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- PDB-8guh: Serine Palmitoyltransferase from Sphingobacterium multivorum comp... -

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Basic information

Entry
Database: PDB / ID: 8guh
TitleSerine Palmitoyltransferase from Sphingobacterium multivorum complexed with Tris
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
Chem-K9E / Serine palmitoyltransferase
Similarity search - Component
Biological speciesSphingobacterium multivorum (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsMurakami, T. / Takahashi, A. / Katayama, A. / Miyahara, I. / Kamiya, N. / Ikushiro, H. / Yano, T.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2022
Title: Crystal structure of Sphingobacterium multivorum serine palmitoyltransferase complexed with tris(hydroxymethyl)aminomethane.
Authors: Ikushiro, H. / Takahashi, A. / Murakami, T. / Katayama, A. / Sawai, T. / Goto, H. / Miyahara, I. / Kamiya, N. / Yano, T.
History
DepositionSep 12, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 19, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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: Serine palmitoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,5468
Polymers43,8231
Non-polymers7237
Water8,215456
1
A: Serine palmitoyltransferase
hetero molecules

A: Serine palmitoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,09116
Polymers87,6462
Non-polymers1,44514
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area10960 Å2
ΔGint-15 kcal/mol
Surface area26460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.321, 61.321, 208.573
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-744-

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-K9E / [4-[[[2-(hydroxymethyl)-1,3-bis(oxidanyl)propan-2-yl]amino]methyl]-6-methyl-5-oxidanyl-pyridin-3-yl]methyl dihydrogen phosphate


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.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 456 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.24 Å3/Da / Density % sol: 45.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: PEG4000, sodium acetate, Tris-HCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-X / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Sep 9, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. obs: 47616 / % possible obs: 96.8 % / Redundancy: 8.9 % / CC1/2: 0.999 / Rpim(I) all: 0.024 / Rrim(I) all: 0.063 / Net I/σ(I): 23.4
Reflection shellResolution: 1.65→1.75 Å / Mean I/σ(I) obs: 6.4 / Num. unique obs: 6313 / CC1/2: 0.956 / Rpim(I) all: 0.128 / Rrim(I) all: 0.222

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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: 1.65→46.031 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.938 / WRfactor Rfree: 0.215 / WRfactor Rwork: 0.17 / SU B: 2.115 / SU ML: 0.072 / Average fsc free: 0.9271 / Average fsc work: 0.9428 / Cross valid method: FREE R-VALUE / ESU R: 0.106 / ESU R Free: 0.109
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2143 4916 10.328 %
Rwork0.1695 42685 -
all0.174 --
obs-47601 96.957 %
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: 15.038 Å2
Baniso -1Baniso -2Baniso -3
1--0.344 Å20 Å20 Å2
2---0.344 Å20 Å2
3---0.687 Å2
Refinement stepCycle: LAST / Resolution: 1.65→46.031 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3035 0 47 456 3538
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0133294
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173138
X-RAY DIFFRACTIONr_angle_refined_deg1.6751.6444460
X-RAY DIFFRACTIONr_angle_other_deg1.471.5897272
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5755429
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.68823.503157
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.16415588
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2411515
X-RAY DIFFRACTIONr_chiral_restr0.0820.2431
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023782
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02715
X-RAY DIFFRACTIONr_nbd_refined0.2180.2705
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1790.22858
X-RAY DIFFRACTIONr_nbtor_refined0.1650.21587
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.21449
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1860.2314
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1370.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1610.226
X-RAY DIFFRACTIONr_nbd_other0.1940.2151
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1850.238
X-RAY DIFFRACTIONr_mcbond_it1.1251.3551663
X-RAY DIFFRACTIONr_mcbond_other1.1221.3521661
X-RAY DIFFRACTIONr_mcangle_it1.6622.0272106
X-RAY DIFFRACTIONr_mcangle_other1.6622.032107
X-RAY DIFFRACTIONr_scbond_it1.9161.6211631
X-RAY DIFFRACTIONr_scbond_other1.9161.6221632
X-RAY DIFFRACTIONr_scangle_it2.8992.3262353
X-RAY DIFFRACTIONr_scangle_other2.8982.3272354
X-RAY DIFFRACTIONr_lrange_it4.58817.9443845
X-RAY DIFFRACTIONr_lrange_other4.58717.9543846
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.6930.3232700.2542362X-RAY DIFFRACTION73.9534
1.693-1.7390.2623190.2192690X-RAY DIFFRACTION87.1416
1.739-1.7890.2653440.1992921X-RAY DIFFRACTION97.4918
1.789-1.8440.2433370.1922971X-RAY DIFFRACTION99.9396
1.844-1.9050.2463210.1892864X-RAY DIFFRACTION99.9686
1.905-1.9720.243250.192763X-RAY DIFFRACTION100
1.972-2.0460.2433250.1922672X-RAY DIFFRACTION99.9666
2.046-2.1290.2352970.1912564X-RAY DIFFRACTION99.9651
2.129-2.2240.2133100.1712450X-RAY DIFFRACTION99.9638
2.224-2.3320.2322450.1722402X-RAY DIFFRACTION99.9622
2.332-2.4580.2222590.1612279X-RAY DIFFRACTION99.9213
2.458-2.6070.1962320.1552155X-RAY DIFFRACTION99.9163
2.607-2.7860.2092470.1552040X-RAY DIFFRACTION100
2.786-3.0090.222250.1561883X-RAY DIFFRACTION99.9526
3.009-3.2950.1872080.1511753X-RAY DIFFRACTION99.949
3.295-3.6810.1962000.151599X-RAY DIFFRACTION100
3.681-4.2470.1521460.1351449X-RAY DIFFRACTION100
4.247-5.1920.1641330.1441251X-RAY DIFFRACTION99.8557
5.192-7.3040.2511050.21006X-RAY DIFFRACTION100
7.304-46.0310.188680.185608X-RAY DIFFRACTION98.6861

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