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- PDB-8iyt: Crystal Structure of Serine Palmitoyltransferase complexed with D... -

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Basic information

Entry
Database: PDB / ID: 8iyt
TitleCrystal Structure of Serine Palmitoyltransferase complexed with D-methylserine
ComponentsSerine palmitoyltransferase
KeywordsTRANSFERASE / sphingolipid
Function / homology
Function and homology information


8-amino-7-oxononanoate synthase activity / serine C-palmitoyltransferase activity / serine C-palmitoyltransferase / sphingolipid metabolic process / biosynthetic process / pyridoxal phosphate binding / plasma membrane / cytoplasm
Similarity search - Function
: / Aminotransferase, class-II, pyridoxal-phosphate binding site / Aminotransferases class-II pyridoxal-phosphate attachment site. / Aminotransferase, class I/classII / Aminotransferase class I and II / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
: / Serine palmitoyltransferase
Similarity search - Component
Biological speciesSphingobacterium multivorum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsTakahashi, A. / Murakami, T. / Katayama, A. / Miyahara, I. / Kamiya, N. / Ikushiro, H. / Yano, T.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Biol.Chem. / Year: 2024
Title: Racemization of the substrate and product by serine palmitoyltransferase from Sphingobacterium multivorum yields two enantiomers of the product from d-serine.
Authors: Ikushiro, H. / Honda, T. / Murai, Y. / Murakami, T. / Takahashi, A. / Sawai, T. / Goto, H. / Ikushiro, S.I. / Miyahara, I. / Hirabayashi, Y. / Kamiya, N. / Monde, K. / Yano, T.
History
DepositionApr 6, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 10, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Serine palmitoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,4216
Polymers43,8231
Non-polymers5995
Water6,918384
1
A: Serine palmitoyltransferase
hetero molecules

A: Serine palmitoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,84312
Polymers87,6462
Non-polymers1,19710
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area9390 Å2
ΔGint-38 kcal/mol
Surface area27120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.843, 61.843, 208.344
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-711-

HOH

21A-725-

HOH

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Components

#1: Protein Serine palmitoyltransferase / SPT


Mass: 43822.883 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sphingobacterium multivorum (bacteria) / Gene: spt, I6J33_20140, NCTC11343_02561, SPHINGO8BC_150128 / Production host: Escherichia coli (E. coli) / References: UniProt: A7BFV6, serine C-palmitoyltransferase
#2: Chemical ChemComp-S5R / (2~{R})-2-methyl-2-[[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylamino]-3-oxidanyl-propanoic acid


Mass: 350.262 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H19N2O8P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 384 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.27 Å3/Da / Density % sol: 45.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG4000, Sodium acetate, Tris-HCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 20, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 44526 / % possible obs: 97.5 % / Redundancy: 10.1 % / CC1/2: 0.999 / Net I/σ(I): 20.5
Reflection shellResolution: 1.7→1.8 Å / Num. unique obs: 7144 / CC1/2: 0.999

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3A2B

3a2b


Resolution: 1.7→46.185 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.953 / SU B: 2.637 / SU ML: 0.084 / Cross valid method: FREE R-VALUE / ESU R: 0.115 / ESU R Free: 0.116
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2186 4294 9.644 %
Rwork0.1733 40229 -
all0.178 --
obs-44523 97.476 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 25.467 Å2
Baniso -1Baniso -2Baniso -3
1-1.059 Å2-0 Å2-0 Å2
2--1.059 Å2-0 Å2
3----2.117 Å2
Refinement stepCycle: LAST / Resolution: 1.7→46.185 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3031 0 39 384 3454
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0133279
X-RAY DIFFRACTIONr_bond_other_d0.0010.0153126
X-RAY DIFFRACTIONr_angle_refined_deg1.7061.6434443
X-RAY DIFFRACTIONr_angle_other_deg1.4231.5897236
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4665429
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.2523.057157
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.37815587
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1841517
X-RAY DIFFRACTIONr_chiral_restr0.0860.2430
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023774
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02719
X-RAY DIFFRACTIONr_nbd_refined0.2110.2653
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1740.22758
X-RAY DIFFRACTIONr_nbtor_refined0.1610.21590
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.21435
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1670.2276
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0040.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1530.221
X-RAY DIFFRACTIONr_nbd_other0.1720.2103
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1550.239
X-RAY DIFFRACTIONr_mcbond_it2.0072.4271665
X-RAY DIFFRACTIONr_mcbond_other2.0082.4251661
X-RAY DIFFRACTIONr_mcangle_it2.6183.642108
X-RAY DIFFRACTIONr_mcangle_other2.6193.6432107
X-RAY DIFFRACTIONr_scbond_it2.8532.7951614
X-RAY DIFFRACTIONr_scbond_other2.8522.7961615
X-RAY DIFFRACTIONr_scangle_it4.2484.0442334
X-RAY DIFFRACTIONr_scangle_other4.2474.0452335
X-RAY DIFFRACTIONr_lrange_it5.35230.5483742
X-RAY DIFFRACTIONr_lrange_other5.35130.5583743
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.7-1.7440.3112790.27729850.2832980.8380.85198.96910.241
1.744-1.7920.3073110.25828770.26332130.8620.87699.22190.221
1.792-1.8440.3072820.23828240.24431400.8570.89498.91720.201
1.844-1.90.2712990.22727390.23230690.8950.90598.98990.198
1.9-1.9630.2522790.20926160.21329290.90.9298.83920.182
1.963-2.0310.2752580.21625950.22128850.9050.92298.89080.19
2.031-2.1080.2722770.21224490.21827660.9090.92798.55390.191
2.108-2.1940.2462690.19723910.20227050.9210.93998.33640.178
2.194-2.2910.2492640.19222490.19725650.9160.93897.97270.173
2.291-2.4030.252120.18721800.19324560.9280.94497.39410.173
2.403-2.5320.2522210.1820500.18723380.9250.94397.13430.169
2.532-2.6850.2052300.16919560.17322620.9470.95596.64010.165
2.685-2.870.2242120.16518040.17120900.940.95596.45930.161
2.87-3.0990.2081820.16117370.16619920.9470.9696.33530.166
3.099-3.3930.1881520.15815980.16118240.960.96495.9430.167
3.393-3.7910.1681630.15414280.15616620.9690.97195.7280.17
3.791-4.3730.1811410.12812770.13315040.9650.97894.28190.152
4.373-5.3430.1641180.1310650.13412780.9780.9892.56650.156
5.343-7.5070.207880.1628780.16610370.9620.97193.15330.197
7.507-46.1850.202570.1415240.1476450.9650.98390.07750.185

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