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- PDB-4bmk: Serine Palmitoyltransferase K265A from S. paucimobilis with bound... -

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Basic information

Entry
Database: PDB / ID: 4bmk
TitleSerine Palmitoyltransferase K265A from S. paucimobilis with bound PLP- Myriocin Aldimine
ComponentsSERINE PALMITOYLTRANSFERASE
KeywordsTRANSFERASE/ANTIBIOTIC / TRANSFERASE-ANTIBIOTIC COMPLEX / TRANSFERASE / EXTERNAL ALDIMINE / INHIBITOR / SPHINGOLIPIDS / NATURAL PRODUCT / ANTIBIOTIC ISP-1
Function / homology
Function and homology information


serine C-palmitoyltransferase / sphingolipid metabolic process / biosynthetic process / acyltransferase activity / pyridoxal phosphate binding / 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
Decarboxylated Myriocin / PYRIDOXAL-5'-PHOSPHATE / Serine palmitoyltransferase
Similarity search - Component
Biological speciesSPHINGOMONAS PAUCIMOBILIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.62 Å
AuthorsWadsworth, J.M. / Clarke, D.J. / McMahon, S.A. / Beattie, A.E. / Lowther, J. / Dunn, T.M. / Naismith, J.H. / Campopiano, D.J.
CitationJournal: J.Am.Chem.Soc. / Year: 2013
Title: The Chemical Basis of Serine Palmitoyltransferase Inhibition by Myriocin.
Authors: Wadsworth, J.M. / Clarke, D.J. / Mcmahon, S.A. / Lowther, J.P. / Beattie, A.E. / Langridge-Smith, P.R.R. / Broughton, H.B. / Dunn, T.M. / Naismith, J.H. / Campopiano, D.J.
History
DepositionMay 9, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 4, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2013Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_conn / struct_ncs_dom_lim / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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
B: SERINE PALMITOYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,0818
Polymers94,6882
Non-polymers1,3946
Water10,215567
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9800 Å2
ΔGint-60.3 kcal/mol
Surface area26920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.910, 98.710, 133.190
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ARG / Beg label comp-ID: ARG / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: _ / Auth seq-ID: 22 - 417 / Label seq-ID: 43 - 438

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein SERINE PALMITOYLTRANSFERASE


Mass: 47343.980 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SPHINGOMONAS PAUCIMOBILIS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q93UV0, serine C-palmitoyltransferase
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Chemical ChemComp-MYB / Decarboxylated Myriocin


Mass: 357.528 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H39NO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 567 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsMISSING N-TERMINAL HIS TAG AND LINKER

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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: 2.25 Å3/Da / Density % sol: 45.2 % / Description: NONE
Crystal growpH: 7.5 / Details: 32% PEG MME 2000, 0.1M HEPES PH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Aug 6, 2012 / Details: MIRRORS
RadiationMonochromator: SINGLE BOUNCE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.62→56.14 Å / Num. obs: 103044 / % possible obs: 98.9 % / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 10.8
Reflection shellResolution: 1.62→1.66 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2.3 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2JG2

2jg2


Resolution: 1.62→56.14 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.94 / SU B: 3.755 / SU ML: 0.065 / Cross valid method: THROUGHOUT / ESU R: 0.095 / ESU R Free: 0.09 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED. DISORDERED REGIONS WERE MODELED STEREOCHEMICALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.21086 5148 5 %RANDOM
Rwork0.18886 ---
obs0.18998 97821 98.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 19.736 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å20 Å20 Å2
2---0.76 Å20 Å2
3---0.67 Å2
Refinement stepCycle: LAST / Resolution: 1.62→56.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5919 0 68 567 6554
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0196105
X-RAY DIFFRACTIONr_bond_other_d0.0040.025886
X-RAY DIFFRACTIONr_angle_refined_deg1.441.9728271
X-RAY DIFFRACTIONr_angle_other_deg0.983313519
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3815803
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.47623.755245
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.542151008
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.2021537
X-RAY DIFFRACTIONr_chiral_restr0.0810.2943
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026963
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021372
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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

Ens-ID: 1 / Number: 22738 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.09 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.62→1.662 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 348 -
Rwork0.269 7239 -
obs--99.66 %
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)
10.51310.031-0.08640.0873-0.13460.4242-0.0052-0.0066-0.0762-0.0194-0.0046-0.02710.0974-0.02110.00990.05880.009-0.00850.0136-0.00260.084716.5354-18.9354-41.0898
20.2256-0.05770.03610.1884-0.06070.20730.0349-0.01350.01140.0528-0.012-0.0014-0.0476-0.0043-0.02290.0726-0.0060.00080.0526-0.00370.028814.40916.3649-27.9495
30.2961-0.0781-0.07081.257-0.14620.4981-0.0055-0.0196-0.07720.04830.0318-0.01590.00660.0554-0.02620.0394-0.01610.00010.04570.00990.04387.8421-19.3792-25.1809
41.49770.0122.513311.4405-4.86386.3041-0.14250.08450.2783-0.4413-0.13350.4291-0.05440.20710.2760.0841-0.0314-0.05780.0513-0.02740.14323.768125.4752-29.5532
50.2405-0.1211-0.00620.1664-0.00750.22580.00780.0133-0.0066-0.0295-0.0094-0.02720.00160.01710.00170.05160.01250.00340.06120.00110.030823.80752.5362-51.9737
61.5853-1.1824-0.86973.34551.61550.86110.1934-0.07580.3114-0.47590.1011-0.5291-0.25750.0518-0.29450.21360.02450.08430.0232-0.01640.098320.735924.5559-60.7416
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A22 - 73
2X-RAY DIFFRACTION2A74 - 315
3X-RAY DIFFRACTION3A316 - 420
4X-RAY DIFFRACTION4B22 - 38
5X-RAY DIFFRACTION5B39 - 315
6X-RAY DIFFRACTION6B316 - 420

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