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- PDB-2w41: Crystal structure of Plasmodium falciparum glycerol kinase with ADP -

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Basic information

Entry
Database: PDB / ID: 2w41
TitleCrystal structure of Plasmodium falciparum glycerol kinase with ADP
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
ADENOSINE-5'-DIPHOSPHATE / glycerol kinase
Similarity search - Component
Biological speciesPLASMODIUM FALCIPARUM (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.41 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,82925
Polymers114,6712
Non-polymers2,15823
Water5,531307
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3240 Å2
ΔGint-22.8 kcal/mol
Surface area48060 Å2
MethodPQS
Unit cell
Length a, b, c (Å)82.529, 57.632, 123.922
Angle α, β, γ (deg.)90.00, 89.75, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 1 / Auth seq-ID: 1 - 501 / Label seq-ID: 7 - 507

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein GLYCEROL KINASE, PUTATIVE


Mass: 57335.402 Da / Num. of mol.: 2
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-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 307 / 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: 2.6 Å3/Da / Density % sol: 52.7 % / Description: NONE
Crystal growpH: 7.5
Details: 50MM KFORMATE, 20% PEG 3350, 25% ETHYLENE GLYCOL, 10MM LDAO, 20MM GLYCEROL, THEN SOAKED WITH 5 MM ADP AND 10 MM MGCL2, 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: Sep 14, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.41→124.03 Å / Num. obs: 39660 / % possible obs: 91.4 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 10.95
Reflection shellResolution: 2.41→2.47 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.84 / Mean I/σ(I) obs: 0.71 / % possible all: 40.5

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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: 2.41→124.03 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.912 / SU B: 9.415 / SU ML: 0.219 / Cross valid method: THROUGHOUT / ESU R: 0.598 / ESU R Free: 0.301 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.258 2120 5.1 %RANDOM
Rwork0.197 ---
obs0.2 39660 91.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.23 Å2
Baniso -1Baniso -2Baniso -3
1--0.28 Å20 Å2-0.05 Å2
2---1.22 Å20 Å2
3---1.49 Å2
Refinement stepCycle: LAST / Resolution: 2.41→124.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8032 0 138 307 8477
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0228291
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.771.96211187
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.40551011
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.37425.444360
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.968151502
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.111528
X-RAY DIFFRACTIONr_chiral_restr0.1140.21274
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026034
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2120.23542
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3050.25575
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1930.2305
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1880.244
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1580.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8391.55194
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.43328166
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.31733607
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.5994.53021
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
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 3968 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
tight positional0.060.05
tight thermal0.110.5
LS refinement shellResolution: 2.4→2.47 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.416 66
Rwork0.283 1280

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