PDB-8h1q: Serine Palmitoyltransferase from Sphingobacterium multivorum comp...

ID or keywords:

Entry

Database: PDB / ID: 8h1q

Title

Serine Palmitoyltransferase from Sphingobacterium multivorum complexed with L-serine

Components

Serine palmitoyltransferase

Keywords

TRANSFERASE / sphingolipid

Function / homology

Function and homology information

8-amino-7-oxononanoate synthase activity / serine C-palmitoyltransferase activity / serine C-palmitoyltransferase / sphingolipid metabolic process / biosynthetic process / pyridoxal phosphate binding / plasma membrane / cytoplasm
Similarity search - Function

Biological species

Sphingobacterium multivorum (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.5 Å

Authors

Murakami, T. / Takahashi, A. / Katayama, A. / Miyahara, I. / Kamiya, N. / Ikushiro, H. / Yano, T.

Funding support

1items

Citation

Journal: J.Biol.Chem. / Year: 2023
Title: Structural insights into the substrate recognition of serine palmitoyltransferase from Sphingobacterium multivorum.
Authors: Ikushiro, H. / Murakami, T. / Takahashi, A. / Katayama, A. / Sawai, T. / Goto, H. / Koolath, S. / Murai, Y. / Monde, K. / Miyahara, I. / Kamiya, N. / Yano, T.

History

Deposition	Oct 3, 2022	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Aug 16, 2023	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8h1q.cif.gz	113.9 KB	Display	PDBx/mmCIF format
PDB format	pdb8h1q.ent.gz	83 KB	Display	PDB format
PDBx/mmJSON format	8h1q.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8h1q_validation.pdf.gz	822.4 KB	Display	wwPDB validaton report
Full document	8h1q_full_validation.pdf.gz	825.1 KB	Display
Data in XML	8h1q_validation.xml.gz	22.3 KB	Display
Data in CIF	8h1q_validation.cif.gz	35 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/h1/8h1q ftp://data.pdbj.org/pub/pdb/validation_reports/h1/8h1q	HTTPS FTP

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Related structure data

Related structure data	8h1wC 8h1yC 8h20C 8h21C 8h29C 3a2bS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	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

44.5 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
Evidence: gel filtration
89.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	61.282, 61.282, 207.788
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	92
Space group name H-M	P4₁2₁2

Components on special symmetry positions

ID	Model	Components
1	1	A-620- HOH
2	1	A-757- HOH

#1: Protein	Serine palmitoyltransferase / SPT Mass: 43822.883 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sphingobacterium multivorum (bacteria) / Gene: spt, I6J33_20140, NCTC11343_02561, SPHINGO8BC_150128 / Production host: Escherichia coli (E. coli) / References: UniProt: A7BFV6, serine C-palmitoyltransferase
#2: Chemical	ChemComp-PLS / [3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL]-SERINE / PYRIDOXYL-SERINE-5-MONOPHOSPHATE Mass: 336.235 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₁H₁₇N₂O₈P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 502 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.26 Å³/Da / Density % sol: 45.48 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG4000, sodium acetate, Tris-HCl

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 10, 2019
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.98 Å / Relative weight: 1
Reflection	Resolution: 1.5→50 Å / Num. obs: 64186 / % possible obs: 99.8 % / Redundancy: 9.3 % / CC_1/2: 0.998 / Net I/σ(I): 15
Reflection shell	Resolution: 1.5→1.59 Å / Num. unique obs: 10153 / CC_1/2: 0.949

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
XDS		data reduction
XDS		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3A2B

3a2b

Resolution: 1.5→45.94 Å / Cor.coef. F_o:F_c: 0.978 / Cor.coef. F_o:F_c free: 0.966 / SU B: 1.202 / SU ML: 0.045 / Cross valid method: FREE R-VALUE / ESU R: 0.07 / ESU R Free: 0.074
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.184	6591	10.273 %
R_work	0.148	57569	-
all	0.151	-	-
obs	-	64160	99.2 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 19.881 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.26 Å²	-0 Å²	-0 Å²
2-	-	0.26 Å²	-0 Å²
3-	-	-	-0.52 Å²

Refinement step

Cycle: LAST / Resolution: 1.5→45.94 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3035	0	46	502	3583

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.013	3462
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	3308
X-RAY DIFFRACTION	r_angle_refined_deg	1.829	1.635	4700
X-RAY DIFFRACTION	r_angle_other_deg	1.572	1.585	7687
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.238	5	463
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	31.087	23.272	162
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.265	15	638
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.641	15	17
X-RAY DIFFRACTION	r_chiral_restr	0.097	0.2	450
X-RAY DIFFRACTION	r_chiral_restr_other	0.257	0.2	1
X-RAY DIFFRACTION	r_gen_planes_refined	0.01	0.02	4039
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	754
X-RAY DIFFRACTION	r_nbd_refined	0.222	0.2	747
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.179	0.2	2898
X-RAY DIFFRACTION	r_nbtor_refined	0.171	0.2	1640
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.082	0.2	1432
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.176	0.2	345
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.137	0.2	26
X-RAY DIFFRACTION	r_nbd_other	0.176	0.2	110
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.175	0.2	54
X-RAY DIFFRACTION	r_xyhbond_nbd_other	0.002	0.2	1
X-RAY DIFFRACTION	r_mcbond_it	1.473	1.793	1759
X-RAY DIFFRACTION	r_mcbond_other	1.473	1.793	1759
X-RAY DIFFRACTION	r_mcangle_it	2.009	2.687	2253
X-RAY DIFFRACTION	r_mcangle_other	2.009	2.687	2254
X-RAY DIFFRACTION	r_scbond_it	2.579	2.139	1703
X-RAY DIFFRACTION	r_scbond_other	2.579	2.14	1704
X-RAY DIFFRACTION	r_scangle_it	3.859	3.079	2447
X-RAY DIFFRACTION	r_scangle_other	3.859	3.081	2448
X-RAY DIFFRACTION	r_lrange_it	5.281	23.862	4056
X-RAY DIFFRACTION	r_lrange_other	5.024	22.864	3920

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.5-1.54	0.249	449	0.223	4227	X-RAY DIFFRACTION	99.7
1.539-1.581	0.21	481	0.18	4076	X-RAY DIFFRACTION	100
1.581-1.627	0.21	480	0.174	3964	X-RAY DIFFRACTION	100
1.627-1.677	0.205	443	0.171	3875	X-RAY DIFFRACTION	100
1.677-1.732	0.208	432	0.166	3769	X-RAY DIFFRACTION	99.9762
1.732-1.792	0.198	427	0.16	3635	X-RAY DIFFRACTION	99.9508
1.792-1.86	0.209	410	0.157	3532	X-RAY DIFFRACTION	99.8227
1.86-1.936	0.188	378	0.152	3399	X-RAY DIFFRACTION	99.8942
1.936-2.022	0.209	380	0.158	3251	X-RAY DIFFRACTION	99.7253
2.022-2.12	0.178	381	0.154	3100	X-RAY DIFFRACTION	99.514
2.12-2.235	0.173	318	0.145	3002	X-RAY DIFFRACTION	99.5801
2.235-2.37	0.172	321	0.139	2823	X-RAY DIFFRACTION	99.4307
2.37-2.533	0.175	277	0.135	2677	X-RAY DIFFRACTION	99.1275
2.533-2.736	0.165	294	0.136	2455	X-RAY DIFFRACTION	98.6719
2.736-2.996	0.188	275	0.142	2272	X-RAY DIFFRACTION	98.5681
2.996-3.348	0.204	246	0.15	2078	X-RAY DIFFRACTION	98.2664
3.348-3.863	0.157	215	0.132	1830	X-RAY DIFFRACTION	97.66
3.863-4.724	0.147	156	0.119	1605	X-RAY DIFFRACTION	96.599
4.724-6.652	0.191	143	0.162	1241	X-RAY DIFFRACTION	96.446
6.652-45.94	0.194	85	0.161	754	X-RAY DIFFRACTION	94.5885

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