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- PDB-3vzb: Crystal structure of Sphingosine Kinase 1 -

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Basic information

Entry
Database: PDB / ID: 3vzb
TitleCrystal structure of Sphingosine Kinase 1
ComponentsSphingosine kinase 1
KeywordsTRANSFERASE/INHIBITOR / lipid kinase / TRANSFERASE-INHIBITOR complex
Function / homology
Function and homology information


sphingosine kinase / sphingosine kinase activity / D-erythro-sphingosine kinase activity / sphingoid catabolic process / regulation of endosomal vesicle fusion / sphingosine metabolic process / lipid kinase activity / sphingosine-1-phosphate receptor activity / negative regulation of ceramide biosynthetic process / regulation of interleukin-1 beta production ...sphingosine kinase / sphingosine kinase activity / D-erythro-sphingosine kinase activity / sphingoid catabolic process / regulation of endosomal vesicle fusion / sphingosine metabolic process / lipid kinase activity / sphingosine-1-phosphate receptor activity / negative regulation of ceramide biosynthetic process / regulation of interleukin-1 beta production / regulation of microglial cell activation / sphingosine biosynthetic process / sphingolipid biosynthetic process / regulation of neuroinflammatory response / Sphingolipid de novo biosynthesis / positive regulation of smooth muscle contraction / regulation of phagocytosis / regulation of tumor necrosis factor-mediated signaling pathway / positive regulation of p38MAPK cascade / DNA biosynthetic process / protein acetylation / blood vessel development / acetyltransferase activity / Association of TriC/CCT with target proteins during biosynthesis / positive regulation of interleukin-17 production / regulation of endocytosis / endocytic vesicle / cellular response to vascular endothelial growth factor stimulus / response to tumor necrosis factor / phosphorylation / clathrin-coated pit / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / positive regulation of mitotic nuclear division / positive regulation of mitotic cell cycle / VEGFR2 mediated cell proliferation / protein phosphatase 2A binding / positive regulation of peptidyl-threonine phosphorylation / positive regulation of protein ubiquitination / calcium-mediated signaling / brain development / PKR-mediated signaling / cellular response to growth factor stimulus / cellular response to hydrogen peroxide / positive regulation of non-canonical NF-kappaB signal transduction / positive regulation of angiogenesis / positive regulation of fibroblast proliferation / presynapse / positive regulation of NF-kappaB transcription factor activity / early endosome membrane / positive regulation of cell growth / cell population proliferation / Extra-nuclear estrogen signaling / calmodulin binding / intracellular signal transduction / positive regulation of cell migration / inflammatory response / intracellular membrane-bounded organelle / lipid binding / negative regulation of apoptotic process / magnesium ion binding / DNA binding / nucleoplasm / ATP binding / membrane / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Tumour Suppressor Smad4 - #40 / : / Diacylglycerol kinase, catalytic domain / Diacylglycerol kinase catalytic domain / DAG-kinase catalytic (DAGKc) domain profile. / Diacylglycerol kinase catalytic domain (presumed) / Probable inorganic polyphosphate/atp-NAD kinase; domain 1 / NAD kinase/diacylglycerol kinase-like domain superfamily / Inorganic polyphosphate/ATP-NAD kinase, N-terminal / Tumour Suppressor Smad4 ...Tumour Suppressor Smad4 - #40 / : / Diacylglycerol kinase, catalytic domain / Diacylglycerol kinase catalytic domain / DAG-kinase catalytic (DAGKc) domain profile. / Diacylglycerol kinase catalytic domain (presumed) / Probable inorganic polyphosphate/atp-NAD kinase; domain 1 / NAD kinase/diacylglycerol kinase-like domain superfamily / Inorganic polyphosphate/ATP-NAD kinase, N-terminal / Tumour Suppressor Smad4 / Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
(2S,3R,4E)-2-aminooctadec-4-ene-1,3-diol / Sphingosine kinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsMin, X. / Walker, N.P. / Wang, Z.
CitationJournal: Structure / Year: 2013
Title: Molecular basis of sphingosine kinase 1 substrate recognition and catalysis.
Authors: Wang, Z. / Min, X. / Xiao, S.H. / Johnstone, S. / Romanow, W. / Meininger, D. / Xu, H. / Liu, J. / Dai, J. / An, S. / Thibault, S. / Walker, N.
History
DepositionOct 10, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 8, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: Database references / Derived calculations
Category: citation / database_2 ...citation / database_2 / struct_ref_seq_dif / struct_site
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sphingosine kinase 1
B: Sphingosine kinase 1
C: Sphingosine kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,39923
Polymers119,5813
Non-polymers1,81820
Water6,918384
1
A: Sphingosine kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,6289
Polymers39,8601
Non-polymers7688
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Sphingosine kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,5668
Polymers39,8601
Non-polymers7067
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Sphingosine kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,2056
Polymers39,8601
Non-polymers3445
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)101.859, 226.263, 106.487
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Sphingosine kinase 1 / SK 1 / SPK 1


Mass: 39860.422 Da / Num. of mol.: 3 / Fragment: UNP RESIDUES 9-364
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: sf9 / Gene: SPHK1, SPHK, SPK / Plasmid: pFastBac HTb / References: UniProt: Q9NYA1, sphingosine kinase
#2: Chemical ChemComp-SQS / (2S,3R,4E)-2-aminooctadec-4-ene-1,3-diol / D-Sphingosine


Mass: 299.492 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H37NO2
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 384 / 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: 2.57 Å3/Da / Density % sol: 52.05 %
Crystal growTemperature: 289 K / Method: sitting drop / pH: 6
Details: 1.0-1.4M ammonium sulfate, 0.3-1.3M NaCl, 0.1M Bis-Tris,, pH 6.0, sitting drop, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC315R / Detector: CCD / Details: 3x3 CCD array
RadiationMonochromator: Double-crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→113.131 Å / Num. all: 82888 / Num. obs: 82888 / % possible obs: 99.7 % / Redundancy: 4.3 % / Rsym value: 0.062 / Net I/σ(I): 13.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRsym valueDiffraction-ID% possible all
2-2.113.50.4881.60.488198.5
2.11-2.244.50.3282.30.3281100
2.24-2.394.50.2153.50.2151100
2.39-2.584.50.1445.10.1441100
2.58-2.834.50.1017.10.1011100
2.83-3.164.40.0699.60.0691100
3.16-3.654.40.04313.20.0431100
3.65-4.474.30.04212.90.042199.9
4.47-6.324.10.049110.049199.8
6.32-48.1754.30.027190.027199.6

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Processing

Software
NameVersionClassificationNB
SCALA3.3.9data scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MAD / Resolution: 2→48.22 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.925 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 4.647 / SU ML: 0.13 / SU R Cruickshank DPI: 0.1947 / Cross valid method: THROUGHOUT / ESU R: 0.192 / ESU R Free: 0.177 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26185 4143 5 %RANDOM
Rwork0.21303 ---
obs0.21545 78720 99.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.712 Å2
Baniso -1Baniso -2Baniso -3
1-0.97 Å20 Å20 Å2
2---0.15 Å20 Å2
3----0.81 Å2
Refinement stepCycle: LAST / Resolution: 2→48.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8142 0 117 384 8643
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0198448
X-RAY DIFFRACTIONr_bond_other_d0.0010.028309
X-RAY DIFFRACTIONr_angle_refined_deg1.3121.98611421
X-RAY DIFFRACTIONr_angle_other_deg0.78319022
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.08551041
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.5222.101357
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.036151398
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1391581
X-RAY DIFFRACTIONr_chiral_restr0.080.21284
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0219345
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021960
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.322 298 -
Rwork0.265 5575 -
obs--97.12 %

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