PDB-8h21: Serine Palmitoyltransferase from Sphingobacterium multivorum comp...

ID or keywords:

Entry

Database: PDB / ID: 8h21

Title

Serine Palmitoyltransferase from Sphingobacterium multivorum complexed with L-alanine

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 /

MOLECULAR REPLACEMENT / Resolution: 1.54 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

-
Download

PDBx/mmCIF format	8h21.cif.gz	111.2 KB	Display	PDBx/mmCIF format
PDB format	pdb8h21.ent.gz	80.8 KB	Display	PDB format
PDBx/mmJSON format	8h21.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	8h21_validation.pdf.gz	800 KB	Display	wwPDB validaton report
Full document	8h21_full_validation.pdf.gz	801.1 KB	Display
Data in XML	8h21_validation.xml.gz	21.8 KB	Display
Data in CIF	8h21_validation.cif.gz	34.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/h2/8h21 ftp://data.pdbj.org/pub/pdb/validation_reports/h2/8h21	HTTPS FTP

-
Related structure data

Related structure data	8h1qC 8h1wC 8h1yC 8h20C 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

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

Unit cell

Length a, b, c (Å)	61.234, 61.234, 208.182
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-701- HOH
2	1	A-724- 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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₂H₆O₂
#3: Chemical	ChemComp-PDA / 2-[(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL)-AMINO]-PROPIONIC ACID / PYRIDOXYL-ALANINE-5-PHOSPHATE Mass: 320.236 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₁H₁₇N₂O₇P / Feature type: SUBJECT OF INVESTIGATION
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 493 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.23 Å³/Da / Density % sol: 44.76 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG4000, sodium acetate, Tris-HCl

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: ROTATING ANODE / Type: RIGAKU FR-X / Wavelength: 1.5418 Å
Detector	Type: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Apr 14, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.5418 Å / Relative weight: 1
Reflection	Resolution: 1.54→50 Å / Num. obs: 58899 / % possible obs: 98.3 % / Redundancy: 17.8 % / CC_1/2: 0.999 / Net I/σ(I): 27.1
Reflection shell	Resolution: 1.54→1.63 Å / Num. unique obs: 8495 / CC_1/2: 0.965

-
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: 1.54→45.956 Å / Cor.coef. F_o:F_c: 0.965 / Cor.coef. F_o:F_c free: 0.947 / SU B: 1.682 / SU ML: 0.061 / Cross valid method: FREE R-VALUE / ESU R: 0.088 / ESU R Free: 0.093
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2164	5972	10.145 %
R_work	0.1722	52896	-
all	0.177	-	-
obs	-	58868	98.39 %

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: 16.383 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.012 Å²	-0 Å²	-0 Å²
2-	-	0.012 Å²	-0 Å²
3-	-	-	-0.025 Å²

Refinement step

Cycle: LAST / Resolution: 1.54→45.956 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3035	0	45	493	3573

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.013	3363
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	3218
X-RAY DIFFRACTION	r_angle_refined_deg	1.769	1.641	4561
X-RAY DIFFRACTION	r_angle_other_deg	1.524	1.588	7465
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.492	5	446
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	32.483	23.442	154
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.109	15	611
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.791	15	15
X-RAY DIFFRACTION	r_chiral_restr	0.09	0.2	440
X-RAY DIFFRACTION	r_gen_planes_refined	0.01	0.02	3896
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	729
X-RAY DIFFRACTION	r_nbd_refined	0.221	0.2	735
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.176	0.2	2960
X-RAY DIFFRACTION	r_nbtor_refined	0.169	0.2	1624
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.08	0.2	1527
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.19	0.2	328
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.095	0.2	2
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.147	0.2	28
X-RAY DIFFRACTION	r_nbd_other	0.178	0.2	120
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.174	0.2	51
X-RAY DIFFRACTION	r_mcbond_it	1.266	1.461	1712
X-RAY DIFFRACTION	r_mcbond_other	1.264	1.459	1708
X-RAY DIFFRACTION	r_mcangle_it	1.827	2.185	2182
X-RAY DIFFRACTION	r_mcangle_other	1.828	2.187	2181
X-RAY DIFFRACTION	r_scbond_it	2.155	1.773	1651
X-RAY DIFFRACTION	r_scbond_other	2.155	1.773	1652
X-RAY DIFFRACTION	r_scangle_it	3.314	2.544	2379
X-RAY DIFFRACTION	r_scangle_other	3.313	2.543	2380
X-RAY DIFFRACTION	r_lrange_it	4.993	19.667	3961
X-RAY DIFFRACTION	r_lrange_other	4.992	19.667	3962

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 (%)
1.54-1.58	0.302	389	0.247	3262	X-RAY DIFFRACTION	84.2215
1.58-1.623	0.265	398	0.22	3573	X-RAY DIFFRACTION	93.7662
1.623-1.67	0.265	394	0.211	3735	X-RAY DIFFRACTION	100
1.67-1.722	0.241	407	0.203	3560	X-RAY DIFFRACTION	100
1.722-1.778	0.255	418	0.2	3477	X-RAY DIFFRACTION	100
1.778-1.84	0.249	363	0.199	3406	X-RAY DIFFRACTION	100
1.84-1.91	0.248	370	0.19	3264	X-RAY DIFFRACTION	100
1.91-1.987	0.235	348	0.19	3178	X-RAY DIFFRACTION	100
1.987-2.076	0.222	341	0.182	3017	X-RAY DIFFRACTION	100
2.076-2.177	0.233	333	0.185	2918	X-RAY DIFFRACTION	100
2.177-2.294	0.222	308	0.173	2759	X-RAY DIFFRACTION	100
2.294-2.433	0.206	309	0.158	2619	X-RAY DIFFRACTION	100
2.433-2.601	0.206	256	0.156	2506	X-RAY DIFFRACTION	99.9638
2.601-2.809	0.205	279	0.158	2314	X-RAY DIFFRACTION	100
2.809-3.076	0.219	260	0.153	2134	X-RAY DIFFRACTION	100
3.076-3.437	0.202	231	0.159	1948	X-RAY DIFFRACTION	100
3.437-3.966	0.177	194	0.146	1753	X-RAY DIFFRACTION	100
3.966-4.849	0.155	158	0.129	1521	X-RAY DIFFRACTION	100
4.849-6.826	0.24	137	0.191	1206	X-RAY DIFFRACTION	100
6.826-45.956	0.188	78	0.196	740	X-RAY DIFFRACTION	99.2718

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi