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- PDB-1jyk: Catalytic Mechanism of CTP:phosphocholine Cytidylyltransferase fr... -

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Basic information

Entry
Database: PDB / ID: 1jyk
TitleCatalytic Mechanism of CTP:phosphocholine Cytidylyltransferase from Streptococcus pneumoniae (LicC)
ComponentsCTP:phosphocholine Cytidylyltransferase
KeywordsTRANSFERASE / LicC / 3D Structure / CTP:phosphocholine cytidylyltransferase
Function / homology
Function and homology information


biosynthetic process / nucleotidyltransferase activity / metal ion binding
Similarity search - Function
CTP:phosphocholine cytidylyltransferase / : / Nucleotidyl transferase domain / Nucleotidyl transferase / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Nucleotide-diphospho-sugar transferases / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
LicC protein / LicC protein
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.5 Å
AuthorsKwak, B.-Y. / Yun, M. / Park, H.-w.
CitationJournal: J.Biol.Chem. / Year: 2002
Title: Structure and mechanism of CTP:phosphocholine cytidylyltransferase (LicC) from Streptococcus pneumoniae.
Authors: Kwak, B.Y. / Zhang, Y.M. / Yun, M. / Heath, R.J. / Rock, C.O. / Jackowski, S. / Park, H.W.
History
DepositionSep 12, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CTP:phosphocholine Cytidylyltransferase


Theoretical massNumber of molelcules
Total (without water)29,8051
Polymers29,8051
Non-polymers00
Water4,270237
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.62, 63.59, 122.38
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121

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Components

#1: Protein CTP:phosphocholine Cytidylyltransferase / licC protein


Mass: 29805.346 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Gene: LicC / Production host: Escherichia coli (E. coli) / References: UniProt: Q97QE9, UniProt: A0A0H2UQB5*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 237 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.78 Å3/Da / Density % sol: 55.78 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: sodium citrate, ammonium sulfate, tartrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP at 291K
Crystal grow
*PLUS
Temperature: 18 ℃ / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
123.3 mg/mlprotein11
250 mMTris11pH7.5
31 mMdithiothreitol11
41 mMEDTA11
50.1 Msodium citrate12
61.85 Mammonium sulfate12
70.2 Msodium potassium tartrate12pH5.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 0.9795, 0.9794
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 20, 2001
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97951
20.97941
ReflectionResolution: 1.5→50 Å / Num. obs: 54137 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 20.6 Å2 / Rsym value: 0.048 / Net I/σ(I): 36.8
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 2.79 % / Num. unique all: 10252 / % possible all: 99.6
Reflection
*PLUS
Lowest resolution: 50 Å / Num. measured all: 1187180 / Rmerge(I) obs: 0.048
Reflection shell
*PLUS
% possible obs: 99.7 %

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Processing

Software
NameClassification
SOLVEphasing
XTALVIEWrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 1.5→20 Å / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflectionSelection details
Rfree0.241 -RANDOM
Rwork0.218 --
all-49170 -
obs-49170 -
Refinement stepCycle: LAST / Resolution: 1.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1903 0 0 237 2140
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_angle_deg1.37
Software
*PLUS
Name: XTALVIEW / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.5 Å / Lowest resolution: 20 Å / σ(F): 2 / % reflection Rfree: 5 % / Rfactor obs: 0.218
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDType
X-RAY DIFFRACTIONo_bond_d
X-RAY DIFFRACTIONo_angle_deg

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