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- PDB-2w40: Crystal structure of Plasmodium falciparum glycerol kinase with b... -

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Basic information

Entry
Database: PDB / ID: 2w40
TitleCrystal structure of Plasmodium falciparum glycerol kinase with bound glycerol
ComponentsGLYCEROL KINASE, PUTATIVE
KeywordsTRANSFERASE / CLOSED CONFORMATION / KINASE / MALARIA / PLASMODIUM / SUGAR KINASE/HSP70/ACTIN SUPERFAMILY / GLYCEROL KINASE / OPEN CONFORMATION
Function / homology
Function and homology information


Triglyceride biosynthesis / glycerol-3-phosphate biosynthetic process / glycerol kinase / glycerol kinase activity / glycerol metabolic process / glycerol catabolic process / triglyceride metabolic process / mitochondrion / ATP binding
Similarity search - Function
Glycerol kinase, metazoa / FGGY family of carbohydrate kinases signature 1. / Glycerol kinase / FGGY family of carbohydrate kinases signature 2. / Carbohydrate kinase, FGGY, conserved site / Carbohydrate kinase, FGGY / Carbohydrate kinase, FGGY, N-terminal / FGGY family of carbohydrate kinases, N-terminal domain / Carbohydrate kinase, FGGY, C-terminal / FGGY family of carbohydrate kinases, C-terminal domain ...Glycerol kinase, metazoa / FGGY family of carbohydrate kinases signature 1. / Glycerol kinase / FGGY family of carbohydrate kinases signature 2. / Carbohydrate kinase, FGGY, conserved site / Carbohydrate kinase, FGGY / Carbohydrate kinase, FGGY, N-terminal / FGGY family of carbohydrate kinases, N-terminal domain / Carbohydrate kinase, FGGY, C-terminal / FGGY family of carbohydrate kinases, C-terminal domain / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesPLASMODIUM FALCIPARUM (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 Å
AuthorsSchnick, C. / Polley, S.D. / Fivelman, Q.L. / Ranford-Cartwright, L. / Wilkinson, S.R. / Brannigan, J.A. / Wilkinson, A.J. / Baker, D.A.
CitationJournal: Mol.Microbiol. / Year: 2009
Title: Structure and Non-Essential Function of Glycerol Kinase in Plasmodium Falciparum Blood Stages.
Authors: Schnick, C. / Polley, S.D. / Fivelman, Q.L. / Ranford-Cartwright, L. / Wilkinson, S.R. / Brannigan, J.A. / Wilkinson, A.J. / Baker, D.A.
History
DepositionNov 18, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 2, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GLYCEROL KINASE, PUTATIVE
B: GLYCEROL KINASE, PUTATIVE
C: GLYCEROL KINASE, PUTATIVE
D: GLYCEROL KINASE, PUTATIVE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)232,38978
Polymers227,4364
Non-polymers4,95374
Water34,7511929
1
A: GLYCEROL KINASE, PUTATIVE
C: GLYCEROL KINASE, PUTATIVE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,28539
Polymers113,7182
Non-polymers2,56737
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4500 Å2
ΔGint-36.9 kcal/mol
Surface area43170 Å2
MethodPQS
2
B: GLYCEROL KINASE, PUTATIVE
D: GLYCEROL KINASE, PUTATIVE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,10439
Polymers113,7182
Non-polymers2,38737
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4320 Å2
ΔGint-26.8 kcal/mol
Surface area43080 Å2
MethodPQS
Unit cell
Length a, b, c (Å)101.915, 100.717, 107.812
Angle α, β, γ (deg.)90.00, 92.56, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
GLYCEROL KINASE, PUTATIVE


Mass: 56858.887 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PLASMODIUM FALCIPARUM (malaria parasite P. falciparum)
Strain: 3D7 / Plasmid: PMAL-C2X / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q8IDI4, glycerol kinase
#2: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 62 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1929 / 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: 2.44 Å3/Da / Density % sol: 49.6 % / Description: NONE
Crystal growpH: 7.5
Details: 20% PEG 3350, 50 MM KFORMATE, 25 % ETHYLENE GLYCOL, 10 MM LDAO, 20 MM GLYCEROL, pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Jul 24, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.49→107.83 Å / Num. obs: 260542 / % possible obs: 73.5 % / Observed criterion σ(I): 2 / Redundancy: 4.3 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 12
Reflection shellResolution: 1.49→1.53 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 2.23 / % possible all: 18

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BU6

1bu6


Resolution: 1.49→107.83 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.952 / SU B: 2.689 / SU ML: 0.047 / Cross valid method: THROUGHOUT / ESU R: 0.132 / ESU R Free: 0.096 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.21 13131 5 %RANDOM
Rwork0.168 ---
obs0.171 247410 73.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.27 Å2
Baniso -1Baniso -2Baniso -3
1-1.07 Å20 Å20.08 Å2
2---1 Å20 Å2
3----0.06 Å2
Refinement stepCycle: LAST / Resolution: 1.49→107.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15930 0 320 1929 18179
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.02216453
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3891.95522228
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.02652050
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.16825.436723
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.888153001
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9231558
X-RAY DIFFRACTIONr_chiral_restr0.0980.22543
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212046
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2030.28043
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3040.211560
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1580.21691
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1930.288
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2060.261
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2531.510328
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.815216324
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.69637031
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.9874.55879
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.49→1.53 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.348 234
Rwork0.239 4484

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