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- PDB-3bq7: SAM domain of Diacylglycerol Kinase delta1 (E35G) -

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Basic information

Entry
Database: PDB / ID: 3bq7
TitleSAM domain of Diacylglycerol Kinase delta1 (E35G)
ComponentsDiacylglycerol kinase delta
KeywordsTRANSFERASE / SAM domain / polymerization domain / Alternative splicing / Cytoplasm / Kinase / Membrane / Metal-binding / Phorbol-ester binding / Phosphoprotein / Zinc / Zinc-finger
Function / homology
Function and homology information


negative regulation of protein kinase C signaling / lipid phosphorylation / diacylglycerol metabolic process / diacylglycerol kinase (ATP) / ATP-dependent diacylglycerol kinase activity / positive regulation of clathrin-dependent endocytosis / phosphatidic acid biosynthetic process / diacylglycerol binding / Effects of PIP2 hydrolysis / protein kinase C-activating G protein-coupled receptor signaling pathway ...negative regulation of protein kinase C signaling / lipid phosphorylation / diacylglycerol metabolic process / diacylglycerol kinase (ATP) / ATP-dependent diacylglycerol kinase activity / positive regulation of clathrin-dependent endocytosis / phosphatidic acid biosynthetic process / diacylglycerol binding / Effects of PIP2 hydrolysis / protein kinase C-activating G protein-coupled receptor signaling pathway / positive regulation of epidermal growth factor receptor signaling pathway / clathrin-coated pit / platelet activation / kinase binding / endocytosis / protein transport / cytoplasmic vesicle / intracellular signal transduction / protein heterodimerization activity / signal transduction / protein homodimerization activity / ATP binding / identical protein binding / metal ion binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Diacylglycerol kinase delta, SAM domain / : / : / Diacylglycerol kinase / Diacylglycerol kinase, accessory domain / Diacylglycerol kinase accessory domain / Diacylglycerol kinase accessory domain (presumed) / Diacylglycerol kinase, catalytic domain / Diacylglycerol kinase catalytic domain / DAG-kinase catalytic (DAGKc) domain profile. ...Diacylglycerol kinase delta, SAM domain / : / : / Diacylglycerol kinase / Diacylglycerol kinase, accessory domain / Diacylglycerol kinase accessory domain / Diacylglycerol kinase accessory domain (presumed) / Diacylglycerol kinase, catalytic domain / Diacylglycerol kinase catalytic domain / DAG-kinase catalytic (DAGKc) domain profile. / Diacylglycerol kinase catalytic domain (presumed) / Transcription Factor, Ets-1 / Inorganic polyphosphate/ATP-NAD kinase, N-terminal / NAD kinase/diacylglycerol kinase-like domain superfamily / Phorbol esters/diacylglycerol binding domain (C1 domain) / Zinc finger phorbol-ester/DAG-type signature. / Zinc finger phorbol-ester/DAG-type profile. / Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains) / Protein kinase C-like, phorbol ester/diacylglycerol-binding domain / SAM domain (Sterile alpha motif) / C1-like domain superfamily / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain / PH domain / Sterile alpha motif/pointed domain superfamily / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / DNA polymerase; domain 1 / PH-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Diacylglycerol kinase delta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.9 Å
AuthorsKnight, M.J. / Bowie, J.U. / Sawaya, M.R.
CitationJournal: Structure / Year: 2008
Title: Regulation of Enzyme Localization by Polymerization: Polymer Formation by the SAM Domain of Diacylglycerol Kinase delta1
Authors: Harada, B.T. / Knight, M.J. / Imai, S. / Qiao, F. / Ramachander, R. / Sawaya, M.R. / Gingery, M. / Sakane, F. / Bowie, J.U.
History
DepositionDec 19, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 25, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.3Oct 20, 2021Group: Advisory / Database references
Category: database_2 / pdbx_unobs_or_zero_occ_atoms / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Diacylglycerol kinase delta
B: Diacylglycerol kinase delta
C: Diacylglycerol kinase delta
D: Diacylglycerol kinase delta
E: Diacylglycerol kinase delta
F: Diacylglycerol kinase delta


Theoretical massNumber of molelcules
Total (without water)57,6076
Polymers57,6076
Non-polymers00
Water0
1
A: Diacylglycerol kinase delta
B: Diacylglycerol kinase delta

A: Diacylglycerol kinase delta
B: Diacylglycerol kinase delta

A: Diacylglycerol kinase delta
B: Diacylglycerol kinase delta


Theoretical massNumber of molelcules
Total (without water)57,6076
Polymers57,6076
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z+2/31
crystal symmetry operation3_555-x+y,-x,z+1/31
2
C: Diacylglycerol kinase delta
F: Diacylglycerol kinase delta

C: Diacylglycerol kinase delta
F: Diacylglycerol kinase delta

C: Diacylglycerol kinase delta
F: Diacylglycerol kinase delta


Theoretical massNumber of molelcules
Total (without water)57,6076
Polymers57,6076
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z+2/31
crystal symmetry operation3_665-x+y+1,-x+1,z+1/31
3
D: Diacylglycerol kinase delta
E: Diacylglycerol kinase delta

D: Diacylglycerol kinase delta
E: Diacylglycerol kinase delta

D: Diacylglycerol kinase delta
E: Diacylglycerol kinase delta


Theoretical massNumber of molelcules
Total (without water)57,6076
Polymers57,6076
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_664-y+1,x-y+1,z-1/31
crystal symmetry operation3_565-x+y,-x+1,z+1/31
4
A: Diacylglycerol kinase delta


Theoretical massNumber of molelcules
Total (without water)9,6011
Polymers9,6011
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
B: Diacylglycerol kinase delta


Theoretical massNumber of molelcules
Total (without water)9,6011
Polymers9,6011
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
C: Diacylglycerol kinase delta


Theoretical massNumber of molelcules
Total (without water)9,6011
Polymers9,6011
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
D: Diacylglycerol kinase delta


Theoretical massNumber of molelcules
Total (without water)9,6011
Polymers9,6011
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
E: Diacylglycerol kinase delta


Theoretical massNumber of molelcules
Total (without water)9,6011
Polymers9,6011
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
9
F: Diacylglycerol kinase delta


Theoretical massNumber of molelcules
Total (without water)9,6011
Polymers9,6011
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)108.079, 108.079, 33.513
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32

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Components

#1: Protein
Diacylglycerol kinase delta / Diglyceride kinase delta / DGK-delta / DAG kinase delta / 130 kDa diacylglycerol kinase


Mass: 9601.126 Da / Num. of mol.: 6 / Fragment: SAM domain / Mutation: E35G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DGKD, KIAA0145 / Plasmid: pET-3c / Cell line (production host): BL21 (DE3) / Production host: Escherichia coli (E. coli) / Strain (production host): pLyseS / References: UniProt: Q16760, diacylglycerol kinase (ATP)

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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: 1.96 Å3/Da / Density % sol: 37.3 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: dibasic ammonium phosphate, tris, NaCl, beta-mercaptoethanol, pH 8.0, vapor diffusion, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1.27 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 14, 2006
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.27 Å / Relative weight: 1
Reflection twinType: hemihedral / Operator: -h,-k,l / Fraction: 0.464
ReflectionResolution: 2.9→90 Å / Num. all: 18986 / Num. obs: 18986 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2 % / Rmerge(I) obs: 0.064 / Χ2: 1.085 / Net I/σ(I): 17.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.9-31.90.34418731.03695.4
3-3.1220.27218731.04997.9
3.12-3.2720.18719041.04898.3
3.27-3.4420.1319321.12298.5
3.44-3.6520.09318841.03298
3.65-3.942.10.07418321.14998.3
3.94-4.332.10.06219781.1298.8
4.33-4.962.10.06218911.07499
4.96-6.252.10.0619111.09298.6
6.25-902.10.05119081.11298.8

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT3.004data extraction
BOSdata collection
PHASERphasing
RefinementStarting model: PDB entry 2F3N

2f3n


Resolution: 2.9→54.04 Å / σ(F): 6 / Stereochemistry target values: Engh & Huber
Details: The data is hemihedral twinning with twinning operator: -h,-k,l and corresponding twinned fraction: 0.464027
RfactorNum. reflection% reflectionSelection details
Rfree0.29 869 9 %random
Rwork0.25 ---
obs0.254 9650 99.4 %-
all-9650 --
Solvent computationBsol: 100.123 Å2
Displacement parametersBiso mean: 73.464 Å2
Baniso -1Baniso -2Baniso -3
1--0.655 Å20 Å20 Å2
2---0.655 Å20 Å2
3---1.31 Å2
Refinement stepCycle: LAST / Resolution: 2.9→54.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3320 0 0 0 3320
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.1861.5
X-RAY DIFFRACTIONc_scbond_it1.5262
X-RAY DIFFRACTIONc_mcangle_it2.1192
X-RAY DIFFRACTIONc_scangle_it2.5632.5
Xplor fileSerial no: 1 / Param file: protein_rep.param

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