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- PDB-4xsv: Human CTP: Phosphoethanolamine Cytidylyltransferase in complex wi... -

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Basic information

Entry
Database: PDB / ID: 4xsv
TitleHuman CTP: Phosphoethanolamine Cytidylyltransferase in complex with CTP
ComponentsEthanolamine-phosphate cytidylyltransferase
KeywordsTRANSFERASE
Function / homology
Function and homology information


ethanolamine-phosphate cytidylyltransferase / ethanolamine-phosphate cytidylyltransferase activity / Synthesis of PE / phosphatidylethanolamine biosynthetic process / phospholipid biosynthetic process / endoplasmic reticulum membrane / cytoplasm
Similarity search - Function
Ethanolamine-phosphate cytidylyltransferase / CTP:phosphocholine cytidylyltransferase domain / Cytidylyltransferase-like / Cytidyltransferase-like domain / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
CYTIDINE-5'-MONOPHOSPHATE / CYTIDINE-5'-TRIPHOSPHATE / Ethanolamine-phosphate cytidylyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsSchuler, H. / Karlberg, T.
CitationJournal: To Be Published
Title: Human CTP: Phosphoethanolamine Cytidylyltransferase
Authors: Schuler, H. / Karlberg, T.
History
DepositionJan 22, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 16, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ethanolamine-phosphate cytidylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,6884
Polymers38,7901
Non-polymers8983
Water37821
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1620 Å2
ΔGint-6 kcal/mol
Surface area14840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.390, 73.390, 140.030
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Ethanolamine-phosphate cytidylyltransferase / CTP:phosphoethanolamine cytidylyltransferase / Phosphorylethanolamine transferase


Mass: 38789.859 Da / Num. of mol.: 1 / Fragment: UNP residues 18-356
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PCYT2 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): R3 pRARE
References: UniProt: Q99447, ethanolamine-phosphate cytidylyltransferase
#2: Chemical ChemComp-C5P / CYTIDINE-5'-MONOPHOSPHATE


Mass: 323.197 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N3O8P
#3: Chemical ChemComp-CTP / CYTIDINE-5'-TRIPHOSPHATE


Mass: 483.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H16N3O14P3
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.43 Å3/Da / Density % sol: 49.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.6
Details: 17% PEG3350, 0.2M magnesium formate, 0.1M HEPES, 0.01M CTP, 0.01M magnesium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.9333 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 25, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9333 Å / Relative weight: 1
ReflectionResolution: 2.7→40 Å / Num. all: 11119 / Num. obs: 11119 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.2 % / Rmerge(I) obs: 0.131 / Rsym value: 0.129 / Net I/σ(I): 16.4
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 9.5 % / Rmerge(I) obs: 0.526 / Mean I/σ(I) obs: 4.6 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ELB

3elb


Resolution: 2.7→39.37 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.874 / SU B: 25.232 / SU ML: 0.252 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.273 / ESU R Free: 0.356 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26417 553 5 %RANDOM
Rwork0.191 ---
obs0.19477 10517 99.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.017 Å2
Baniso -1Baniso -2Baniso -3
1-2.04 Å2-0 Å20 Å2
2--2.04 Å2-0 Å2
3----4.09 Å2
Refinement stepCycle: 1 / Resolution: 2.7→39.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2445 0 56 21 2522
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0192556
X-RAY DIFFRACTIONr_bond_other_d0.0010.022397
X-RAY DIFFRACTIONr_angle_refined_deg1.5121.9713472
X-RAY DIFFRACTIONr_angle_other_deg0.7853.0015490
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9915304
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.64723.525122
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.93615425
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4431519
X-RAY DIFFRACTIONr_chiral_restr0.0750.2387
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212849
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02603
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_it1.8732.9111222
X-RAY DIFFRACTIONr_mcbond_other1.872.9091221
X-RAY DIFFRACTIONr_mcangle_it3.1184.3541524
X-RAY DIFFRACTIONr_mcangle_other3.1174.3551525
X-RAY DIFFRACTIONr_scbond_it2.143.1741334
X-RAY DIFFRACTIONr_scbond_other2.1393.1741334
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.6114.6781949
X-RAY DIFFRACTIONr_long_range_B_refined5.41122.9942789
X-RAY DIFFRACTIONr_long_range_B_other5.41323.0022787
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.343 39 -
Rwork0.234 749 -
obs--99.75 %
Refinement TLS params.Method: refined / Details: Chain A / Origin x: -30.1108 Å / Origin y: -7.3232 Å / Origin z: -4.6773 Å
111213212223313233
T0.0081 Å20.0023 Å2-0.0049 Å2-0.0258 Å2-0.0052 Å2--0.0287 Å2
L0.3605 °20.0732 °2-0.1626 °2-0.0895 °2-0.0524 °2--0.5015 °2
S0.0264 Å °-0.0092 Å °0.0077 Å °0.0029 Å °-0.0444 Å °0.0041 Å °-0.039 Å °-0.01 Å °0.018 Å °

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