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- PDB-6ig4: Structure of mitochondrial CDP-DAG synthase Tam41, delta 74 -

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Basic information

Entry
Database: PDB / ID: 6ig4
TitleStructure of mitochondrial CDP-DAG synthase Tam41, delta 74
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
tetracyanoplatinate(II) / : / Phosphatidate cytidylyltransferase, mitochondrial
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.261 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 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,12912
Polymers71,8662
Non-polymers2,26310
Water4,792266
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3200 Å2
ΔGint-94 kcal/mol
Surface area25190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.069, 116.538, 108.548
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-402-

PT

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Components

#1: Protein Phosphatidate cytidylyltransferase, mitochondrial / CDP-diacylglycerol synthase / CDP-DAG synthase / Mitochondrial translocator assembly and ...CDP-diacylglycerol synthase / CDP-DAG synthase / Mitochondrial translocator assembly and maintenance protein 41 homolog / TAM41


Mass: 35932.812 Da / Num. of mol.: 2
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-3G0 / tetracyanoplatinate(II) / [Pt(CN)4]2-


Mass: 299.148 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4N4Pt
#3: Chemical
ChemComp-PT / PLATINUM (II) ION


Mass: 195.078 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Pt
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 266 / 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: 2.4 Å3/Da / Density % sol: 48.75 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 15% Tacsimate, pH 7.0, 20 mM CdCl2, 10 mM K2Pt(CN)4

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Data collection

DiffractionMean temperature: 173.15 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.978 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.26→50 Å / Num. obs: 32658 / % possible obs: 100 % / Redundancy: 13 % / Rmerge(I) obs: 0.124 / Net I/σ(I): 23.3
Reflection shellResolution: 2.26→2.3 Å / Redundancy: 13.2 % / Rmerge(I) obs: 0.468 / Mean I/σ(I) obs: 5.5 / Num. unique obs: 1605 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.261→34.677 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.43
RfactorNum. reflection% reflectionSelection details
Rfree0.2201 1649 5.06 %Random selection
Rwork0.1813 ---
obs0.1833 32582 99.67 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.261→34.677 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4477 0 34 266 4777
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0114605
X-RAY DIFFRACTIONf_angle_d1.1266229
X-RAY DIFFRACTIONf_dihedral_angle_d20.1551696
X-RAY DIFFRACTIONf_chiral_restr0.067681
X-RAY DIFFRACTIONf_plane_restr0.009795
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2605-2.3270.29091320.21332495X-RAY DIFFRACTION98
2.327-2.40210.26441440.20382539X-RAY DIFFRACTION100
2.4021-2.4880.28051270.19172587X-RAY DIFFRACTION100
2.488-2.58750.29951430.19762541X-RAY DIFFRACTION100
2.5875-2.70530.27471460.1972538X-RAY DIFFRACTION100
2.7053-2.84780.2471390.19462578X-RAY DIFFRACTION100
2.8478-3.02620.2321230.18532569X-RAY DIFFRACTION100
3.0262-3.25970.24521340.18052583X-RAY DIFFRACTION100
3.2597-3.58740.20441230.17092603X-RAY DIFFRACTION100
3.5874-4.10580.20841440.16352597X-RAY DIFFRACTION100
4.1058-5.17010.17481530.15292620X-RAY DIFFRACTION100
5.1701-34.68080.17851410.20092683X-RAY DIFFRACTION98

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