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

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Basic information

Entry
Database: PDB / ID: 1jyl
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
Chem-CDC / LicC protein / LicC protein
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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: CTP:phosphocholine Cytidylyltransferase
B: CTP:phosphocholine Cytidylyltransferase
C: CTP:phosphocholine Cytidylyltransferase
D: CTP:phosphocholine Cytidylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,89712
Polymers118,8464
Non-polymers2,0518
Water3,207178
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.2, 69.0, 81.6
Angle α, β, γ (deg.)93.4, 92.8, 97.1
Int Tables number1
Cell settingtriclinic
Space group name H-MP1

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Components

#1: Protein
CTP:phosphocholine Cytidylyltransferase / licC protein


Mass: 29711.557 Da / Num. of mol.: 4
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: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-CDC / [2-CYTIDYLATE-O'-PHOSPHONYLOXYL]-ETHYL-TRIMETHYL-AMMONIUM


Mass: 488.324 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H26N4O11P2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 178 / 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: 2.26 Å3/Da / Density % sol: 45.53 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: sodium acetate, PEG 4000, sodium cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP at 291K
Crystal grow
*PLUS
Temperature: 18 ℃ / pH: 7.5 / 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: APS / Beamline: 19-BM / Wavelength: 0.979 Å
DetectorDetector: CCD / Date: Jun 11, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.4→20 Å / Num. obs: 37757 / % possible obs: 94.5 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 29.24 Å2 / Rsym value: 0.094 / Net I/σ(I): 12.2
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 1.82 % / Mean I/σ(I) obs: 2.02 / Num. unique all: 1522 / Rsym value: 0.33 / % possible all: 77.2
Reflection
*PLUS
Lowest resolution: 20 Å / Num. measured all: 194300 / Rmerge(I) obs: 0.094
Reflection shell
*PLUS
% possible obs: 77.2 %

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Processing

Software
NameClassification
X-PLORmodel building
XTALVIEWrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→20 Å / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflectionSelection details
Rfree0.239 -RANDOM
Rwork0.208 --
all-35102 -
obs-35102 -
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7602 0 128 178 7908
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_angle_deg1.51
Software
*PLUS
Name: XTALVIEW / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 20 Å / σ(F): 2 / % reflection Rfree: 5 % / Rfactor obs: 0.208
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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