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- PDB-2jg2: HIGH RESOLUTION STRUCTURE OF SPT WITH PLP INTERNAL ALDIMINE -

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Basic information

Entry
Database: PDB / ID: 2jg2
TitleHIGH RESOLUTION STRUCTURE OF SPT WITH PLP INTERNAL ALDIMINE
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
PYRIDOXAL-5'-PHOSPHATE / Serine palmitoyltransferase
Similarity search - Component
Biological speciesPSEUDOMONAS PAUCIMOBILIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 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 7, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 1, 2007Provider: repository / Type: Initial release
Revision 1.1Nov 11, 2015Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Other / Structure summary / Version format compliance
Revision 1.2Apr 9, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)45,6043
Polymers45,3331
Non-polymers2712
Water7,368409
1
A: SERINE PALMITOYLTRANSFERASE
hetero molecules

A: SERINE PALMITOYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,2096
Polymers90,6662
Non-polymers5434
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area9040 Å2
ΔGint-61.9 kcal/mol
Surface area27150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.190, 107.552, 90.322
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-2388-

HOH

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Components

#1: Protein SERINE PALMITOYLTRANSFERASE


Mass: 45332.879 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: PLP FORMING INTERNAL ALDIMINE WITH LYS265 / 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: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 409 / Source method: isolated from a natural source / Formula: H2O
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: 1.9 Å3/Da / Density % sol: 35 %
Crystal growpH: 7.5
Details: 21.27% PEG 3350, 0.1M HEPES PH 6.5, MG-CHLORIDE 0.11M

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9785
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 9, 2006 / 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: 1.3→30 Å / Num. obs: 88217 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 7.9 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 19.7
Reflection shellResolution: 1.3→1.37 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2.9 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→18.79 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.968 / SU B: 1.649 / SU ML: 0.031 / Cross valid method: THROUGHOUT / ESU R: 0.052 / ESU R Free: 0.05
Stereochemistry target values: MAXIMUM LIKELIHOODWITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.185 4422 5 %RANDOM
Rwork0.153 ---
obs0.155 83750 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.65 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0.02 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.3→18.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3007 0 16 409 3432
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0223122
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2211.9694228
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1095407
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.0723.538130
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.47715530
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1661522
X-RAY DIFFRACTIONr_chiral_restr0.110.2473
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.022358
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2150.21495
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.310.22198
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1430.2333
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2570.2112
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1940.256
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.911.52041
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.34523176
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.52531217
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.7264.51049
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
LS refinement shellResolution: 1.3→1.33 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.319 355
Rwork0.27 6020
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)
12.61650.47164.88826.19794.595911.390.0393-0.1977-0.1160.43090.13390.09390.1978-0.0704-0.17320.0643-0.03640.04630.03810.0081-0.0154-15.7083.27738.063
21.77470.8454-0.63972.6588-1.52042.5398-0.0508-0.1156-0.06020.10630.12170.0570.1989-0.1338-0.0710.05330.00210.01730.0554-0.04160.0221-7.76320.44245.793
30.4815-0.06690.13140.47540.09240.5222-0.00080.00110.0909-0.0197-0.0291-0.0427-0.06050.02060.030.0106-0.0050.01830.01720.0070.04217.19325.25923.718
42.9266-1.103-0.62041.5381-0.42180.51440.0736-0.0146-0.0659-0.00680.01170.09780.0978-0.0497-0.08530.03370.00820.00370.00740.01110.03549.3120.01526.201
50.6158-0.3-0.04031.55370.56430.85790.0349-0.05990.00820.109-0.0271-0.11440.1240.0507-0.00780.02390.0153-0.00540.0110.00280.017720.6551.18730.868
60.5263-0.05550.16190.61650.02160.54280.00810.03490.0250.0029-0.0076-0.12290.02110.1094-0.00050.011900.02490.03350.00650.048114.73618.73522.036
75.33322.66831.66096.4725-4.69598.26730.04630.16520.0669-0.0830.0557-0.0285-0.19980.4169-0.1020.016-0.0394-0.00730.0716-0.05020.097322.02131.9835.419
81.1908-0.3195-0.21442.2391-0.44381.5316-0.1519-0.16160.03590.32030.1713-0.14440.14570.048-0.01950.07460.0325-0.05470.0399-0.04230.022815.69918.27750.169
91.8996-0.6103-0.09254.05180.22691.7978-0.0923-0.2206-0.13580.30090.06150.18440.221-0.06210.03070.06220.0060.0130.0613-0.0285-0.00370.62920.42852.057
101.27754.08351.566313.05295.00671.92040.5832-0.3275-0.3281-0.1474-0.70911.25540.3625-0.92510.1260.1409-0.0014-0.00220.10950.00640.11481.8167.06145.422
110.83360.0098-0.24462.1714-0.30341.1937-0.0891-0.11190.05090.27690.0892-0.25410.01610.0108-00.0420.0261-0.04890.0224-0.04140.016810.16324.51650.103
120.01830.2620.43443.87385.5214.3726-0.006-0.5694-0.3530.7423-0.2704-0.83260.53160.61870.27640.1592-0.00260.00840.140.00270.11186.31419.33663.206
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A22 - 34
2X-RAY DIFFRACTION2A35 - 55
3X-RAY DIFFRACTION3A56 - 147
4X-RAY DIFFRACTION4A148 - 174
5X-RAY DIFFRACTION5A175 - 231
6X-RAY DIFFRACTION6A232 - 313
7X-RAY DIFFRACTION7A314 - 321
8X-RAY DIFFRACTION8A322 - 357
9X-RAY DIFFRACTION9A358 - 377
10X-RAY DIFFRACTION10A378 - 383
11X-RAY DIFFRACTION11A384 - 412
12X-RAY DIFFRACTION12A413 - 419

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