PDB-8jor: Structure of an acyltransferase involved in mannosylerythritol li...

ID or keywords:

Entry

Database: PDB / ID: 8jor

Title

Structure of an acyltransferase involved in mannosylerythritol lipid formation from Pseudozyma tsukubaensis in type A crystal

Components

Acyltransferase

Keywords

TRANSFERASE / acyltransferase

Function / homology

Chloramphenicol acetyltransferase-like domain superfamily / acyltransferase activity / Acyltransferase

Function and homology information

Biological species

Pseudozyma tsukubaensis (fungus)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.45 Å

Authors

Nakamichi, Y. / Saika, A. / Watanabe, M. / Fujii, T. / Morita, T.

Funding support

1items

Citation

Journal: Front Bioeng Biotechnol / Year: 2023
Title: Structural identification of catalytic His158 of PtMAC2p from Pseudozyma tsukubaensis , an acyltransferase involved in mannosylerythritol lipids formation.
Authors: Nakamichi, Y. / Saika, A. / Watanabe, M. / Fujii, T. / Morita, T.

History

Deposition	Jun 8, 2023	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Apr 17, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	8jor.cif.gz	250 KB	Display	PDBx/mmCIF format
PDB format	pdb8jor.ent.gz	197.7 KB	Display	PDB format
PDBx/mmJSON format	8jor.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	8jor_validation.pdf.gz	435.9 KB	Display	wwPDB validaton report
Full document	8jor_full_validation.pdf.gz	438 KB	Display
Data in XML	8jor_validation.xml.gz	27.8 KB	Display
Data in CIF	8jor_validation.cif.gz	43.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/jo/8jor ftp://data.pdbj.org/pub/pdb/validation_reports/jo/8jor	HTTPS FTP

-
Related structure data

Related structure data	8josC 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
Related items in Molecule of the Month	#153 - Sep 2012 Pyruvate Dehydrogenase Complex similarity (1) #154 - Oct 2012 Citric Acid Cycle similarity (1)

Deposited unit

A: Acyltransferase

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	53.043, 83.073, 131.035
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Acyltransferase Mass: 62716.453 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudozyma tsukubaensis (fungus) / Gene: PtMAC2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2Z6ERP5
#2: Chemical	ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₀H₂₂O₆ / Comment: precipitant*YM
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 702 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.3 Å³/Da / Density % sol: 46.56 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 21% PEG 3350, 300mM lithium chloride

-
Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

SPring-8

/ Beamline: BL44XU / Wavelength: 0.9 Å

Detector

Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 20, 2021

Radiation

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

Radiation wavelength

Wavelength: 0.9 Å / Relative weight: 1

Reflection

Resolution: 1.45→44.73 Å / Num. obs: 103745 / % possible obs: 99.8 % / Redundancy: 7.4 % / B_iso Wilson estimate: 17.53 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.075 / R_pim(I) all: 0.03 / R_rim(I) all: 0.081 / Net I/σ(I): 15.68

Reflection shell

Diffraction-ID: 1

Resolution (Å)	R_merge(I) obs	Mean I/σ(I) obs	Num. unique obs	CC_1/2	R_rim(I) all	% possible all
1.45-1.53	1.177	2.29	16481	0.729	1.262	99.2
1.53-1.64	0.73		15610	0.868	0.785
1.64-1.77	0.418		14586	0.954	0.448
1.77-1.94	0.233		13437	0.983	0.249
1.94-2.17	0.126		12189	0.993	0.135
2.17-2.5	0.077		10829	0.996	0.083
2.5-3.06	0.053		9216	0.998	0.056
3.06-4.32	0.037		7214	0.999	0.04
4.32-44.73	0.033		4183	0.999	0.035	99.6

-
Processing

Software

Name	Version	Classification
PHENIX	1.20.1_4487	refinement
XDS	Jan 10, 2022	data scaling
XDS	Jan 10, 2022	data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.45→35.08 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.33 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1943	5187	5 %	0
R_work	0.1708	-	-	-
obs	0.172	103733	99.79 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.45→35.08 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4242	0	16	702	4960

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	4633
X-RAY DIFFRACTION	f_angle_d	0.897	6328
X-RAY DIFFRACTION	f_dihedral_angle_d	10.541	673
X-RAY DIFFRACTION	f_chiral_restr	0.081	696
X-RAY DIFFRACTION	f_plane_restr	0.009	849

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 (%)
1.45-1.46	0.351	168	0.2981	3179	X-RAY DIFFRACTION	98
1.46-1.48	0.3226	169	0.2718	3225	X-RAY DIFFRACTION	99
1.48-1.5	0.2732	169	0.2523	3207	X-RAY DIFFRACTION	100
1.5-1.52	0.2673	173	0.2306	3292	X-RAY DIFFRACTION	99
1.52-1.54	0.2359	170	0.2136	3224	X-RAY DIFFRACTION	100
1.54-1.56	0.2185	172	0.2049	3260	X-RAY DIFFRACTION	100
1.56-1.58	0.2081	169	0.2033	3225	X-RAY DIFFRACTION	100
1.58-1.6	0.2385	174	0.1912	3293	X-RAY DIFFRACTION	100
1.6-1.63	0.2138	170	0.193	3224	X-RAY DIFFRACTION	100
1.63-1.66	0.2347	172	0.1805	3287	X-RAY DIFFRACTION	100
1.66-1.68	0.2146	171	0.1785	3230	X-RAY DIFFRACTION	100
1.68-1.72	0.2128	171	0.1732	3255	X-RAY DIFFRACTION	100
1.72-1.75	0.1817	172	0.175	3265	X-RAY DIFFRACTION	100
1.75-1.78	0.1877	172	0.1736	3274	X-RAY DIFFRACTION	100
1.78-1.82	0.1865	173	0.1779	3287	X-RAY DIFFRACTION	100
1.82-1.87	0.2089	171	0.1835	3259	X-RAY DIFFRACTION	100
1.87-1.91	0.1908	172	0.177	3264	X-RAY DIFFRACTION	100
1.91-1.96	0.2205	174	0.1716	3306	X-RAY DIFFRACTION	100
1.96-2.02	0.1665	173	0.1634	3282	X-RAY DIFFRACTION	100
2.02-2.09	0.1897	171	0.1631	3247	X-RAY DIFFRACTION	100
2.09-2.16	0.2015	173	0.1664	3294	X-RAY DIFFRACTION	100
2.16-2.25	0.1919	175	0.1653	3325	X-RAY DIFFRACTION	100
2.25-2.35	0.199	173	0.1636	3281	X-RAY DIFFRACTION	100
2.35-2.47	0.1738	174	0.174	3299	X-RAY DIFFRACTION	100
2.47-2.63	0.1901	174	0.1759	3315	X-RAY DIFFRACTION	100
2.63-2.83	0.1992	175	0.1816	3321	X-RAY DIFFRACTION	100
2.83-3.12	0.2137	177	0.1765	3356	X-RAY DIFFRACTION	100
3.12-3.57	0.1829	175	0.1606	3342	X-RAY DIFFRACTION	100
3.57-4.49	0.166	179	0.1423	3391	X-RAY DIFFRACTION	100
4.49-35.08	0.1762	186	0.1579	3537	X-RAY DIFFRACTION	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	1.7346	0.2807	0.2581	0.9015	0.18	0.8485	0.0094	0.0325	-0.0949	-0.0657	-0.007	-0.0253	0.0989	0.0379	-0.011	0.1367	0.0278	0.0062	0.1038	-0.0118	0.0923	38.7897	33.2298	35.3346
2	0.8703	0.189	-0.5351	0.168	-0.0728	0.9609	-0.0037	0.0313	-0.0733	-0.008	-0.0092	-0.0133	0.1187	-0.0108	0.0163	0.1345	0.0019	-0.02	0.0871	-0.0155	0.1163	30.0391	30.4084	35.5144
3	0.4938	-0.8254	-0.5418	2.0739	1.4572	1.2241	0.0435	0.042	0.02	-0.1179	-0.0312	0.015	-0.1247	0.0468	-0.0026	0.0952	-0.0021	-0.0122	0.1141	0.0058	0.1081	39.1782	47.3079	42.9433
4	0.6435	0.259	0.1025	1.0534	0.4629	0.8057	0.006	-0.0357	-0.0101	0.0903	-0.0117	0.0535	0.0334	-0.0578	0.01	0.1123	0.0096	-0.0009	0.1033	0.0159	0.0992	24.7195	43.8082	59.263

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 227 through 340 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 341 through 447 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 448 through 539 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid -7 through 226 )

-
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