PDB-8h20: Serine Palmitoyltransferase from Sphingobacterium multivorum comp...

ID or keywords:

Entry

Database: PDB / ID: 8h20

Title

Serine Palmitoyltransferase from Sphingobacterium multivorum complexed with Glycine

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: 1.45 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 4, 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	8h20.cif.gz	108.7 KB	Display	PDBx/mmCIF format
PDB format	pdb8h20.ent.gz	78.9 KB	Display	PDB format
PDBx/mmJSON format	8h20.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8h20_validation.pdf.gz	783.4 KB	Display	wwPDB validaton report
Full document	8h20_full_validation.pdf.gz	784.9 KB	Display
Data in XML	8h20_validation.xml.gz	21.1 KB	Display
Data in CIF	8h20_validation.cif.gz	32.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/h2/8h20 ftp://data.pdbj.org/pub/pdb/validation_reports/h2/8h20	HTTPS FTP

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Related structure data

Related structure data	8h1qC 8h1wC 8h1yC 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

44.6 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
Evidence: homology
89.3 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	61.573, 61.573, 207.774
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-721- HOH
2	1	A-771- 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-PLG / N-GLYCINE-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YL-METHANE] / N-PYRIDOXYL-GLYCINE-5-MONOPHOSPHATE Mass: 306.209 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₀H₁₅N₂O₇P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 415 / 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: 2.25 Å³/Da / Density % sol: 45.26 %
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: Mar 20, 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: 1.45→50 Å / Num. obs: 72011 / % possible obs: 100 % / Redundancy: 9.6 % / CC_1/2: 0.999 / Net I/σ(I): 22.8
Reflection shell	Resolution: 1.45→1.54 Å / Num. unique obs: 11434 / CC_1/2: 0.969

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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: 1.45→46.059 Å / Cor.coef. F_o:F_c: 0.971 / Cor.coef. F_o:F_c free: 0.957 / SU B: 1.661 / SU ML: 0.062 / Cross valid method: FREE R-VALUE / ESU R: 0.076 / ESU R Free: 0.082
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2289	7291	10.125 %
R_work	0.1882	64717	-
all	0.192	-	-
obs	-	72008	99.978 %

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: 20.116 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.695 Å²	-0 Å²	0 Å²
2-	-	0.695 Å²	0 Å²
3-	-	-	-1.389 Å²

Refinement step

Cycle: LAST / Resolution: 1.45→46.059 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3035	0	52	415	3502

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.013	0.013	3313
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	3182
X-RAY DIFFRACTION	r_angle_refined_deg	1.894	1.643	4477
X-RAY DIFFRACTION	r_angle_other_deg	1.532	1.588	7373
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.451	5	432
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	32.003	23.399	153
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.407	15	602
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	12.998	15	15
X-RAY DIFFRACTION	r_chiral_restr	0.099	0.2	432
X-RAY DIFFRACTION	r_gen_planes_refined	0.01	0.02	3792
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	713
X-RAY DIFFRACTION	r_nbd_refined	0.228	0.2	717
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.18	0.2	2894
X-RAY DIFFRACTION	r_nbtor_refined	0.168	0.2	1608
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.082	0.2	1520
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.167	0.2	280
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.117	0.2	25
X-RAY DIFFRACTION	r_nbd_other	0.172	0.2	118
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.208	0.2	44
X-RAY DIFFRACTION	r_mcbond_it	1.652	1.834	1677
X-RAY DIFFRACTION	r_mcbond_other	1.652	1.834	1677
X-RAY DIFFRACTION	r_mcangle_it	2.176	2.749	2126
X-RAY DIFFRACTION	r_mcangle_other	2.176	2.75	2127
X-RAY DIFFRACTION	r_scbond_it	2.734	2.21	1636
X-RAY DIFFRACTION	r_scbond_other	2.733	2.212	1637
X-RAY DIFFRACTION	r_scangle_it	4.141	3.17	2351
X-RAY DIFFRACTION	r_scangle_other	4.14	3.172	2352
X-RAY DIFFRACTION	r_lrange_it	5.249	24.032	3838
X-RAY DIFFRACTION	r_lrange_other	5.248	24.046	3839

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 (%)
1.45-1.488	0.352	550	0.312	4654	X-RAY DIFFRACTION	99.9232
1.488-1.528	0.369	457	0.303	4670	X-RAY DIFFRACTION	100
1.528-1.573	0.328	509	0.293	4434	X-RAY DIFFRACTION	100
1.573-1.621	0.315	486	0.269	4379	X-RAY DIFFRACTION	100
1.621-1.674	0.266	484	0.237	4175	X-RAY DIFFRACTION	100
1.674-1.733	0.279	445	0.234	4063	X-RAY DIFFRACTION	100
1.733-1.798	0.263	468	0.23	3913	X-RAY DIFFRACTION	100
1.798-1.871	0.263	428	0.224	3832	X-RAY DIFFRACTION	100
1.871-1.955	0.249	439	0.22	3600	X-RAY DIFFRACTION	100
1.955-2.05	0.248	386	0.215	3537	X-RAY DIFFRACTION	99.9745
2.05-2.16	0.243	376	0.201	3305	X-RAY DIFFRACTION	100
2.16-2.291	0.226	341	0.196	3219	X-RAY DIFFRACTION	99.9719
2.291-2.449	0.236	339	0.18	2968	X-RAY DIFFRACTION	100
2.449-2.645	0.222	298	0.172	2819	X-RAY DIFFRACTION	99.9679
2.645-2.896	0.219	319	0.162	2552	X-RAY DIFFRACTION	99.9652
2.896-3.237	0.216	280	0.168	2358	X-RAY DIFFRACTION	99.9621
3.237-3.735	0.208	244	0.156	2078	X-RAY DIFFRACTION	100
3.735-4.568	0.148	186	0.131	1825	X-RAY DIFFRACTION	100
4.568-6.433	0.199	162	0.155	1447	X-RAY DIFFRACTION	100
6.433-46.059	0.191	94	0.164	889	X-RAY DIFFRACTION	99.5947

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