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- PDB-6ig2: Structure of mitochondrial CDP-DAG synthase Tam41 complexed with ... -

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Basic information

Entry
Database: PDB / ID: 6ig2
TitleStructure of mitochondrial CDP-DAG synthase Tam41 complexed with CTP, delta 74, F240A
ComponentsPhosphatidate cytidylyltransferase, mitochondrial
KeywordsTRANSFERASE / mitochondrial inner membrane / CDP-Diacylglycerol synthase / NTase fold
Function / homology
Function and homology information


phosphatidate cytidylyltransferase / phosphatidate cytidylyltransferase activity / CDP-diacylglycerol biosynthetic process / extrinsic component of mitochondrial inner membrane / cardiolipin biosynthetic process / phosphatidic acid binding / cardiolipin binding / mitochondrial membrane organization / mitochondrial matrix / mitochondrion
Similarity search - Function
Phosphatidate cytidylyltransferase, mitochondrial / Phosphatidate cytidylyltransferase, mitochondrial
Similarity search - Domain/homology
CYTIDINE-5'-TRIPHOSPHATE / Phosphatidate cytidylyltransferase, mitochondrial
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.882 Å
AuthorsJiao, H.Z. / Yin, Y. / Liu, Z.F.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China31670749 China
Chinese Academy of SciencesXDB08020302 China
CitationJournal: Structure / Year: 2019
Title: Structures of the Mitochondrial CDP-DAG Synthase Tam41 Suggest a Potential Lipid Substrate Pathway from Membrane to the Active Site.
Authors: Jiao, H. / Yin, Y. / Liu, Z.
History
DepositionSep 23, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 10, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 21, 2019Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.2Nov 22, 2023Group: 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

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Assembly

Deposited unit
A: Phosphatidate cytidylyltransferase, mitochondrial
B: Phosphatidate cytidylyltransferase, mitochondrial
C: Phosphatidate cytidylyltransferase, mitochondrial
D: Phosphatidate cytidylyltransferase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,9105
Polymers143,4274
Non-polymers4831
Water3,891216
1
A: Phosphatidate cytidylyltransferase, mitochondrial
B: Phosphatidate cytidylyltransferase, mitochondrial


Theoretical massNumber of molelcules
Total (without water)71,7132
Polymers71,7132
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2580 Å2
ΔGint-17 kcal/mol
Surface area25950 Å2
MethodPISA
2
C: Phosphatidate cytidylyltransferase, mitochondrial
D: Phosphatidate cytidylyltransferase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,1973
Polymers71,7132
Non-polymers4831
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3570 Å2
ΔGint-16 kcal/mol
Surface area25860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.266, 187.418, 186.570
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number17
Space group name H-MP2122

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Components

#1: Protein
Phosphatidate cytidylyltransferase, mitochondrial / Tam41 / CDP-diacylglycerol synthase / CDP-DAG synthase / Mitochondrial translocator assembly and ...Tam41 / CDP-diacylglycerol synthase / CDP-DAG synthase / Mitochondrial translocator assembly and maintenance protein 41 homolog


Mass: 35856.719 Da / Num. of mol.: 4 / Mutation: F240A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Strain: 972 / ATCC 24843 / Gene: tam41, SPBC1A4.06c / Production host: Escherichia coli (E. coli)
References: UniProt: O74339, phosphatidate cytidylyltransferase
#2: Chemical ChemComp-CTP / CYTIDINE-5'-TRIPHOSPHATE


Mass: 483.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H16N3O14P3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 216 / 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: 3.37 Å3/Da / Density % sol: 63.53 %
Crystal growTemperature: 289.15 K / Method: evaporation, recrystallization
Details: 0.1 M HEPES-Na, pH 7.5, 9% Tacsimate, pH 7.0, 2% PEG 3350, incubated with 10 mM MgCl2, 5 mM CTP for 1 h before crystallization
PH range: 7.0-7.5

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Data collection

DiffractionMean temperature: 173.15 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.977 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 24, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 2.88→50 Å / Num. obs: 44684 / % possible obs: 100 % / Redundancy: 6.5 % / Rpim(I) all: 0.042 / Net I/σ(I): 20.7
Reflection shellResolution: 2.9→3 Å / Redundancy: 6.8 % / Mean I/σ(I) obs: 1.9 / Num. unique obs: 4338 / Rpim(I) all: 0.482 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6IG4

6ig4


Resolution: 2.882→47.604 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.92
RfactorNum. reflection% reflectionSelection details
Rfree0.2588 2135 5.05 %Random selection
Rwork0.2164 ---
obs0.2185 42315 94.2 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.882→47.604 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8946 0 29 216 9191
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0029184
X-RAY DIFFRACTIONf_angle_d0.47712433
X-RAY DIFFRACTIONf_dihedral_angle_d24.8033402
X-RAY DIFFRACTIONf_chiral_restr0.041362
X-RAY DIFFRACTIONf_plane_restr0.0031592
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8818-2.94880.3682930.30611643X-RAY DIFFRACTION59
2.9488-3.02250.34011090.27931942X-RAY DIFFRACTION70
3.0225-3.10420.31181410.26882452X-RAY DIFFRACTION88
3.1042-3.19560.29921650.25842692X-RAY DIFFRACTION98
3.1956-3.29870.30651550.26082801X-RAY DIFFRACTION99
3.2987-3.41650.30121410.24792787X-RAY DIFFRACTION99
3.4165-3.55330.30721340.23992811X-RAY DIFFRACTION100
3.5533-3.71490.36731440.27662832X-RAY DIFFRACTION100
3.7149-3.91070.29151430.21842835X-RAY DIFFRACTION100
3.9107-4.15560.21091580.1852811X-RAY DIFFRACTION100
4.1556-4.47620.19071410.17262849X-RAY DIFFRACTION100
4.4762-4.92630.18981630.16462852X-RAY DIFFRACTION100
4.9263-5.63820.2371560.18472877X-RAY DIFFRACTION100
5.6382-7.09970.2421460.22062925X-RAY DIFFRACTION100
7.0997-47.61030.22631460.23071X-RAY DIFFRACTION99

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