PDB-8acx: Pathogen effector of Zymoseptoria tritici: Zt-KP4

ID or keywords:

Entry

Database: PDB / ID: 8acx

Title

Pathogen effector of Zymoseptoria tritici: Zt-KP4

Components

Hce2 domain-containing protein

Keywords

UNKNOWN FUNCTION / FUNGAL TOXIN ZYMOSEPTORIA TRITICI KP4-LIKE

Function / homology

Ecp2 effector protein / Pathogen effector; putative necrosis-inducing factor / Ecp2 effector protein domain-containing protein

Function and homology information

Biological species

Zymoseptoria tritici (fungus)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.9 Å

Authors

Hoh, F. / Padilla, A. / De Guillen, K.

Funding support

France, 1items

Citation

Journal: To Be Published
Title: Structure of ZT-PK4:a pathogen effector protein of Zymoseptoria tritici at 1.9 A
Authors: De Guillen, K. / Padilla, A. / Hoh, F.

History

Deposition	Jul 7, 2022	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jan 17, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	8acx.cif.gz	342.4 KB	Display	PDBx/mmCIF format
PDB format	pdb8acx.ent.gz	279.4 KB	Display	PDB format
PDBx/mmJSON format	8acx.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ac/8acx ftp://data.pdbj.org/pub/pdb/validation_reports/ac/8acx	HTTPS FTP

-
Related structure data

Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Hce2 domain-containing protein

B: Hce2 domain-containing protein

C: Hce2 domain-containing protein

D: Hce2 domain-containing protein

E: Hce2 domain-containing protein

F: Hce2 domain-containing protein

G: Hce2 domain-containing protein

H: Hce2 domain-containing protein

121 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Hce2 domain-containing protein

D: Hce2 domain-containing protein

defined by author&software
Evidence: gel filtration
30.3 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Hce2 domain-containing protein

G: Hce2 domain-containing protein

defined by author&software
Evidence: gel filtration
30.3 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: Hce2 domain-containing protein

F: Hce2 domain-containing protein

defined by author&software
Evidence: gel filtration
30.3 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

E: Hce2 domain-containing protein

H: Hce2 domain-containing protein

defined by author&software
Evidence: gel filtration
30.3 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	109.108, 109.108, 252.755
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	146
Space group name H-M	H3

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	ASN	ASN	SER	SER	A	A	23 - 147	20 - 144
2	1	ASN	ASN	SER	SER	B	B	23 - 147	20 - 144
1	2	ASN	ASN	SER	SER	A	A	23 - 147	20 - 144
2	2	ASN	ASN	SER	SER	C	C	22 - 147	19 - 144
1	3	CYS	CYS	SER	SER	A	A	24 - 147	21 - 144
2	3	CYS	CYS	SER	SER	D	D	24 - 147	21 - 144
1	4	ASN	ASN	SER	SER	A	A	23 - 147	20 - 144
2	4	ASN	ASN	SER	SER	E	E	23 - 147	20 - 144
1	5	SER	SER	HIS	HIS	A	A	27 - 146	24 - 143
2	5	SER	SER	HIS	HIS	F	F	27 - 146	24 - 143
1	6	ASN	ASN	SER	SER	A	A	22 - 147	19 - 144
2	6	ASN	ASN	SER	SER	G	G	22 - 147	19 - 144
1	7	CYS	CYS	HIS	HIS	A	A	24 - 146	21 - 143
2	7	CYS	CYS	HIS	HIS	H	H	24 - 146	21 - 143
1	8	ASN	ASN	SER	SER	B	B	22 - 147	19 - 144
2	8	ASN	ASN	SER	SER	C	C	22 - 147	19 - 144
1	9	CYS	CYS	SER	SER	B	B	24 - 147	21 - 144
2	9	CYS	CYS	SER	SER	D	D	24 - 147	21 - 144
1	10	LEU	LEU	SER	SER	B	B	20 - 147	17 - 144
2	10	LEU	LEU	SER	SER	E	E	20 - 147	17 - 144
1	11	SER	SER	GLY	GLY	B	B	27 - 145	24 - 142
2	11	SER	SER	GLY	GLY	F	F	27 - 145	24 - 142
1	12	ASN	ASN	SER	SER	B	B	23 - 147	20 - 144
2	12	ASN	ASN	SER	SER	G	G	23 - 147	20 - 144
1	13	ASP	ASP	HIS	HIS	B	B	25 - 146	22 - 143
2	13	ASP	ASP	HIS	HIS	H	H	25 - 146	22 - 143
1	14	ASN	ASN	HIS	HIS	C	C	23 - 146	20 - 143
2	14	ASN	ASN	HIS	HIS	D	D	23 - 146	20 - 143
1	15	LEU	LEU	SER	SER	C	C	20 - 147	17 - 144
2	15	LEU	LEU	SER	SER	E	E	20 - 147	17 - 144
1	16	SER	SER	GLY	GLY	C	C	27 - 145	24 - 142
2	16	SER	SER	GLY	GLY	F	F	27 - 145	24 - 142
1	17	ASN	ASN	SER	SER	C	C	22 - 147	19 - 144
2	17	ASN	ASN	SER	SER	G	G	23 - 147	20 - 144
1	18	ASN	ASN	GLY	GLY	C	C	23 - 145	20 - 142
2	18	ASN	ASN	GLY	GLY	H	H	23 - 145	20 - 142
1	19	CYS	CYS	SER	SER	D	D	24 - 147	21 - 144
2	19	CYS	CYS	SER	SER	E	E	24 - 147	21 - 144
1	20	SER	SER	GLY	GLY	D	D	27 - 145	24 - 142
2	20	SER	SER	GLY	GLY	F	F	27 - 145	24 - 142
1	21	CYS	CYS	SER	SER	D	D	24 - 147	21 - 144
2	21	CYS	CYS	SER	SER	G	G	24 - 147	21 - 144
1	22	ASN	ASN	HIS	HIS	D	D	23 - 146	20 - 143
2	22	ASN	ASN	HIS	HIS	H	H	23 - 146	20 - 143
1	23	SER	SER	GLY	GLY	E	E	27 - 145	24 - 142
2	23	SER	SER	GLY	GLY	F	F	27 - 145	24 - 142
1	24	ASN	ASN	SER	SER	E	E	22 - 147	19 - 144
2	24	ASN	ASN	SER	SER	G	G	22 - 147	19 - 144
1	25	CYS	CYS	HIS	HIS	E	E	24 - 146	21 - 143
2	25	CYS	CYS	HIS	HIS	H	H	24 - 146	21 - 143
1	26	SER	SER	HIS	HIS	F	F	27 - 146	24 - 143
2	26	SER	SER	HIS	HIS	G	G	27 - 146	24 - 143
1	27	SER	SER	HIS	HIS	F	F	27 - 146	24 - 143
2	27	SER	SER	HIS	HIS	H	H	27 - 146	24 - 143
1	28	ASP	ASP	HIS	HIS	G	G	25 - 146	22 - 143
2	28	ASP	ASP	HIS	HIS	H	H	25 - 146	22 - 143

NCS ensembles :

#1: Protein	Hce2 domain-containing protein Mass: 15147.969 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Zymoseptoria tritici (fungus) / Gene: ZT1E4_G10522 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2H1H404
#2: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 157 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.39 Å³/Da / Density % sol: 48.52 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / Details: sodium acetate and PEG 300

-
Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

ESRF

/ Beamline: MASSIF-1 / Wavelength: 1 Å

Detector

Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Oct 3, 2018

Radiation

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

Radiation wavelength

Wavelength: 1 Å / Relative weight: 1

Reflection twin

Crystal-ID	ID	Operator	Domain-ID	Fraction
1	1	H, K, L	1	0.71
1	1	K, H, -L	2	0.29

Reflection

Resolution: 1.9→46.44 Å / Num. obs: 86240 / % possible obs: 97 % / Redundancy: 9.25 % / CC_1/2: 0.999 / Net I/σ(I): 14.9

Reflection shell

Resolution: 1.9→2.01 Å / Num. unique obs: 2800 / CC_1/2: 0.381

-
Phasing

Phasing	Method: molecular replacement

-
Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing
PDB_EXTRACT	3.27	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: Itasser model

Resolution: 1.9→46.44 Å / Cor.coef. F_o:F_c: 0.974 / Cor.coef. F_o:F_c free: 0.965 / SU B: 6.876 / SU ML: 0.096 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.041 / ESU R Free: 0.027 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2199	1042	1.3 %	RANDOM
R_work	0.1709	-	-	-
obs	0.1715	81506	93.91 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso max: 83.57 Å² / B_iso mean: 56.59 Å² / B_iso min: 49.1 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-3.8 Å²	-0 Å²	-0 Å²
2-	-	-3.8 Å²	-0 Å²
3-	-	-	7.6 Å²

Refinement step

Cycle: final / Resolution: 1.9→46.44 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6616	0	0	157	6773
B_iso mean	-	-	-	56.25	-
Num. residues	-	-	-	-	881

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.014	0.013	6716
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.015	6369
X-RAY DIFFRACTION	r_angle_refined_deg	1.889	1.62	9098
X-RAY DIFFRACTION	r_angle_other_deg	1.317	1.591	14592
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	8.224	5	866
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.084	22.033	300
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.633	15	1072
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	24.442	15	42
X-RAY DIFFRACTION	r_chiral_restr	0.084	0.2	897
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.02	7634
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1558
X-RAY DIFFRACTION	r_rigid_bond_restr	5.296	3	13085

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-ID	Dom-ID	Auth asym-ID	Number	Rms dev position (Å)
1	1	A	3277	0.09
1	2	B	3277	0.09
2	1	A	3149	0.09
2	2	C	3149	0.09
3	1	A	3161	0.1
3	2	D	3161	0.1
4	1	A	3266	0.09
4	2	E	3266	0.09
5	1	A	2961	0.09
5	2	F	2961	0.09
6	1	A	3316	0.11
6	2	G	3316	0.11
7	1	A	3109	0.1
7	2	H	3109	0.1
8	1	B	3297	0.07
8	2	C	3297	0.07
9	1	B	3211	0.1
9	2	D	3211	0.1
10	1	B	3401	0.08
10	2	E	3401	0.08
11	1	B	3075	0.08
11	2	F	3075	0.08
12	1	B	3372	0.09
12	2	G	3372	0.09
13	1	B	3208	0.08
13	2	H	3208	0.08
14	1	C	3206	0.09
14	2	D	3206	0.09
15	1	C	3398	0.09
15	2	E	3398	0.09
16	1	C	2910	0.09
16	2	F	2910	0.09
17	1	C	3252	0.09
17	2	G	3252	0.09
18	1	C	3164	0.09
18	2	H	3164	0.09
19	1	D	3262	0.09
19	2	E	3262	0.09
20	1	D	3027	0.09
20	2	F	3027	0.09
21	1	D	3220	0.1
21	2	G	3220	0.1
22	1	D	3167	0.12
22	2	H	3167	0.12
23	1	E	3030	0.1
23	2	F	3030	0.1
24	1	E	3350	0.1
24	2	G	3350	0.1
25	1	E	3208	0.09
25	2	H	3208	0.09
26	1	F	2945	0.1
26	2	G	2945	0.1
27	1	F	2965	0.08
27	2	H	2965	0.08
28	1	G	3177	0.1
28	2	H	3177	0.1

LS refinement shell

Resolution: 1.904→1.954 Å / R_factor R_free error: 0 / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.583	42	-
R_work	0.592	3367	-
all	-	3409	-
obs	-	-	52.01 %

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	0.6996	-0.5233	0.1428	1.0418	0.1046	0.9304	0.0122	0.0881	0.1256	-0.0661	0.0258	-0.0107	-0.188	0.0271	-0.0379	0.0524	-0.0114	0.0067	0.0757	0.0125	0.0588	50.5126	70.7681	74.2475
2	1.2965	0.2794	-0.2064	1.2987	-0.0113	0.6975	-0.0135	0.0542	-0.0808	-0.0674	-0.007	0.0826	0.0034	-0.0775	0.0205	0.0102	0.0029	-0.011	0.012	-0.0058	0.0243	14.8966	37.3338	79.5436
3	1.2231	0.0674	-0.3058	0.7717	-0.2177	1.1392	-0.0547	0.1147	0.0803	-0.0865	-0.0006	-0.0133	0.0014	-0.0108	0.0553	0.0563	-0.0065	-0.0012	0.0316	0.0172	0.0242	51.5408	52.7536	51.213
4	0.6573	0.3996	0.2331	1.1254	-0.2562	1.2752	0.057	-0.1036	0.0746	0.1284	0	-0.009	-0.1253	-0.0318	-0.057	0.0508	0.0216	0.0018	0.0834	-0.0197	0.0484	47.3316	69.2641	96.2643
5	1.3576	-0.4905	-0.0653	0.9191	-0.1518	0.9284	-0.0328	-0.0588	0.0472	0.1159	0.0044	0.0688	-0.0165	-0.0753	0.0284	0.0674	0.0128	0.0074	0.0426	-0.0173	0.0168	27.1052	38.0784	114.3459
6	1.3238	-0.1458	-0.4678	0.9136	-0.4021	0.8015	-0.0943	0.1591	0.0271	-0.0119	0.0536	0.1531	0.0106	-0.1746	0.0406	0.0679	-0.0299	-0.0059	0.1001	-0.0179	0.0704	31.1162	46.2041	56.7923
7	0.9692	-0.0594	0.3157	1.4606	-0.1905	0.7986	0.0001	-0.026	0.0946	0.0562	-0.0486	0.0091	-0.1152	-0.0123	0.0486	0.0254	-0.0081	0.0048	0.0266	-0.0137	0.0193	21.8001	55.9174	90.2109
8	1.2233	0.2082	-0.1909	0.4043	-0.013	1.0165	-0.0174	-0.1432	0.0636	0.1348	0.0061	0.0617	-0.0101	-0.0515	0.0113	0.0713	0.0037	0.0027	0.0908	-0.0178	0.0341	52.5374	52.477	119.3815

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	22 - 147
2	X-RAY DIFFRACTION	2	B	20 - 147
3	X-RAY DIFFRACTION	3	C	19 - 147
4	X-RAY DIFFRACTION	4	D	23 - 147
5	X-RAY DIFFRACTION	5	E	20 - 147
6	X-RAY DIFFRACTION	6	F	27 - 146
7	X-RAY DIFFRACTION	7	G	21 - 147
8	X-RAY DIFFRACTION	8	H	23 - 146

-
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