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

ID or keywords:

Entry

Database: PDB / ID: 2jg2

Title

HIGH RESOLUTION STRUCTURE OF SPT WITH PLP INTERNAL ALDIMINE

Components

SERINE PALMITOYLTRANSFERASE

Keywords

TRANSFERASE / 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 / cytoplasm
Similarity search - Function

Biological species

PSEUDOMONAS PAUCIMOBILIS (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.3 Å

Authors

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. ...

Citation

Journal: 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

Deposition	Feb 7, 2007	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	May 1, 2007	Provider: repository / Type: Initial release
Revision 1.1	Nov 11, 2015	Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Other / Structure summary / Version format compliance

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	2jg2.cif.gz	174.8 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	2jg2_validation.pdf.gz	449.6 KB	Display	wwPDB validaton report
Full document	2jg2_full_validation.pdf.gz	454.5 KB	Display
Data in XML	2jg2_validation.xml.gz	20.7 KB	Display
Data in CIF	2jg2_validation.cif.gz	31.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/jg/2jg2 ftp://data.pdbj.org/pub/pdb/validation_reports/jg/2jg2	HTTPS FTP

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Related structure data

Related structure data	2jgtC C: citing same article (ref.)
Similar structure data	2w8j-1 6i2j-d 1fc4-d 7bxs-d 2zdh-2 2w8w-1 3a2b-1 6p7y-1 5wja-d 3tfu-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: SERINE PALMITOYLTRANSFERASE

hetero molecules

45.6 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: SERINE PALMITOYLTRANSFERASE

hetero molecules

A: SERINE PALMITOYLTRANSFERASE

hetero molecules

defined by author&software
91.2 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

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 number	20
Space group name H-M	C222₁

Components on special symmetry positions

ID	Model	Components
1	1	A-2388- HOH

#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

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 1.9 Å³/Da / Density % sol: 35 %
Crystal grow	pH: 7.5 Details: 21.27% PEG 3350, 0.1M HEPES PH 6.5, MG-CHLORIDE 0.11M

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9785
Detector	Type: MARRESEARCH / Detector: CCD / Date: Oct 9, 2006 / Details: MIRRORS
Radiation	Monochromator: SI(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9785 Å / Relative weight: 1
Reflection	Resolution: 1.3→30 Å / Num. obs: 88217 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 7.9 % / R_merge(I) obs: 0.08 / Net I/σ(I): 19.7
Reflection shell	Resolution: 1.3→1.37 Å / Redundancy: 5.2 % / R_merge(I) obs: 0.5 / Mean I/σ(I) obs: 2.9 / % possible all: 100

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0005	refinement
MOSFLM		data reduction
SCALA		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.3→18.79 Å / Cor.coef. F_o:F_c: 0.975 / Cor.coef. F_o:F_c 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.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.185	4422	5 %	RANDOM
R_work	0.153	-	-	-
obs	0.155	83750	99.6 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 13.65 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0 Å²	0 Å²	0 Å²
2-	-	0.02 Å²	0 Å²
3-	-	-	-0.01 Å²

Refinement step

Cycle: LAST / Resolution: 1.3→18.79 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3007	0	16	409	3432

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.02	0.022	3122
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.221	1.969	4228
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.109	5	407
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.07	23.538	130
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.477	15	530
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.166	15	22
X-RAY DIFFRACTION	r_chiral_restr	0.11	0.2	473
X-RAY DIFFRACTION	r_gen_planes_refined	0.012	0.02	2358
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.215	0.2	1495
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.31	0.2	2198
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.143	0.2	333
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.257	0.2	112
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.194	0.2	56
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	1.91	1.5	2041
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	2.345	2	3176
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	3.525	3	1217
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	4.726	4.5	1049
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.3→1.33 Å / Total num. of bins used: 20 /

	R_factor	Num. reflection
R_free	0.319	355
R_work	0.27	6020

Refinement TLS params.

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

ID	L11 (°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)
1	2.6165	0.4716	4.8882	6.1979	4.5959	11.39	0.0393	-0.1977	-0.116	0.4309	0.1339	0.0939	0.1978	-0.0704	-0.1732	0.0643	-0.0364	0.0463	0.0381	0.0081	-0.0154	-15.708	3.277	38.063
2	1.7747	0.8454	-0.6397	2.6588	-1.5204	2.5398	-0.0508	-0.1156	-0.0602	0.1063	0.1217	0.057	0.1989	-0.1338	-0.071	0.0533	0.0021	0.0173	0.0554	-0.0416	0.0221	-7.763	20.442	45.793
3	0.4815	-0.0669	0.1314	0.4754	0.0924	0.5222	-0.0008	0.0011	0.0909	-0.0197	-0.0291	-0.0427	-0.0605	0.0206	0.03	0.0106	-0.005	0.0183	0.0172	0.007	0.0421	7.193	25.259	23.718
4	2.9266	-1.103	-0.6204	1.5381	-0.4218	0.5144	0.0736	-0.0146	-0.0659	-0.0068	0.0117	0.0978	0.0978	-0.0497	-0.0853	0.0337	0.0082	0.0037	0.0074	0.0111	0.0354	9.312	0.015	26.201
5	0.6158	-0.3	-0.0403	1.5537	0.5643	0.8579	0.0349	-0.0599	0.0082	0.109	-0.0271	-0.1144	0.124	0.0507	-0.0078	0.0239	0.0153	-0.0054	0.011	0.0028	0.0177	20.655	1.187	30.868
6	0.5263	-0.0555	0.1619	0.6165	0.0216	0.5428	0.0081	0.0349	0.025	0.0029	-0.0076	-0.1229	0.0211	0.1094	-0.0005	0.0119	0	0.0249	0.0335	0.0065	0.0481	14.736	18.735	22.036
7	5.3332	2.6683	1.6609	6.4725	-4.6959	8.2673	0.0463	0.1652	0.0669	-0.083	0.0557	-0.0285	-0.1998	0.4169	-0.102	0.016	-0.0394	-0.0073	0.0716	-0.0502	0.0973	22.021	31.98	35.419
8	1.1908	-0.3195	-0.2144	2.2391	-0.4438	1.5316	-0.1519	-0.1616	0.0359	0.3203	0.1713	-0.1444	0.1457	0.048	-0.0195	0.0746	0.0325	-0.0547	0.0399	-0.0423	0.0228	15.699	18.277	50.169
9	1.8996	-0.6103	-0.0925	4.0518	0.2269	1.7978	-0.0923	-0.2206	-0.1358	0.3009	0.0615	0.1844	0.221	-0.0621	0.0307	0.0622	0.006	0.013	0.0613	-0.0285	-0.0037	0.629	20.428	52.057
10	1.2775	4.0835	1.5663	13.0529	5.0067	1.9204	0.5832	-0.3275	-0.3281	-0.1474	-0.7091	1.2554	0.3625	-0.9251	0.126	0.1409	-0.0014	-0.0022	0.1095	0.0064	0.1148	1.816	7.061	45.422
11	0.8336	0.0098	-0.2446	2.1714	-0.3034	1.1937	-0.0891	-0.1119	0.0509	0.2769	0.0892	-0.2541	0.0161	0.0108	-0	0.042	0.0261	-0.0489	0.0224	-0.0414	0.0168	10.163	24.516	50.103
12	0.0183	0.262	0.4344	3.8738	5.52	14.3726	-0.006	-0.5694	-0.353	0.7423	-0.2704	-0.8326	0.5316	0.6187	0.2764	0.1592	-0.0026	0.0084	0.14	0.0027	0.1118	6.314	19.336	63.206

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	22 - 34
2	X-RAY DIFFRACTION	2	A	35 - 55
3	X-RAY DIFFRACTION	3	A	56 - 147
4	X-RAY DIFFRACTION	4	A	148 - 174
5	X-RAY DIFFRACTION	5	A	175 - 231
6	X-RAY DIFFRACTION	6	A	232 - 313
7	X-RAY DIFFRACTION	7	A	314 - 321
8	X-RAY DIFFRACTION	8	A	322 - 357
9	X-RAY DIFFRACTION	9	A	358 - 377
10	X-RAY DIFFRACTION	10	A	378 - 383
11	X-RAY DIFFRACTION	11	A	384 - 412
12	X-RAY DIFFRACTION	12	A	413 - 419

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