PDB-8h29: Serine Palmitoyltransferase from Sphingobacterium multivorum comp...

ID or keywords:

Entry

Database: PDB / ID: 8h29

Title

Serine Palmitoyltransferase from Sphingobacterium multivorum complexed with L-threonine

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 / sphingosine biosynthetic process / ceramide 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 5, 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	8h29.cif.gz	111.1 KB	Display	PDBx/mmCIF format
PDB format	pdb8h29.ent.gz	80.8 KB	Display	PDB format
PDBx/mmJSON format	8h29.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8h29_validation.pdf.gz	826.7 KB	Display	wwPDB validaton report
Full document	8h29_full_validation.pdf.gz	828.7 KB	Display
Data in XML	8h29_validation.xml.gz	21.5 KB	Display
Data in CIF	8h29_validation.cif.gz	33.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/h2/8h29 ftp://data.pdbj.org/pub/pdb/validation_reports/h2/8h29	HTTPS FTP

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Related structure data

Related structure data	8h1qC 8h1wC 8h1yC 8h20C 8h21C 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

44.7 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
89.5 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	61.083, 61.083, 207.890
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-765- HOH
2	1	A-799- 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-2BO / N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)-L-threonine Mass: 350.262 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₂H₁₉N₂O₈P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 465 / 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: 2.24 Å³/Da / Density % sol: 45.15 %
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-5A / Wavelength: 0.98 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 11, 2020
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: 70978 / % possible obs: 99.9 % / Redundancy: 9.3 % / CC_1/2: 1 / Net I/σ(I): 31.4
Reflection shell	Resolution: 1.45→1.54 Å / Num. unique obs: 11258 / CC_1/2: 0.967

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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→43.23 Å / Cor.coef. F_o:F_c: 0.977 / Cor.coef. F_o:F_c free: 0.969 / SU B: 0.971 / SU ML: 0.038 / Cross valid method: FREE R-VALUE / ESU R: 0.06 / ESU R Free: 0.064
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.174	7165	10.103 %
R_work	0.1446	63757	-
all	0.148	-	-
obs	-	70922	99.924 %

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: 17.457 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.003 Å²	0 Å²	-0 Å²
2-	-	-0.003 Å²	-0 Å²
3-	-	-	0.006 Å²

Refinement step

Cycle: LAST / Resolution: 1.45→43.23 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3027	0	59	465	3551

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.013	0.013	3366
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.015	3212
X-RAY DIFFRACTION	r_angle_refined_deg	1.867	1.645	4561
X-RAY DIFFRACTION	r_angle_other_deg	1.585	1.587	7448
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.425	5	444
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	31.535	23.526	156
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.562	15	605
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.645	15	15
X-RAY DIFFRACTION	r_chiral_restr	0.102	0.2	441
X-RAY DIFFRACTION	r_gen_planes_refined	0.01	0.02	3891
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	724
X-RAY DIFFRACTION	r_nbd_refined	0.229	0.2	726
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.18	0.2	2962
X-RAY DIFFRACTION	r_nbtor_refined	0.173	0.2	1628
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.084	0.2	1424
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.185	0.2	292
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.159	0.2	23
X-RAY DIFFRACTION	r_nbd_other	0.192	0.2	137
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.176	0.2	44
X-RAY DIFFRACTION	r_mcbond_it	1.318	1.568	1707
X-RAY DIFFRACTION	r_mcbond_other	1.318	1.566	1703
X-RAY DIFFRACTION	r_mcangle_it	1.786	2.351	2174
X-RAY DIFFRACTION	r_mcangle_other	1.786	2.355	2173
X-RAY DIFFRACTION	r_scbond_it	2.47	1.871	1659
X-RAY DIFFRACTION	r_scbond_other	2.469	1.872	1660
X-RAY DIFFRACTION	r_scangle_it	3.461	2.69	2387
X-RAY DIFFRACTION	r_scangle_other	3.461	2.692	2388
X-RAY DIFFRACTION	r_lrange_it	5.059	20.766	3904
X-RAY DIFFRACTION	r_lrange_other	5.058	20.775	3905

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 (%)
1.45-1.487	0.225	531	0.194	4635	X-RAY DIFFRACTION	100
1.487-1.528	0.22	441	0.18	4578	X-RAY DIFFRACTION	100
1.528-1.572	0.202	496	0.165	4390	X-RAY DIFFRACTION	100
1.572-1.621	0.191	483	0.157	4253	X-RAY DIFFRACTION	100
1.621-1.674	0.188	485	0.157	4116	X-RAY DIFFRACTION	100
1.674-1.733	0.191	438	0.154	4055	X-RAY DIFFRACTION	99.9778
1.733-1.798	0.183	462	0.149	3874	X-RAY DIFFRACTION	100
1.798-1.871	0.166	427	0.143	3711	X-RAY DIFFRACTION	99.9758
1.871-1.954	0.169	430	0.144	3575	X-RAY DIFFRACTION	99.9501
1.954-2.049	0.181	368	0.145	3467	X-RAY DIFFRACTION	100
2.049-2.16	0.161	380	0.144	3296	X-RAY DIFFRACTION	100
2.16-2.291	0.176	327	0.14	3130	X-RAY DIFFRACTION	99.9422
2.291-2.448	0.182	336	0.138	2955	X-RAY DIFFRACTION	99.9696
2.448-2.644	0.169	305	0.128	2741	X-RAY DIFFRACTION	99.8034
2.644-2.895	0.171	308	0.135	2533	X-RAY DIFFRACTION	99.7893
2.895-3.236	0.178	270	0.142	2304	X-RAY DIFFRACTION	99.9612
3.236-3.733	0.163	241	0.133	2062	X-RAY DIFFRACTION	99.8266
3.733-4.564	0.128	186	0.121	1797	X-RAY DIFFRACTION	99.7987
4.564-6.423	0.194	157	0.167	1410	X-RAY DIFFRACTION	99.0518
6.423-43.23	0.181	94	0.174	875	X-RAY DIFFRACTION	99.1812

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