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- PDB-4r7b: Crystal structure of pneumococcal LicA in complex with choline -

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Basic information

Entry
Database: PDB / ID: 4r7b
TitleCrystal structure of pneumococcal LicA in complex with choline
ComponentsCholine kinase
KeywordsTRANSFERASE / protein kinase-like fold
Function / homology
Function and homology information


choline kinase activity / kinase activity / phosphorylation / 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 ION / Choline kinase / Choline kinase
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 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 1.1Nov 8, 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

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Assembly

Deposited unit
A: Choline kinase
B: Choline kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,4304
Polymers71,2222
Non-polymers2082
Water5,621312
1


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


Theoretical massNumber of molelcules
Total (without water)35,7152
Polymers35,6111
Non-polymers1041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Choline kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7152
Polymers35,6111
Non-polymers1041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.386, 96.690, 98.595
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: Chemical ChemComp-CHT / CHOLINE ION / Choline


Mass: 104.171 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H14NO
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 312 / 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: 2.36 Å3/Da / Density % sol: 47.78 %
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: 0.97924 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 15, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97924 Å / Relative weight: 1
ReflectionResolution: 2.01→50 Å / Num. all: 44656 / Num. obs: 44656 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shellResolution: 2.01→2.08 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.571 / Mean I/σ(I) obs: 3.362 / Rsym value: 0.571 / % possible all: 98

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.5.0110refinement
HKL-2000data reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4R77

4r77


Resolution: 2.01→29.78 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.936 / SU B: 4.171 / SU ML: 0.116 / Cross valid method: THROUGHOUT / ESU R: 0.196 / ESU R Free: 0.168 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23738 2255 5.1 %RANDOM
Rwork0.20049 ---
obs0.20231 42212 97.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.236 Å2
Baniso -1Baniso -2Baniso -3
1-2.82 Å20 Å20 Å2
2---2.8 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.01→29.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4678 0 14 312 5004
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0224780
X-RAY DIFFRACTIONr_angle_refined_deg1.1381.9676452
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3825570
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.62425.583240
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.88815892
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1311516
X-RAY DIFFRACTIONr_chiral_restr0.0850.2704
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023580
X-RAY DIFFRACTIONr_mcbond_it0.5861.52844
X-RAY DIFFRACTIONr_mcangle_it1.15824600
X-RAY DIFFRACTIONr_scbond_it1.81131936
X-RAY DIFFRACTIONr_scangle_it3.0914.51852
LS refinement shellResolution: 2.011→2.063 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 184 -
Rwork0.263 3046 -
obs--97.64 %

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