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- PDB-3a2b: Crystal Structure of Serine Palmitoyltransferase from Sphingobact... -

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Basic information

Entry
Database: PDB / ID: 3a2b
TitleCrystal Structure of Serine Palmitoyltransferase from Sphingobacterium multivorum with substrate L-serine
ComponentsSerine palmitoyltransferase
KeywordsTRANSFERASE / vitamin B6-dependent enzyme Fold type I / Acyltransferase / Pyridoxal phosphate
Function / homology
Function and homology information


8-amino-7-oxononanoate synthase activity / serine C-palmitoyltransferase activity / serine C-palmitoyltransferase / sphingosine biosynthetic process / ceramide 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 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain ...Aminotransferase, class-II, pyridoxal-phosphate binding site / Aminotransferases class-II pyridoxal-phosphate attachment site. / Aminotransferase, class I/classII / Aminotransferase class I and II / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PYRIDOXAL-5'-PHOSPHATE / SERINE / Serine palmitoyltransferase
Similarity search - Component
Biological speciesSphingobacterium multivorum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsOkamoto, A. / Hoseki, J.
CitationJournal: J.Biochem. / Year: 2009
Title: Structural Insights into the Enzymatic Mechanism of Serine Palmitoyltransferase from Sphingobacterium multivorum
Authors: Ikushiro, H. / Islam, M.M. / Okamoto, A. / Hoseki, J. / Murakawa, T. / Fujii, S. / Miyahara, I. / Hayashi, H.
History
DepositionMay 9, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 14, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 650HELIX DETERMINATION METHOD: AUTHOR DETERMINED
Remark 700SHEET DETERMINATION METHOD: AUTHOR DETERMINED
Remark 750TURN DETERMINATION METHOD: AUTHOR DETERMINED

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serine palmitoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,0443
Polymers43,6921
Non-polymers3522
Water5,134285
1
A: Serine palmitoyltransferase
hetero molecules

A: Serine palmitoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,0886
Polymers87,3832
Non-polymers7044
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area9900 Å2
ΔGint-52 kcal/mol
Surface area26190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.670, 61.670, 207.760
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-637-

HOH

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Components

#1: Protein Serine palmitoyltransferase


Mass: 43691.688 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sphingobacterium multivorum (bacteria) / Strain: GTC97 / Gene: spt / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)(pLysS) / References: UniProt: A7BFV6, serine C-palmitoyltransferase
#2: Chemical ChemComp-SER / SERINE


Type: L-peptide linking / Mass: 105.093 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO3
#3: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 285 / 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: 2.26 Å3/Da / Density % sol: 45.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 21.6%W/V PEG 4000, 0.2M Sodium acetate, 0.1M Tris-HCl buffer, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Mar 10, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.29→58.722 Å / Num. all: 19738 / Num. obs: 18611 / % possible obs: 99.4 % / Redundancy: 1.81 % / Biso Wilson estimate: 18.5 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 30.35
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 1.85 % / Rmerge(I) obs: 0.107 / Mean I/σ(I) obs: 16.43 / % possible all: 99.1

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Processing

Software
NameVersionClassification
MOLREPphasing
CNS1.1refinement
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FC4

1fc4


Resolution: 2.3→19.86 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 2225645.7 / Data cutoff low absF: 0 / Isotropic thermal model: restrained / Cross valid method: THROUGHOUT / σ(F): 0 / Details: CNS bulk solvent model used
RfactorNum. reflection% reflectionSelection details
Rfree0.27 951 5.1 %random
Rwork0.211 ---
all-18667 --
obs-18598 99.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 28.5691 Å2 / ksol: 0.303489 e/Å3
Displacement parametersBiso mean: 27.07 Å2
Baniso -1Baniso -2Baniso -3
1-5.57 Å20 Å20 Å2
2--5.57 Å20 Å2
3----11.14 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.28 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 2.3→19.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3019 0 22 285 3326
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.13
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.331.5
X-RAY DIFFRACTIONc_mcangle_it2.092
X-RAY DIFFRACTIONc_scbond_it2.122
X-RAY DIFFRACTIONc_scangle_it2.942.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection obs% reflection obs (%)
2.3-2.40.29311450.23628380.027221098.8
2.4-2.530.3721150.2430.035228999.8
2.53-2.690.2981010.230.03229599.9
2.69-2.90.2771310.2120.0242289100
2.9-3.190.2971180.2190.0272314100
3.19-3.650.2661290.1970.023234799.9

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