PDB-8rkz: Crystal structure of a cysteine hydrolase from Phytophthora infestans

ID or keywords:

Entry

Database: PDB / ID: 8rkz

Title

Crystal structure of a cysteine hydrolase from Phytophthora infestans

Components

Isochorismatase family

Keywords

HYDROLASE / Phytophthora infestans / cysteine hydrolase

Function / homology

: / Isochorismatase-like / Isochorismatase-like superfamily / Isochorismatase domain / Isochorismatase family

Function and homology information

Biological species

Phytophthora infestans (potato late blight agent)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.3 Å

Authors

Altegoer, F. / Weiland, P. / Bange, G.

Funding support

Germany, 1items

Citation

Journal: To Be Published
Title: Structural and functional characterization of an isochorismate (ISC)-like protein in a plant-pathogenic fungus
Authors: Rubio Elizalde, I. / Christ, M. / Weiland, P. / Jalomo, E. / Voll, L. / Altegoer, F. / Bange, G.

History

Deposition	Jan 2, 2024	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jan 15, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8rkz.cif.gz	1.4 MB	Display	PDBx/mmCIF format
PDB format	pdb8rkz.ent.gz	1 MB	Display	PDB format
PDBx/mmJSON format	8rkz.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

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

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Related structure data

Related structure data	8rl0C C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

G: Isochorismatase family

H: Isochorismatase family

L: Isochorismatase family

M: Isochorismatase family

D: Isochorismatase family

J: Isochorismatase family

I: Isochorismatase family

K: Isochorismatase family

A: Isochorismatase family

P: Isochorismatase family

O: Isochorismatase family

N: Isochorismatase family

B: Isochorismatase family

C: Isochorismatase family

F: Isochorismatase family

E: Isochorismatase family

368 kDa, 16 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

G: Isochorismatase family

H: Isochorismatase family

L: Isochorismatase family

M: Isochorismatase family

defined by author&software
91.9 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

D: Isochorismatase family

J: Isochorismatase family

I: Isochorismatase family

K: Isochorismatase family

defined by author&software
91.9 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

A: Isochorismatase family

P: Isochorismatase family

O: Isochorismatase family

N: Isochorismatase family

defined by author&software
91.9 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

B: Isochorismatase family

C: Isochorismatase family

F: Isochorismatase family

E: Isochorismatase family

defined by author&software
91.9 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	81.340, 218.350, 101.590
Angle α, β, γ (deg.)	90.000, 102.410, 90.000
Int Tables number	4
Space group name H-M	P12₁1
Space group name Hall	P2yb
Symmetry operation	#1: x,y,z #2: -x,y+1/2,-z

#1: Protein	Isochorismatase family Mass: 22984.545 Da / Num. of mol.: 16 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Phytophthora infestans (potato late blight agent) Gene: GN244_ATG15348, GN958_ATG18013 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A833SVL6
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1201 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	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: 2.4 Å³/Da / Density % sol: 48.66 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M di-Ammonium tartrate; 20 % (w/v) PEG 3350

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
Detector	Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 21, 2019
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9184 Å / Relative weight: 1
Reflection	Resolution: 2.3→47.83 Å / Num. obs: 152006 / % possible obs: 99.36 % / Redundancy: 3.8 % / B_iso Wilson estimate: 33.64 Å² / CC_1/2: 0.991 / R_merge(I) obs: 0.1907 / Net I/σ(I): 6.91
Reflection shell	Resolution: 2.3→2.382 Å / R_merge(I) obs: 1.169 / Mean I/σ(I) obs: 1.13 / Num. unique obs: 15213 / CC_1/2: 0.497

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Processing

Software

Name	Version	Classification
PHENIX	1.20.1_4487	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.3→47.83 Å / SU ML: 0.2942 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.8164
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2347	7595	5 %
R_work	0.1909	144327	-
obs	0.193	151922	99.38 %

Solvent computation

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

Displacement parameters

B_iso mean: 43.77 Å²

Refinement step

Cycle: LAST / Resolution: 2.3→47.83 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	24553	0	0	1201	25754

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0041	24971
X-RAY DIFFRACTION	f_angle_d	0.645	33801
X-RAY DIFFRACTION	f_chiral_restr	0.0457	4116
X-RAY DIFFRACTION	f_plane_restr	0.0051	4262
X-RAY DIFFRACTION	f_dihedral_angle_d	5.0223	3335

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 (%)
2.3-2.33	0.3524	256	0.3001	4857	X-RAY DIFFRACTION	99.49
2.33-2.35	0.3519	251	0.2846	4783	X-RAY DIFFRACTION	99.49
2.35-2.38	0.3193	253	0.2756	4802	X-RAY DIFFRACTION	99.65
2.38-2.41	0.2872	253	0.2604	4796	X-RAY DIFFRACTION	99.63
2.41-2.44	0.3282	250	0.2536	4774	X-RAY DIFFRACTION	99.35
2.44-2.48	0.2856	255	0.2531	4842	X-RAY DIFFRACTION	99.49
2.48-2.51	0.3171	253	0.2638	4797	X-RAY DIFFRACTION	99.41
2.51-2.55	0.3362	253	0.2666	4822	X-RAY DIFFRACTION	99.43
2.55-2.59	0.3246	252	0.2655	4782	X-RAY DIFFRACTION	99.49
2.59-2.63	0.2757	253	0.2482	4810	X-RAY DIFFRACTION	99.2
2.63-2.68	0.2833	252	0.2343	4775	X-RAY DIFFRACTION	99.02
2.68-2.73	0.2856	251	0.2336	4785	X-RAY DIFFRACTION	99.04
2.73-2.78	0.2915	250	0.2315	4748	X-RAY DIFFRACTION	98.27
2.78-2.84	0.2877	256	0.2226	4845	X-RAY DIFFRACTION	99.86
2.84-2.9	0.2696	253	0.2202	4823	X-RAY DIFFRACTION	99.88
2.9-2.97	0.269	252	0.2188	4788	X-RAY DIFFRACTION	99.76
2.97-3.04	0.2516	255	0.2192	4837	X-RAY DIFFRACTION	99.76
3.04-3.12	0.2708	255	0.2132	4850	X-RAY DIFFRACTION	99.69
3.12-3.21	0.2468	253	0.2097	4792	X-RAY DIFFRACTION	99.47
3.21-3.32	0.2347	252	0.1979	4794	X-RAY DIFFRACTION	99.33
3.32-3.44	0.2367	252	0.186	4795	X-RAY DIFFRACTION	99.14
3.44-3.57	0.2092	252	0.1694	4783	X-RAY DIFFRACTION	98.96
3.57-3.74	0.2166	253	0.172	4827	X-RAY DIFFRACTION	99.04
3.74-3.93	0.2121	254	0.1635	4819	X-RAY DIFFRACTION	99.82
3.93-4.18	0.1998	253	0.1543	4821	X-RAY DIFFRACTION	99.92
4.18-4.5	0.1784	257	0.138	4880	X-RAY DIFFRACTION	99.86
4.5-4.95	0.1655	253	0.1321	4796	X-RAY DIFFRACTION	99.1
4.95-5.67	0.1899	253	0.1682	4821	X-RAY DIFFRACTION	98.91
5.67-7.14	0.2334	255	0.186	4842	X-RAY DIFFRACTION	99.71
7.14-47.83	0.1725	255	0.1394	4841	X-RAY DIFFRACTION	98.3

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	1.48764697676	-0.0532763462869	-0.470840902291	3.05619069031	0.213180367657	2.04774643857	-0.0878302452565	-0.055251814133	-0.116165217316	0.127155165062	-0.0287516766344	0.438758216481	0.0928260499961	-0.229073035043	0.103191417127	0.229586514285	0.00864589329227	0.051417656213	0.29820954174	-0.024744862037	0.25908930462	-25.8484055557	-43.3635234731	83.4155123352
2	1.40442392161	-0.391707786411	-0.22465270083	2.55632271489	0.49120558142	1.1751699674	-0.0592711752705	-0.261294209538	0.217598010059	0.0646672879256	0.209702661341	-0.509086239976	-0.0982398118054	0.318099635979	-0.101809170978	0.233994856324	-0.00915403654674	-0.0647205802786	0.416000146849	-0.0873952473933	0.298890195415	17.7555914574	-36.2684205454	76.4575481189
3	2.35057041665	-0.312364437198	-0.958126367186	1.36988268599	0.504078151414	2.05821260957	-0.28282939152	-0.195456115454	-0.474412861058	0.2909984181	0.0970513673302	0.0610671517471	0.350453490794	0.0917702323603	0.150425143995	0.36648266749	0.0516213425447	0.061835626124	0.250419286237	0.0226432316372	0.308075423238	-0.978379584216	-61.9164472828	77.8800089253
4	1.97923126774	-0.338085495355	-0.361454794253	2.2469607955	0.362422961633	1.62388690568	0.0365571845344	-0.104183710918	0.266347167313	0.0691288759053	0.107663047252	-0.0981149804884	-0.182227239129	0.0460714239256	-0.119688976675	0.32692628204	-0.0149885434385	-0.0153146722885	0.245591568329	-0.0555268159454	0.210066836178	-7.18058780328	-17.7214999076	81.821983208
5	2.04218265664	0.267022474895	0.153629349679	1.86964230287	0.241444236798	2.07829070613	-0.0736239011569	0.0452774404991	0.183423587815	-0.0400409432127	-0.000238736106706	0.263865075496	-0.134218647317	-0.226230435749	0.0603085977964	0.213490900518	0.00233275132163	0.0230444397205	0.223250529559	0.00796144121659	0.249136814634	-20.1856563586	-122.952742052	69.0841833298
6	1.37201648323	-0.073621255093	0.285219486455	1.94952238029	-0.0787880965922	1.82497747666	-0.00477178980774	0.199657214388	0.0119904117228	-0.243721256275	0.0166009600464	-0.00738026402295	0.0642307601243	0.102114759281	-0.00955454377365	0.311560104969	-0.0467436030833	0.0252976768282	0.263966445094	-0.0109646535788	0.191421304211	3.17722339972	-126.88734873	47.8986842885
7	1.64970368576	-0.0596037878517	0.325987965463	1.72923738322	0.313690173003	1.76186899153	-0.00434331447291	-0.0122178063946	0.00205120159544	0.0395054842768	-0.00787226480628	-0.367268375538	-0.00450192458326	0.231708250818	0.000887983632057	0.229134575707	-0.0211162020518	0.0211547309758	0.251039996198	-0.00809981806723	0.29707068825	23.8070128157	-131.407564803	71.5253694517
8	1.71840385686	0.0394637718086	-0.516363700936	2.03159073922	0.0775668326849	1.08915844596	0.0565481706403	-0.347316048936	0.0799353728807	0.35462627591	-0.030874326906	-0.0126563661158	-0.0745121249267	0.0399361683771	-0.0251057561596	0.326158108064	-0.0211312330665	0.00734987785321	0.332460671415	-0.0176885505934	0.174580783473	0.487314498949	-127.585350982	92.4117340466
9	0.897026278958	0.373910006567	-0.688736253853	2.60140759958	-0.74736253893	1.9408655008	0.0445796578491	-0.018021252133	0.0820406389441	-0.118175084325	-0.0778733808168	-0.0643911339536	-0.0723268857468	0.0192476630481	0.0220585752702	0.198749161058	0.0235939835725	-0.0206124940611	0.203046823437	-0.00639531692136	0.218470462386	12.7647516426	-45.9423170924	42.809223353
10	1.40629140983	0.279904631625	-0.0307172464455	2.59747464263	-0.151654993879	1.17717848596	-0.0351705323856	0.0254098864805	-0.210326391575	-0.442708970066	-0.137557821838	-0.96661679264	0.316216218829	0.324362988933	0.138592273692	0.462234557034	0.120379727389	0.217071927341	0.346927050255	0.0928150811223	0.591110091158	30.9396430279	-71.480592983	41.4408753002
11	1.91560200822	0.461670078952	-0.244625492404	3.06860015873	-0.637428502438	1.65130332875	-0.173668598855	0.0436927303695	-0.310764807558	-0.779773059458	-0.00701088682714	-0.021289726128	0.533677024	-0.0876091410437	0.143682847997	0.669343070669	-0.00102644462556	0.100262490126	0.236161554962	-0.00732635454928	0.276759029614	5.20962472712	-89.931870062	41.7594770578
12	1.69529923811	0.109718673442	-0.590179661847	2.32096485538	-0.100919356393	1.74491880307	-0.123863075713	0.211143436139	-0.0117080559265	-0.380335195161	0.127868743164	0.614091325263	0.185185518529	-0.445860471086	-0.0155926872761	0.285765720264	-0.0743839611141	-0.131699795542	0.370291663543	-0.024407059479	0.380176774098	-13.2097263151	-64.3093733853	43.2115027365
13	1.65837574672	0.166715686446	0.183384210356	1.83451758412	-0.187402834589	1.66930872703	0.00477154124729	0.036484164418	0.230663959735	-0.103824282112	-0.0299767525109	-0.138051881487	-0.101744433155	-0.037452636988	0.0226005663482	0.295446651663	0.013073152091	0.00324141469298	0.238824956118	0.0174535826635	0.326962680971	18.1485128714	-94.2723219039	75.3496665202
14	2.05772426849	-0.839636858274	0.518864379409	2.00065148891	-0.209633584635	1.37687827215	-0.0757212673366	-0.312754008129	0.210036548969	0.289566966016	0.0127484938734	-0.197285174305	-0.097310022917	0.0473191331749	0.0413860516208	0.350667255987	-0.0127942342727	-0.0270783552958	0.293212060777	-0.100310691193	0.359732478111	32.2897842104	-93.9801447317	117.719514691
15	1.69318737271	0.0245286398356	-0.238331766061	1.73186343561	0.403755976366	2.13002786077	-0.0529687824739	0.137006699644	0.177495198057	-0.0292055462842	0.0216388180858	-0.299256189335	-0.0212224104953	0.36699983436	0.035519059825	0.257038722484	-0.0255176913221	0.00677399765828	0.338895156579	0.00993914820857	0.502277074215	46.4881207354	-93.3952592155	89.3137486076
16	1.98119213242	-0.0574562530812	-0.504645925418	1.69483398064	0.0530201294186	2.11487885547	0.0166151268611	-0.188444676416	0.23457752445	0.227121338747	-0.0626377282552	0.230921159771	0.0110615699644	-0.272137037045	0.040778118932	0.278163030532	-0.0149279110815	0.0320262084411	0.295861018133	-0.0707130410136	0.327057389849	3.98456469153	-94.2289808781	103.812382835

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

ID	Refine TLS-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	(chain 'G' and resid 8 through 205)	G	A	8 - 205	1 - 198
2	2	(chain 'H' and resid 8 through 205)	H	B	8 - 205	1 - 198
3	3	(chain 'L' and resid 8 through 205)	L	C	8 - 205	1 - 198
4	4	(chain 'M' and resid 8 through 205)	M	D	8 - 205	1 - 198
5	5	(chain 'D' and resid 8 through 205)	D	E	8 - 205	1 - 198
6	6	(chain 'J' and resid 8 through 205)	J	F	8 - 205	1 - 198
7	7	(chain 'I' and resid 8 through 205)	I	G	8 - 205	1 - 198
8	8	(chain 'K' and resid 8 through 205)	K	H	8 - 205	1 - 196
9	9	(chain 'A' and resid 8 through 208)	A	I	8 - 208	1 - 201
10	10	(chain 'P' and resid 8 through 205)	P	J	8 - 205	1 - 198
11	11	(chain 'O' and resid 8 through 205)	O	K	8 - 205	1 - 198
12	12	(chain 'N' and resid 8 through 205)	N	L	8 - 205	1 - 198
13	13	(chain 'B' and resid 8 through 205)	B	M	8 - 205	1 - 198
14	14	(chain 'C' and resid 8 through 205)	C	N	8 - 205	1 - 198
15	15	(chain 'F' and resid 8 through 205)	F	O	8 - 205	1 - 198
16	16	(chain 'E' and resid 8 through 205)	E	P	8 - 205	1 - 198

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