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- PDB-2qg7: Plasmodium vivax ethanolamine kinase Pv091845 -

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Basic information

Entry
Database: PDB / ID: 2qg7
TitlePlasmodium vivax ethanolamine kinase Pv091845
Componentsethanolamine kinase Pv091845
KeywordsTRANSFERASE / malaria / ethanolamine kinase / Pv091845 / SGC / Structural Genomics Consortium
Function / homology
Function and homology information


Choline/ethanolamine kinase / Aminoglycoside 3'-phosphotransferase; Chain: A, domain 2 / Aminoglycoside phosphotransferase (APH), C-terminal lobe / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Protein kinase-like domain superfamily / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Ethanolamine kinase, putative
Similarity search - Component
Biological speciesPlasmodium vivax (malaria parasite P. vivax)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.407 Å
AuthorsLunin, V.V. / Wernimont, A.K. / Mulichak, A. / Lew, J. / Wasney, G. / Senisterra, G. / Kozieradzki, I. / Vedadi, M. / Bochkarev, A. / Arrowsmith, C.H. ...Lunin, V.V. / Wernimont, A.K. / Mulichak, A. / Lew, J. / Wasney, G. / Senisterra, G. / Kozieradzki, I. / Vedadi, M. / Bochkarev, A. / Arrowsmith, C.H. / Sundstrom, M. / Weigelt, J. / Edwards, A.E. / Hui, R. / Hills, T. / Artz, J. / Xiao, T. / Structural Genomics Consortium (SGC)
CitationJournal: TO BE PUBLISHED
Title: Plasmodium vivax ethanolamine kinase Pv091845
Authors: Lunin, V.V. / Wernimont, A.K. / Mulichak, A. / Lew, J. / Wasney, G. / Senisterra, G. / Kozieradzki, I. / Vedadi, M. / Bochkarev, A. / Arrowsmith, C.H. / Sundstrom, M. / Weigelt, J. / ...Authors: Lunin, V.V. / Wernimont, A.K. / Mulichak, A. / Lew, J. / Wasney, G. / Senisterra, G. / Kozieradzki, I. / Vedadi, M. / Bochkarev, A. / Arrowsmith, C.H. / Sundstrom, M. / Weigelt, J. / Edwards, A.E. / Hui, R. / Hills, T. / Artz, J. / Xiao, T.
History
DepositionJun 28, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 30, 2023Group: 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ethanolamine kinase Pv091845
B: ethanolamine kinase Pv091845
D: ethanolamine kinase Pv091845
E: ethanolamine kinase Pv091845
hetero molecules


Theoretical massNumber of molelcules
Total (without water)209,5375
Polymers209,4414
Non-polymers961
Water8,215456
1
A: ethanolamine kinase Pv091845
E: ethanolamine kinase Pv091845
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,8163
Polymers104,7202
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2750 Å2
ΔGint-41 kcal/mol
Surface area33260 Å2
MethodPISA
2
B: ethanolamine kinase Pv091845
D: ethanolamine kinase Pv091845


Theoretical massNumber of molelcules
Total (without water)104,7202
Polymers104,7202
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2500 Å2
ΔGint-21 kcal/mol
Surface area33560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.031, 172.702, 93.353
Angle α, β, γ (deg.)90.00, 110.72, 90.00
Int Tables number4
Space group name H-MP1211
DetailsOne dimer is formed by molecules A and E, another by molecules B and D

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Components

#1: Protein
ethanolamine kinase Pv091845


Mass: 52360.160 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium vivax (malaria parasite P. vivax)
Plasmid: p15-mhl / Production host: Escherichia coli (E. coli) / Strain (production host): dh5a / References: UniProt: A5K4Q6
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 456 / 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: 2.77 Å3/Da / Density % sol: 55.63 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.4M Na Citrate, 0.1M Hepes pH7.5, 2mM TCEP, 1mM MgCl2, 4mm CaCl2, 4mM ethanolamine chloride, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-BM / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Mar 10, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 85067 / Num. obs: 85067 / % possible obs: 95.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rsym value: 0.058 / Net I/σ(I): 20.28
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 1.4 % / Mean I/σ(I) obs: 2 / Num. unique all: 5104 / Rsym value: 0.262 / % possible all: 57.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCQuantumdata collection
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2CK0

2ck0


Resolution: 2.407→24.93 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.9 / SU B: 11.577 / SU ML: 0.266 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.371 / ESU R Free: 0.285 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28974 4237 5 %RANDOM
Rwork0.23011 ---
all0.2331 80452 --
obs0.2331 80452 96.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 61.755 Å2
Baniso -1Baniso -2Baniso -3
1--0.56 Å20 Å21.16 Å2
2--1.83 Å20 Å2
3----0.45 Å2
Refinement stepCycle: LAST / Resolution: 2.407→24.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12177 0 5 456 12638
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.02212437
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3421.96116759
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.74851455
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.76124.694620
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.331152347
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2941559
X-RAY DIFFRACTIONr_chiral_restr0.0930.21829
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.029259
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1810.25448
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2990.28557
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1340.2504
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1510.270
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1950.221
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3491.57566
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.67211886
X-RAY DIFFRACTIONr_scbond_it2.52335399
X-RAY DIFFRACTIONr_scangle_it3.6324.54873
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.407→2.47 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.373 201 -
Rwork0.311 3940 -
obs--63.98 %

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