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- PDB-4r77: Crystal structure of choline kinase LicA from Streptococcus pneumoniae -

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Basic information

Entry
Database: PDB / ID: 4r77
TitleCrystal structure of choline kinase LicA from Streptococcus pneumoniae
ComponentsCholine kinase
KeywordsTRANSFERASE / a protein kinase-like fold / choline/ethanolamine kinase / ATP/choline binding
Function / homology
Function and homology information


choline kinase activity / kinase activity / nucleotide binding
Similarity search - Function
: / 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
Choline kinase / Choline kinase
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.94 Å
AuthorsWang, L. / Jiang, Y.L. / Zhou, C.Z. / Chen, Y.X.
CitationJournal: Plos One / Year: 2015
Title: Structural and enzymatic characterization of the choline kinase LicA from Streptococcus pneumoniae
Authors: Wang, L. / Jiang, Y.L. / Zhang, J.R. / Zhou, C.Z. / Chen, Y.X.
History
DepositionAug 27, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 12, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Choline kinase
A: Choline kinase


Theoretical massNumber of molelcules
Total (without water)71,2222
Polymers71,2222
Non-polymers00
Water5,116284
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Choline kinase


Theoretical massNumber of molelcules
Total (without water)35,6111
Polymers35,6111
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
A: Choline kinase


Theoretical massNumber of molelcules
Total (without water)35,6111
Polymers35,6111
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)69.347, 96.466, 97.590
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Choline kinase


Mass: 35610.867 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Gene: licA / Production host: Escherichia coli (E. coli)
References: UniProt: Q93MI3, UniProt: Q8DPI4*PLUS, choline kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 284 / 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: 2.29 Å3/Da / Density % sol: 46.32 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M HEPES, 1.2M sodium citrate, 4% glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97923 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 15, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97923 Å / Relative weight: 1
ReflectionResolution: 1.94→50 Å / Num. all: 47710 / Num. obs: 47710 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shellResolution: 1.94→2.01 Å / Redundancy: 3 % / Rmerge(I) obs: 0.529 / Mean I/σ(I) obs: 2.8 / Rsym value: 0.529 / % possible all: 97.8

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.5.0110refinement
HKL-2000data reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.94→36.88 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.926 / SU B: 4.121 / SU ML: 0.118 / Cross valid method: THROUGHOUT / ESU R: 0.181 / ESU R Free: 0.167 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25452 2395 5 %RANDOM
Rwork0.20805 ---
obs0.2104 45131 96.97 %-
all-46551 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.183 Å2
Baniso -1Baniso -2Baniso -3
1-1.58 Å20 Å20 Å2
2---1.5 Å20 Å2
3----0.08 Å2
Refinement stepCycle: LAST / Resolution: 1.94→36.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4591 0 0 284 4875
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0224683
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1041.9656320
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3475557
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.77525.451233
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.98215876
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6031516
X-RAY DIFFRACTIONr_chiral_restr0.0770.2693
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023500
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6051.52789
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.17524512
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.71731894
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.8954.51808
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: 1.942→1.992 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 162 -
Rwork0.284 3325 -
obs--97.35 %

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