24 - 48624 - 486
d_22EDOEDOEDOEDOBK504

NCS oper: (Code: givenMatrix: (-0.993642826891, 0.077810745027, -0.0813598213216), (-0.0322578738098, -0.889176698113, -0.456425491302), (-0.107858064809, -0.450899420593, 0.886034057113)Vector: 140. ...NCS oper: (Code: given
Matrix: (-0.993642826891, 0.077810745027, -0.0813598213216), (-0.0322578738098, -0.889176698113, -0.456425491302), (-0.107858064809, -0.450899420593, 0.886034057113)
Vector: 140.774217359, 19.5243238713, 11.3613079115)

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Components

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Protein / Sugars , 2 types, 4 molecules AB

#1: Protein Phosphotransferase


Mass: 55330.094 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium (eukaryote) / Strain: isolate NF54 / Gene: CK202_5141, PFNF54_05159 / Production host: Escherichia coli (E. coli)
References: UniProt: W7JZC2, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor
#2: Sugar ChemComp-GLC / alpha-D-glucopyranose / alpha-D-glucose / D-glucose / glucose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranoseCOMMON NAMEGMML 1.0
a-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 31 molecules

#3: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 50.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 20% PEG 3350, 200 mM sodium citrate, 0.1 mM sodium citrate buffer (pH 3.4-4.0), 10 mM glucose, 10 mM ATP, 5 mM DTT
PH range: 3.4-4.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 17, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.796→49.48 Å / Num. obs: 27459 / % possible obs: 99.67 % / Redundancy: 10.1 % / Biso Wilson estimate: 95.84 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.1198 / Net I/σ(I): 13.1
Reflection shellResolution: 2.796→2.896 Å / Rmerge(I) obs: 3.411 / Num. unique obs: 2644 / CC1/2: 0.305

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PHENIX1.19.2_4158refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6VYG

6vyg


Resolution: 2.8→49.48 Å / SU ML: 0.5384 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.6589
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2677 2746 10 %
Rwork0.1992 24710 -
obs0.206 27456 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 89.78 Å2
Refinement stepCycle: LAST / Resolution: 2.8→49.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7321 0 76 24 7421
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01017548
X-RAY DIFFRACTIONf_angle_d1.170110177
X-RAY DIFFRACTIONf_chiral_restr0.05971108
X-RAY DIFFRACTIONf_plane_restr0.00871296
X-RAY DIFFRACTIONf_dihedral_angle_d16.72272763
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 2.16061356931 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.840.49071280.47221155X-RAY DIFFRACTION94.2
2.84-2.90.47281360.39051225X-RAY DIFFRACTION100
2.9-2.950.4041360.34521220X-RAY DIFFRACTION99.85
2.95-3.010.36661350.311210X-RAY DIFFRACTION99.93
3.01-3.080.35531340.3071209X-RAY DIFFRACTION100
3.08-3.150.37631380.27951245X-RAY DIFFRACTION100
3.15-3.230.3331370.24231227X-RAY DIFFRACTION100
3.23-3.310.33391350.24281215X-RAY DIFFRACTION99.93
3.31-3.410.31521370.24021240X-RAY DIFFRACTION100
3.41-3.520.30561350.24751212X-RAY DIFFRACTION100
3.52-3.650.30241380.2361241X-RAY DIFFRACTION100
3.65-3.790.27121370.19471236X-RAY DIFFRACTION100
3.79-3.970.28251370.18121235X-RAY DIFFRACTION100
3.97-4.180.26281380.18171238X-RAY DIFFRACTION100
4.18-4.440.23441360.1781227X-RAY DIFFRACTION100
4.44-4.780.24481400.16861253X-RAY DIFFRACTION100
4.78-5.260.2771390.17321257X-RAY DIFFRACTION100
5.26-6.020.26851400.18861260X-RAY DIFFRACTION100
6.02-7.580.24991410.19311269X-RAY DIFFRACTION100
7.59-49.480.19931490.16291336X-RAY DIFFRACTION100

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