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- PDB-4q2e: CRYSTAL STRUCTURE OF AN INTRAMEMBRANE CDP-DAG SYNTHETASE CENTRAL ... -

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Basic information

Entry
Database: PDB / ID: 4q2e
TitleCRYSTAL STRUCTURE OF AN INTRAMEMBRANE CDP-DAG SYNTHETASE CENTRAL FOR PHOSPHOLIPID BIOSYNTHESIS (S200C/S258C, active mutant)
ComponentsPhosphatidate cytidylyltransferase
KeywordsTRANSFERASE / intramembrane enzyme / CdsA fold / phospholipid biosynthesis lipid metabolism / CTP and phosphatidic acid binding / Nucleotidyltransferase / membrane
Function / homology
Function and homology information


phosphatidate cytidylyltransferase / phosphatidate cytidylyltransferase activity / CDP-diacylglycerol biosynthetic process / plasma membrane
Similarity search - Function
Phosphatidate cytidylyltransferase / Cytidylyltransferase family / Phosphatidate cytidylyltransferase signature.
Similarity search - Domain/homology
: / : / Phosphatidate cytidylyltransferase
Similarity search - Component
Biological speciesThermotoga maritima MSB8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.4 Å
AuthorsLiu, X. / Yin, Y. / Wu, J. / Liu, Z.
CitationJournal: Nat Commun / Year: 2014
Title: Structure and mechanism of an intramembrane liponucleotide synthetase central for phospholipid biosynthesis
Authors: Liu, X. / Yin, Y. / Wu, J. / Liu, Z.
History
DepositionApr 8, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 2, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 30, 2014Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Mar 20, 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_asym_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_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_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
A: Phosphatidate cytidylyltransferase
B: Phosphatidate cytidylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,98412
Polymers64,6542
Non-polymers1,33010
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5580 Å2
ΔGint-210 kcal/mol
Surface area24130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)142.080, 142.080, 198.373
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Phosphatidate cytidylyltransferase / CDP-DAG synthase / CDP-DG synthase / CDP-diacylglycerol synthase / CDS / CDP-diglyceride ...CDP-DAG synthase / CDP-DG synthase / CDP-diacylglycerol synthase / CDS / CDP-diglyceride pyrophosphorylase / CDP-diglyceride synthase / CTP:phosphatidate cytidylyltransferase


Mass: 32326.900 Da / Num. of mol.: 2 / Mutation: S220C, S243C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima MSB8 (bacteria) / Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099 / Gene: cdsA, TM_1397 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3)
References: UniProt: Q9X1B7, phosphatidate cytidylyltransferase
#2: Chemical
ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Hg
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K

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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: 4.47 Å3/Da / Density % sol: 72.48 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 8%-13% PEG3350, 100mM NaCl, 20mM HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jun 8, 2013 / Details: Mono-chromator and mirrors
RadiationMonochromator: Cryo-cooled channel-cut Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 3.4→45 Å / Num. all: 16764 / Num. obs: 16580 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Biso Wilson estimate: 72.7 Å2 / Rmerge(I) obs: 0.099 / Net I/σ(I): 14.1
Reflection shellResolution: 3.4→3.48 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.729 / Mean I/σ(I) obs: 2.1 / Num. unique all: 1099 / % possible all: 99.8

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Processing

Software
NameVersionClassification
SERGUIdata collection
PHENIXmodel building
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 3.4→45 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 5175072.22 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.338 854 5.2 %RANDOM
Rwork0.299 ---
all0.299 16764 --
obs0.299 16580 98.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 62.2071 Å2 / ksol: 0.25 e/Å3
Displacement parametersBiso mean: 113.8 Å2
Baniso -1Baniso -2Baniso -3
1--5.3 Å20 Å20 Å2
2---5.3 Å20 Å2
3---10.61 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.73 Å0.63 Å
Luzzati d res low-5 Å
Luzzati sigma a1.2 Å0.97 Å
Refinement stepCycle: LAST / Resolution: 3.4→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4180 0 10 0 4190
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_dihedral_angle_d20
X-RAY DIFFRACTIONc_improper_angle_d1.55
X-RAY DIFFRACTIONc_mcbond_it1.41.5
X-RAY DIFFRACTIONc_mcangle_it2.572
X-RAY DIFFRACTIONc_scbond_it1.842
X-RAY DIFFRACTIONc_scangle_it2.092.5
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 3.4→3.61 Å / Rfactor Rfree error: 0.036 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.422 140 5.2 %
Rwork0.395 2567 -
obs--99.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2ion.paramion.top
X-RAY DIFFRACTION3hglink.parhglink.top

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