PDB-6sld: Structure of the Phosphatidylcholine Binding Mutant of Yeast Sec1...

ID or keywords:

Entry

Database: PDB / ID: 6sld

Title

Structure of the Phosphatidylcholine Binding Mutant of Yeast Sec14 Homolog Sfh1 (S175I,T177I) in Complex with Phosphatidylinositol

Components

CRAL-TRIO domain-containing protein YKL091C

Keywords

LIPID TRANSPORT /

Sec14 / Sfh1 /

Phosphatidylcholine /

Phosphatidylinositol

Function / homology

Function and homology information

phosphatidylcholine binding /

phosphatidylinositol binding /

nucleus
Similarity search - Function

Biological species

Saccharomyces cerevisiae (brewer's yeast)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.4 Å

Authors

Berger, J. / Fitz, M. / Johnen, P. / Shanmugaratnam, S. / Hocker, B. / Stiel, A.C. / Schaaf, G.

Funding support

Germany, 4items

Organization	Grant number	Country
German Research Foundation	Emmy Noether grant 1274/2-1	Germany
German Research Foundation	SCHA 1274/5-1	Germany
German Research Foundation	GRK 2064	Germany
German Research Foundation	Germany's Excellence Strategy, EXC-2070_390732324_PhenoRob	Germany

Citation

Journal: To Be Published
Title: Structure of the Phosphatidylcholine Binding Mutant of Yeast Sec14 Homolog Sfh1 (S175I,T177I) in Complex with Phosphatidylinositol
Authors: Berger, J. / Fitz, M. / Johnen, P. / Shanmugaratnam, S. / Hocker, B. / Stiel, A.C. / Schaaf, G.

History

Deposition	Aug 19, 2019	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Aug 19, 2020	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	6sld.cif.gz	202.4 KB	Display	PDBx/mmCIF format
PDB format	pdb6sld.ent.gz	171.3 KB	Display	PDB format
PDBx/mmJSON format	6sld.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/sl/6sld ftp://data.pdbj.org/pub/pdb/validation_reports/sl/6sld	HTTPS FTP

-
Related structure data

Similar structure data	3b7q-1 3b7n-d 2qje-d 3q8g-d 3gvr-d 3b7q-2 3ttr-d 3v5a-d 2p1s-d 2zmb-d Search similar-shape structures by Omokage search (details) 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: CRAL-TRIO domain-containing protein YKL091C

hetero molecules

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

1

Idetical with deposited unit
defined by author

Unit cell

Length a, b, c (Å)	48.220, 70.810, 90.190
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	CRAL-TRIO domain-containing protein YKL091C Mass: 35825.082 Da / Num. of mol.: 1 / Mutation: S175I,T177I Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: YKL091C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE)-RIL / References: UniProt: P33324
#2: Chemical	ChemComp-B7N / (1R)-2-{[(S)-hydroxy{[(1S,2R,3R,4S,5S,6R)-2,3,4,5,6-pentahydroxycyclohexyl]oxy}phosphoryl]oxy}-1-[(octadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate Mass: 865.122 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄₅H₈₅O₁₃P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 391 / 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: 2.15 Å³/Da / Density % sol: 42.76 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.8 Details: 40% (w/v) PEG3350, 10% Glycerol (w/v), 100mM Kaliumphosphate 100mM Ammoniumacetat

-
Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

SLS

/ Beamline: X10SA / Wavelength: 1.00005 Å

Detector

Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 27, 2015

Radiation

Monochromator: DOUBLE-CRYSTAL SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1.00005 Å / Relative weight: 1

Reflection

Resolution: 1.396→45.095 Å / Num. obs: 61867 / % possible obs: 99.7 % / Redundancy: 12.746 % / B_iso Wilson estimate: 14.08 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.092 / R_rim(I) all: 0.095 / Χ²: 1.044 / Net I/σ(I): 17.47

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. possible	Num. unique obs	CC_1/2	R_rim(I) all	% possible all
1.4-1.43	11.732	1.274	1.92	50696	4521	4321	0.728	1.331	95.6
1.43-1.47	12.848	1.031	2.72	56814	4422	4422	0.856	1.073	100
1.47-1.51	12.47	0.811	3.48	53857	4320	4319	0.905	0.846	100
1.51-1.56	11.942	0.661	4.25	49762	4172	4167	0.931	0.69	99.9
1.56-1.61	13.443	0.538	5.47	54591	4061	4061	0.957	0.56	100
1.61-1.67	13.414	0.439	6.7	52329	3901	3901	0.97	0.456	100
1.67-1.73	13.372	0.355	8.15	50920	3808	3808	0.981	0.369	100
1.73-1.8	13.193	0.274	10.37	48089	3645	3645	0.986	0.285	100
1.8-1.88	12.554	0.212	12.87	44088	3512	3512	0.991	0.221	100
1.88-1.97	12.488	0.154	17.01	41923	3358	3357	0.995	0.16	100
1.97-2.08	13.781	0.122	21.84	44429	3225	3224	0.997	0.127	100
2.08-2.21	13.569	0.099	26.3	41167	3034	3034	0.997	0.103	100
2.21-2.36	13.228	0.083	30.81	37806	2858	2858	0.998	0.086	100
2.36-2.55	12.659	0.076	33.12	33913	2679	2679	0.998	0.079	100
2.55-2.79	11.454	0.065	35.06	28040	2449	2448	0.998	0.068	100
2.79-3.12	13.132	0.055	42.37	29705	2262	2262	0.999	0.058	100
3.12-3.6	12.656	0.046	48.77	25148	1987	1987	0.999	0.048	100
3.6-4.41	11.976	0.04	52.52	20670	1726	1726	0.999	0.042	100
4.41-6.24	11.167	0.038	50.92	15020	1346	1345	0.999	0.04	99.9
6.24-45.095	12.148	0.035	54.64	9609	792	791	0.999	0.037	99.9

-
Phasing

Phasing

Method:

molecular replacement

Phasing MR

	Highest resolution	Lowest resolution
Rotation	6.51 Å	45.1 Å
Translation	6.51 Å	45.1 Å

-
Processing

Software

Name	Version	Classification
XDS		data reduction
XSCALE		data scaling
PHASER	2.5.6	phasing
PHENIX		refinement
PDB_EXTRACT	3.25	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.4→45.095 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 15.97

	R_factor	Num. reflection	% reflection
R_free	0.1635	3094	5 %
R_work	0.1435	-	-
obs	0.1445	61865	99.66 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Displacement parameters

B_iso max: 83.73 Å² / B_iso mean: 18.7986 Å² / B_iso min: 6.92 Å²

Refinement step

Cycle: final / Resolution: 1.4→45.095 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2525	0	143	391	3059
B_iso mean	-	-	28.18	29.95	-
Num. residues	-	-	-	-	307

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	2656
X-RAY DIFFRACTION	f_angle_d	1.039	3582
X-RAY DIFFRACTION	f_chiral_restr	0.078	381
X-RAY DIFFRACTION	f_plane_restr	0.007	452
X-RAY DIFFRACTION	f_dihedral_angle_d	13.998	1030

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	% reflection obs (%)
1.4-1.4179	0.3092	130	0.2792	2461	93
1.4179-1.4411	0.2086	138	0.2359	2626	100
1.4411-1.466	0.265	140	0.2134	2657	100
1.466-1.4926	0.2584	138	0.2014	2626	100
1.4926-1.5214	0.2189	139	0.1866	2639	100
1.5214-1.5524	0.2227	141	0.1768	2674	100
1.5524-1.5862	0.2055	138	0.1695	2623	100
1.5862-1.6231	0.2077	140	0.1564	2661	100
1.6231-1.6637	0.1884	141	0.156	2688	100
1.6637-1.7086	0.1636	139	0.1493	2636	100
1.7086-1.7589	0.1787	141	0.1443	2668	100
1.7589-1.8157	0.1665	139	0.1388	2655	100
1.8157-1.8806	0.1711	141	0.1375	2667	100
1.8806-1.9559	0.1451	139	0.1255	2658	100
1.9559-2.0449	0.1481	142	0.1237	2680	100
2.0449-2.1527	0.1665	140	0.1214	2676	100
2.1527-2.2876	0.1552	142	0.1244	2688	100
2.2876-2.4642	0.1531	142	0.1245	2693	100
2.4642-2.7121	0.1645	143	0.1296	2720	100
2.7121-3.1045	0.151	143	0.138	2725	100
3.1045-3.911	0.1233	145	0.1279	2757	100
3.911-45.095	0.1609	153	0.1572	2893	100

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	0.152	-0.0663	-0.1943	0.092	-0.014	0.4064	-0.0229	-0.055	0.0464	-0.0428	-0.0343	0.028	-0.0448	-0.0638	-0	0.1207	-0.0164	-0.015	0.1166	-0.0017	0.1173	-34.6808	13.1819	-24.1355
2	0.6903	-0.1859	0.2954	0.6067	0.4748	0.9693	-0.0102	0.0102	0.0666	-0.0571	-0.044	0.1613	-0.082	-0.0197	-0.0019	0.1064	-0.0031	-0.0261	0.0819	0.0055	0.084	-31.1521	4.4356	-34.3874
3	0.3293	0.0306	0.3148	0.1622	-0.0008	0.3056	0.0342	0.0973	-0.0345	-0.2044	0.0066	-0.0537	0.2941	0.0903	-0.0004	0.145	0.0146	-0.0265	0.093	-0.004	0.0844	-24.9607	-5.7845	-30.113
4	0.9474	-0.1383	0.3584	0.7336	0.1764	0.8197	0.032	0.0094	-0.0812	0.0503	-0.0321	-0.0551	0.1409	0.034	0.0024	0.0918	-0.0088	0.0126	0.0806	0.007	0.087	-23.2933	-1.4326	-8.5028
5	0.1848	0.2189	0.2852	0.5836	0.2876	0.445	-0.0114	0.0738	-0.0332	-0.0042	0.0244	-0.0936	0.0345	0.1539	-0	0.0904	0.0052	0.0008	0.1381	0.0073	0.1009	-12.148	2.5205	-14.9513
6	0.593	0.1771	0.0688	0.4796	0.1235	0.6585	-0.0215	-0.0041	0.0027	0.0206	-0.0035	-0.0229	0.0039	0.0643	-0	0.0736	0.0032	-0.0022	0.0806	0.005	0.0791	-19.9459	9.0052	-5.989

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 4 through 26 )	A	4 - 26
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 27 through 64 )	A	27 - 64
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 65 through 83 )	A	65 - 83
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 84 through 174 )	A	84 - 174
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 175 through 217 )	A	175 - 217
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 218 through 310 )	A	218 - 310

-
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

-
Phasing

-
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

-Phasing

-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

-
Phasing

-
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