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- PDB-2jgt: Low resolution structure of SPT -

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Basic information

Entry
Database: PDB / ID: 2jgt
TitleLow resolution structure of SPT
ComponentsSERINE PALMITOYLTRANSFERASE
KeywordsTRANSFERASE / SPT / PLP / SSPF / SPHINGOLIPID / PYRIDOXAL PHOSPHATE / SERINE PALMITOYL TRANSFERASE
Function / homology
Function and homology information


serine C-palmitoyltransferase / sphingolipid metabolic process / biosynthetic process / acyltransferase activity / pyridoxal phosphate binding / 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 ...: / 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
Serine palmitoyltransferase
Similarity search - Component
Biological speciesPSEUDOMONAS PAUCIMOBILIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsYard, B.A. / Carter, L.G. / Johnson, K.A. / Overton, I.M. / Mcmahon, S.A. / Dorward, M. / Liu, H. / Puech, D. / Oke, M. / Barton, G.J. ...Yard, B.A. / Carter, L.G. / Johnson, K.A. / Overton, I.M. / Mcmahon, S.A. / Dorward, M. / Liu, H. / Puech, D. / Oke, M. / Barton, G.J. / Naismith, J.H. / Campopiano, D.J.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: The Structure of Serine Palmitoyltransferase; Gateway to Sphingolipid Biosynthesis.
Authors: Yard, B.A. / Carter, L.G. / Johnson, K.A. / Overton, I.M. / Dorward, M. / Liu, H. / Mcmahon, S.A. / Oke, M. / Puech, D. / Barton, G.J. / Naismith, J.H. / Campopiano, D.J.
History
DepositionFeb 14, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 1, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SERINE PALMITOYLTRANSFERASE
B: SERINE PALMITOYLTRANSFERASE


Theoretical massNumber of molelcules
Total (without water)90,6942
Polymers90,6942
Non-polymers00
Water70339
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)93.866, 109.537, 187.031
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B
13A
23B
14A
24B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A22 - 95
2111B22 - 95
1121A111 - 146
2121B111 - 146
1131A150 - 286
2131B150 - 286
1141A294 - 419
2141B294 - 419

NCS ensembles :
ID
1
2
3
4

NCS oper: (Code: given
Matrix: (-0.01732, -0.84203, 0.53915), (-0.84537, -0.27561, -0.45759), (0.5339, -0.46371, -0.70705)
Vector: -8.76372, -46.01311, -55.8794)

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Components

#1: Protein SERINE PALMITOYLTRANSFERASE


Mass: 45346.906 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS PAUCIMOBILIS (bacteria) / Plasmid: PET-28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): HMS 174 (DES) / References: UniProt: Q93UV0, serine C-palmitoyltransferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / 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: 2.6 Å3/Da / Density % sol: 53 %
Crystal growDetails: 10% PEG 8K, 0.17 M MAGNESIUM CHLORIDE, 0.1 M TRIS PH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9785
DetectorType: MARRESEARCH / Detector: CCD / Details: MIRRORS
RadiationMonochromator: SI(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 19635 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Redundancy: 7.8 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 21
Reflection shellResolution: 3→3.07 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 5 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FC4

1fc4


Resolution: 3→19.99 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.896 / SU B: 43.158 / SU ML: 0.377 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.463
Stereochemistry target values: MAXIMUM LIKELIHOODWITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.276 996 5.1 %RANDOM
Rwork0.25 ---
obs0.251 18544 99.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 85.86 Å2
Baniso -1Baniso -2Baniso -3
1--0.18 Å20 Å20 Å2
2--0.15 Å20 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 3→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5524 0 0 39 5563
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0225628
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3161.9617607
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.4385726
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.76923.537229
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.72815939
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3481536
X-RAY DIFFRACTIONr_chiral_restr0.0760.2863
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024216
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2290.22605
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3040.23866
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1660.2203
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2310.253
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.380.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3711.53699
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.64925764
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.6532151
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.1184.51843
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A394tight positional0.060.05
12B394tight positional0.060.05
21A272tight positional0.020.05
22B272tight positional0.020.05
31A966tight positional0.050.05
41A935tight positional0.090.05
42B935tight positional0.090.05
11A394tight thermal0.040.5
12B394tight thermal0.040.5
21A272tight thermal0.050.5
22B272tight thermal0.050.5
31A966tight thermal0.030.5
41A935tight thermal0.050.5
42B935tight thermal0.050.5
LS refinement shellResolution: 3→3.07 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.395 57 -
Rwork0.316 1325 -
obs--99.42 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.42921.4395-0.92993.2229-1.90164.2040.3858-0.3886-0.01110.5113-0.5163-0.1988-0.30920.73270.1305-0.1805-0.18110.052-0.11680.0162-0.2134-5.062-37.006-9.479
23.60141.8144-0.21813.71840.90712.24580.0119-0.2216-0.85460.22990.031-0.76830.19980.5893-0.0428-0.30230.0105-0.061-0.19290.077-0.076417.224-27.103-34.867
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A22 - 419
2X-RAY DIFFRACTION2B22 - 419

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