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- PDB-4mvd: Crystal Structure of a Mammalian Cytidylyltransferase -

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Basic information

Entry
Database: PDB / ID: 4mvd
TitleCrystal Structure of a Mammalian Cytidylyltransferase
ComponentsCholine-phosphate cytidylyltransferase A
KeywordsTRANSFERASE / Rossmann Fold / Amphipathic helix / Four-helix bundle / Lipid Membrane Binding / Cytidine 5'-diphosphocholine synthesis / Phosphatidylcholine homeostasis / Lipid Membrane Surface / Endoplasmic Reticulum / Nucleus
Function / homology
Function and homology information


Synthesis of PC / choline-phosphate cytidylyltransferase / choline-phosphate cytidylyltransferase activity / CDP-choline pathway / glycogen granule / phosphatidylcholine biosynthetic process / phosphatidylcholine binding / extrinsic component of membrane / molecular function inhibitor activity / nuclear envelope ...Synthesis of PC / choline-phosphate cytidylyltransferase / choline-phosphate cytidylyltransferase activity / CDP-choline pathway / glycogen granule / phosphatidylcholine biosynthetic process / phosphatidylcholine binding / extrinsic component of membrane / molecular function inhibitor activity / nuclear envelope / calmodulin binding / lipid binding / endoplasmic reticulum membrane / endoplasmic reticulum / protein homodimerization activity / identical protein binding / nucleus / cytosol
Similarity search - Function
Choline-phosphate cytidylyltransferase Pcy1-like / CTP:phosphocholine cytidylyltransferase domain / Cytidylyltransferase-like / Cytidyltransferase-like domain / Rossmann-like alpha/beta/alpha sandwich fold
Similarity search - Domain/homology
Chem-CDC / Choline-phosphate cytidylyltransferase A
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 8 Å
AuthorsLee, J. / Cornell, R.B.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Structural Basis for Autoinhibition of CTP:Phosphocholine Cytidylyltransferase (CCT), the Regulatory Enzyme in Phosphatidylcholine Synthesis, by Its Membrane-binding Amphipathic Helix.
Authors: Lee, J. / Taneva, S.G. / Holland, B.W. / Tieleman, D.P. / Cornell, R.B.
History
DepositionSep 23, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2014Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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
B: Choline-phosphate cytidylyltransferase A
A: Choline-phosphate cytidylyltransferase A
D: Choline-phosphate cytidylyltransferase A
C: Choline-phosphate cytidylyltransferase A
F: Choline-phosphate cytidylyltransferase A
E: Choline-phosphate cytidylyltransferase A
H: Choline-phosphate cytidylyltransferase A
G: Choline-phosphate cytidylyltransferase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)308,39516
Polymers304,4888
Non-polymers3,9078
Water0
1
B: Choline-phosphate cytidylyltransferase A
A: Choline-phosphate cytidylyltransferase A
D: Choline-phosphate cytidylyltransferase A
C: Choline-phosphate cytidylyltransferase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,1988
Polymers152,2444
Non-polymers1,9534
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
F: Choline-phosphate cytidylyltransferase A
E: Choline-phosphate cytidylyltransferase A
H: Choline-phosphate cytidylyltransferase A
G: Choline-phosphate cytidylyltransferase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,1988
Polymers152,2444
Non-polymers1,9534
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)107.780, 107.780, 575.710
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein
Choline-phosphate cytidylyltransferase A / CCT-alpha / CTP:phosphocholine cytidylyltransferase A / CCT A / CT A / Phosphorylcholine transferase A


Mass: 38061.051 Da / Num. of mol.: 8 / Fragment: CCT1-312 / Mutation: Deletion (313-367)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Ctpct, Pcyt1, Pcyt1a / Plasmid: pET-14b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta BL21 (DE3)
References: UniProt: P19836, choline-phosphate cytidylyltransferase
#2: Chemical
ChemComp-CDC / [2-CYTIDYLATE-O'-PHOSPHONYLOXYL]-ETHYL-TRIMETHYL-AMMONIUM / Citicoline


Mass: 488.324 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C14H26N4O11P2

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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: 5.49 Å3/Da / Density % sol: 77.6 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M MES (pH 6.5), 1.8 M Ammonium Sulphate, 3 % dioxane, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 1.105 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jun 7, 2012 / Details: ultra-low expansion titanium silicate flat mirror
RadiationMonochromator: ACCEL/BRUKER double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.105 Å / Relative weight: 1
ReflectionResolution: 8→107.8 Å / Num. all: 6966 / Num. obs: 6964 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Rmerge(I) obs: 0.18 / Net I/σ(I): 9.3
Reflection shellResolution: 8→8.4 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 3 / Num. unique all: 1018 / % possible all: 100

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Processing

Software
NameVersionClassification
MXData Collectordata collection
PHASERphasing
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 8→107.8 Å / Cor.coef. Fo:Fc: 0.631 / Cor.coef. Fo:Fc free: 0.581 / SU B: 0.016 / SU ML: 0 / Cross valid method: THROUGHOUT / ESU R: 3.845 / ESU R Free: 4.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.40659 329 4.8 %RANDOM
Rwork0.3788 ---
all0.38019 6917 --
obs0.38019 6585 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.453 Å2
Baniso -1Baniso -2Baniso -3
1-18.72 Å20 Å20 Å2
2--18.72 Å20 Å2
3----37.44 Å2
Refinement stepCycle: LAST / Resolution: 8→107.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10013 0 248 0 10261
LS refinement shellResolution: 8.001→8.207 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 23 -
Rwork0.363 492 -
obs--100 %

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