PDB-9g7g: Structure of the clippase PaJOS from Pigmentiphaga aceris

ID or keywords:

Entry

Database: PDB / ID: 9g7g

Title

Structure of the clippase PaJOS from Pigmentiphaga aceris

Components

PaJOS
Polyubiquitin-B

Keywords

HYDROLASE / Ubiquitin / Clippase

Function / homology

Function and homology information

symbiont entry into host cell via disruption of host cell glycocalyx / symbiont entry into host cell via disruption of host cell envelope / virus tail
Similarity search - Function

Biological species

Pigmentiphaga aceris (bacteria)

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.89 Å

Authors

Baumann, U. / Uthoff, M. / Hermanns, T. / Hofmann, K.

Funding support

Germany, 1items

Citation

Journal: Mol.Cell / Year: 2025
Title: A family of bacterial Josephin-like deubiquitinases with an irreversible cleavage mode.
Authors: Hermanns, T. / Kolek, S. / Uthoff, M. / de Heiden, R.A. / Mulder, M.P.C. / Baumann, U. / Hofmann, K.

History

Deposition	Jul 21, 2024	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Apr 23, 2025	Provider: repository / Type: Initial release
Revision 2.0	May 21, 2025	Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Experimental preparation / Structure summary Category: atom_site / exptl_crystal_grow ...atom_site / exptl_crystal_grow / pdbx_modification_feature / pdbx_nonpoly_scheme / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_validate_close_contact / struct_conn Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _exptl_crystal_grow.temp / _pdbx_modification_feature.auth_asym_id / _pdbx_modification_feature.auth_seq_id / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_nonpoly_scheme.pdb_strand_id / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9g7g.cif.gz	1.4 MB	Display	PDBx/mmCIF format
PDB format	pdb9g7g.ent.gz	1.2 MB	Display	PDB format
PDBx/mmJSON format	9g7g.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9g7g_validation.pdf.gz	3.1 MB	Display	wwPDB validaton report
Full document	9g7g_full_validation.pdf.gz	3.1 MB	Display
Data in XML	9g7g_validation.xml.gz	143 KB	Display
Data in CIF	9g7g_validation.cif.gz	186.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/g7/9g7g ftp://data.pdbj.org/pub/pdb/validation_reports/g7/9g7g	HTTPS FTP

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Related structure data

Related structure data	9f5tC 9fn4C 9fpaC 9ft5 PDB Unreleased entry C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#234 - Jun 2019 MDM2 and Cancer similarity (1) #60 - Dec 2004 Ubiquitin similarity (1)

Deposited unit

A: PaJOS

B: Polyubiquitin-B

C: PaJOS

D: Polyubiquitin-B

E: PaJOS

F: Polyubiquitin-B

G: PaJOS

H: Polyubiquitin-B

I: PaJOS

J: Polyubiquitin-B

K: PaJOS

L: Polyubiquitin-B

M: PaJOS

N: Polyubiquitin-B

O: PaJOS

P: Polyubiquitin-B

Q: PaJOS

R: Polyubiquitin-B

S: PaJOS

T: Polyubiquitin-B

U: PaJOS

V: Polyubiquitin-B

W: PaJOS

X: Polyubiquitin-B

hetero molecules

436 kDa, 24 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: PaJOS

B: Polyubiquitin-B

hetero molecules

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

2

C: PaJOS

D: Polyubiquitin-B

hetero molecules

defined by author&software
36.4 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

E: PaJOS

F: Polyubiquitin-B

hetero molecules

defined by author&software
36.4 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

G: PaJOS

H: Polyubiquitin-B

hetero molecules

defined by author&software
36.4 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

5

I: PaJOS

J: Polyubiquitin-B

hetero molecules

defined by author&software
36.4 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

6

K: PaJOS

L: Polyubiquitin-B

hetero molecules

defined by author&software
36.4 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

7

M: PaJOS

N: Polyubiquitin-B

hetero molecules

defined by author&software
36.4 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

8

O: PaJOS

P: Polyubiquitin-B

hetero molecules

defined by author&software
36.4 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

9

Q: PaJOS

R: Polyubiquitin-B

hetero molecules

defined by author&software
36.4 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

10

S: PaJOS

T: Polyubiquitin-B

hetero molecules

defined by author&software
36.4 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

11

U: PaJOS

V: Polyubiquitin-B

hetero molecules

defined by author&software
36.4 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

12

W: PaJOS

X: Polyubiquitin-B

hetero molecules

defined by author&software
36.4 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	131.946, 81.316, 167.392
Angle α, β, γ (deg.)	90.00, 90.23, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	PaJOS Mass: 27797.758 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pigmentiphaga aceris (bacteria) / Gene: FXN63_18770 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A5C0B1L0
#2: Protein	Polyubiquitin-B Mass: 8519.778 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: UBB / Production host: Escherichia coli B (bacteria) / References: UniProt: P0CG47
#3: Chemical	ChemComp-AYE / prop-2-en-1-amine / ALLYLAMINE Mass: 57.094 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C₃H₇N / Feature type: SUBJECT OF INVESTIGATION
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 598 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
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: 2.06 Å³/Da / Density % sol: 40.31 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.2 M magnesium chloride, 0.1 M TRIS pH 8.5, 30 % w/v PEG4000

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

SLS

/ Beamline: X06SA / Wavelength: 1 Å

Detector

Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 6, 2022

Radiation

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

Radiation wavelength

Wavelength: 1 Å / Relative weight: 1

Reflection

Resolution: 1.89→80 Å / Num. obs: 271333 / % possible obs: 95.9 % / Redundancy: 6.6 % / CC_1/2: 0.999 / R_merge(I) obs: 0.072 / R_rim(I) all: 0.078 / Net I/σ(I): 11.63

Reflection shell

Resolution (Å)	R_merge(I) obs	Num. unique obs	CC_1/2	R_rim(I) all	Diffraction-ID
1.89-1.94	1.742	15799	0.373	1.982	1
1.94-1.99	1.258	17406	0.57	1.414	1
1.99-2.05	0.96	18565	0.737	1.059	1
2.05-2.11	0.8	19032	0.87	0.865	1
2.11-2.18	0.617	18478	0.917	0.665	1
2.18-2.26	0.477	17899	0.946	0.514	1
2.26-2.35	0.353	17258	0.967	0.381	1
2.35-2.44	0.284	16616	0.976	0.306	1
2.44-2.55	0.22	15896	0.985	0.238	1
2.55-2.67	0.173	14953	0.989	0.188	1
2.67-2.82	0.136	14611	0.995	0.146	1
2.82-2.99	0.107	13715	0.996	0.116	1
2.99-3.2	0.081	12828	0.997	0.088	1
3.2-3.45	0.063	12043	0.998	0.069	1
3.45-3.78	0.05	10773	0.998	0.055	1
3.78-4.23	0.043	10019	0.999	0.047	1
4.23-4.88	0.038	8897	0.999	0.041	1
4.88-5.98	0.039	7538	0.999	0.043	1
5.98-8.46	0.036	5687	0.999	0.039	1
8.46-80	0.028	3320	1	0.03	1

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Processing

Software

Name	Version	Classification
PHENIX	(dev_5407: ???)	refinement
XSCALE		data scaling
XDS		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.89→49.03 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.34 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2309	2116	0.78 %
R_work	0.2041	-	-
obs	0.2043	270643	95.61 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.89→49.03 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	28197	0	48	598	28843

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	29000
X-RAY DIFFRACTION	f_angle_d	0.923	39549
X-RAY DIFFRACTION	f_dihedral_angle_d	12.655	10549
X-RAY DIFFRACTION	f_chiral_restr	0.061	4528
X-RAY DIFFRACTION	f_plane_restr	0.009	5232

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 (%)
1.89-1.93	0.4499	112	0.4206	13676	X-RAY DIFFRACTION	73
1.93-1.98	0.3708	121	0.3657	15698	X-RAY DIFFRACTION	84
1.98-2.04	0.3615	134	0.3146	17230	X-RAY DIFFRACTION	92
2.04-2.1	0.3246	146	0.2836	18340	X-RAY DIFFRACTION	98
2.1-2.16	0.3402	145	0.2669	18484	X-RAY DIFFRACTION	99
2.16-2.24	0.2779	146	0.2555	18510	X-RAY DIFFRACTION	99
2.24-2.33	0.2832	146	0.2441	18538	X-RAY DIFFRACTION	99
2.33-2.44	0.2613	147	0.231	18492	X-RAY DIFFRACTION	99
2.44-2.57	0.2731	144	0.2287	18465	X-RAY DIFFRACTION	99
2.57-2.73	0.2737	144	0.2355	18330	X-RAY DIFFRACTION	98
2.73-2.94	0.279	145	0.2471	18609	X-RAY DIFFRACTION	99
2.94-3.23	0.2641	146	0.2305	18562	X-RAY DIFFRACTION	99
3.23-3.7	0.2424	143	0.1967	18458	X-RAY DIFFRACTION	98
3.7-4.66	0.1497	147	0.1465	18508	X-RAY DIFFRACTION	98
4.66-49.03	0.1668	150	0.1514	18627	X-RAY DIFFRACTION	97

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	2.0193	0.3184	0.001	2.1315	0.1872	1.1481	0.0642	-0.1189	0.1872	0.0397	0.0102	0.0194	-0.0529	-0.0027	-0.0667	0.2413	0.0244	-0.0289	0.3861	-0.0332	0.2978	-47.2913	21.8875	-87.6888
2	5.9618	1.9249	2.0645	4.199	1.3472	3.6712	-0.1032	0.2365	-0.1065	-0.1662	-0.0223	0.4275	0.0738	-0.582	0.1387	0.2908	-0.01	-0.0619	0.5516	-0.0625	0.3614	-64.7624	8.0338	-99.9535
3	2.1734	-0.1065	0.1295	2.116	-0.7192	1.2878	0.0569	0.0052	0.1502	0.0062	-0.0832	0.0252	-0.0754	0.1347	0.0342	0.2828	0.0072	-0.0366	0.4569	-0.0162	0.2863	-15.9694	20.7345	-81.7948
4	6.1529	-2.367	3.3419	4.0249	-1.9452	3.5937	-0.0622	0.1529	0.048	0.1119	-0.1241	-0.4539	-0.1153	0.6145	0.1711	0.2928	0.0023	-0.0156	0.6495	0.0523	0.3024	0.4039	6.6843	-68.1534
5	2.4399	-0.2577	-0.0713	2.1915	0.7379	1.493	0.1306	-0.0475	0.245	-0.0025	-0.1073	-0.1749	-0.1676	-0.0286	-0.0141	0.2865	-0.0325	-0.0396	0.2858	0.0319	0.3358	-27.2411	59.9313	-141.7759
6	6.2282	2.6478	3.3228	5.0107	3.1102	4.6322	-0.0177	-0.2507	0.1955	-0.0385	-0.2772	0.353	-0.0997	-0.491	0.2896	0.2658	0.0244	-0.0289	0.3486	-0.0024	0.2624	-43.5474	45.3122	-155.12
7	1.3748	-0.1163	0.0547	2.0363	-0.1401	1.4717	-0.0875	-0.0097	0.0389	-0.0554	-0.06	-0.2297	0.0639	0.1521	0.1627	0.2881	-0.0062	-0.0196	0.3829	0.0019	0.3126	-29.8176	62.6647	-100.0172
8	2.5737	-0.3838	-1.7683	4.7	-0.3283	1.7891	-0.1555	-0.0676	-0.5727	-0.0367	0.0767	0.593	0.171	-0.4132	0.1016	0.3036	-0.0375	0.0016	0.4915	-0.0288	0.4108	-54.6527	59.9343	-94.9748
9	2.2267	0.3908	-0.0668	2.5799	0.1257	1.0937	0.0555	-0.1196	0.2617	0.013	-0.035	-0.0495	-0.1066	-0.027	-0.0215	0.272	-0.0333	-0.0042	0.3629	-0.0286	0.2721	-90.7588	20.4306	-143.4021
10	5.6249	1.5953	2.1258	3.9463	1.0843	3.753	-0.2867	0.3518	-0.0421	-0.4566	0.139	0.6594	0.1014	-0.4439	0.1259	0.3404	-0.0692	-0.0526	0.4501	-0.0276	0.3582	-108.6578	6.5369	-155.3106
11	1.91	-0.2988	0.5914	2.456	-0.4841	1.3599	-0.0278	0.0667	0.1881	-0.0488	0.0038	-0.0447	-0.1124	0.1203	0.0149	0.2593	-0.0574	-0.0167	0.3549	-0.0287	0.2973	-59.4339	19.4428	-138.1067
12	6.6467	-3.1174	2.9233	3.7551	-2.0448	3.3785	-0.1454	0.0451	0.2318	0.0412	0.025	-0.4312	-0.0994	0.2492	0.1293	0.2581	-0.0455	-0.0322	0.3442	-0.0443	0.3265	-42.9984	5.555	-124.4277
13	2.0572	-0.2093	-0.0933	2.1352	-0.3787	1.5716	-0.0305	0.0283	-0.0033	-0.0801	-0.2525	-0.3526	0.1845	0.198	0.2921	0.3343	-0.0016	0.0045	0.3803	0.0647	0.3042	-73.3735	61.3706	-155.6756
14	8.7748	1.2207	-1.9342	4.2492	-0.9319	2.4099	-0.2136	0.1027	-0.6144	-0.2102	-0.0271	0.5473	0.3374	-0.5817	0.2358	0.3562	-0.1008	0.0019	0.4521	-0.0939	0.3692	-98.0222	58.1208	-150.5587
15	3.418	-0.2666	0.5271	2.2581	-0.1749	1.42	0.0099	-0.0111	0.9067	0.0223	-0.0853	-0.0682	-0.203	0.0817	0.0358	0.2268	-0.0111	-0.0242	0.2291	-0.0084	0.5459	4.2173	62.2299	-136.8168
16	6.8881	-1.3034	2.1424	3.2483	-1.8208	2.9709	-0.057	-0.3528	0.3507	0.0469	-0.1252	-0.3244	-0.1751	0.492	0.1663	0.2843	-0.0303	-0.0617	0.4866	-0.0705	0.3933	22.015	49.4474	-123.9409
17	2.0904	0.7652	0.6482	2.468	0.6515	2.3591	0.243	-0.5763	0.0746	0.3214	-0.5674	0.4567	0.5404	-1.1011	0.2274	0.4975	-0.2918	0.006	0.949	-0.1419	0.3847	-80.0848	63.8759	-121.1337
18	2.5638	-1.3605	-2.3314	3.1789	0.5026	3.9346	0.076	-0.5255	-0.7002	0.4112	-0.1253	-0.3714	0.5749	0.191	0.0413	0.5222	-0.0654	-0.1018	0.462	0.0473	0.5141	-55.8181	57.8142	-125.4745
19	5.8083	1.376	-1.6235	2.4977	-0.4254	3.2927	-0.5419	-0.494	-0.6229	0.0195	-0.1472	0.2907	0.4773	-0.2089	0.4732	0.3514	0.042	0.0846	0.3202	-0.0225	0.4206	-12.8609	22.4212	-122.679
20	5.8455	-0.157	-0.819	3.4855	-0.2778	1.7848	-0.7282	-0.7235	-1.2446	0.329	0.2906	-0.3159	0.4039	0.5643	0.3761	0.4479	0.1593	0.132	0.4942	0.0979	0.5135	12.0383	19.0417	-127.5215
21	2.0227	-0.0539	0.3334	2.0448	-0.6489	2.2556	-0.0452	0.1517	-0.0003	-0.1732	-0.2508	-0.3459	0.426	0.7119	0.2696	0.4426	0.0864	0.0402	0.7626	0.1215	0.3319	-94.7221	24.8424	-102.13
22	6.1592	1.1754	-2.9888	4.5919	-0.4765	3.9197	-0.2123	0.3343	-0.5479	-0.196	-0.0292	0.39	0.5124	-0.5725	0.2284	0.4851	-0.1037	-0.0027	0.5697	0.0053	0.3912	-118.8528	18.4926	-97.6044
23	4.2035	-2.1708	-0.4078	4.2742	0.5669	2.1336	0.1353	0.5168	0.0455	-0.4132	-0.2573	-0.3055	0.399	0.3448	0.1088	0.4724	0.111	-0.0216	0.4701	0.0245	0.3346	-5.0933	23.4375	-156.9329
24	6.0181	2.9015	0.0964	4.404	0.8982	2.9359	-0.1493	0.5169	-1.3487	-0.1146	-0.2587	1.1438	0.5645	-0.627	0.3632	0.6283	-0.0488	0.0025	0.5625	-0.2278	1.1362	-29.2502	16.2995	-152.3169

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain 'A' and resid 28 through 261)
2	X-RAY DIFFRACTION	2	(chain 'B' and resid 1 through 75)
3	X-RAY DIFFRACTION	3	(chain 'C' and resid 28 through 260)
4	X-RAY DIFFRACTION	4	(chain 'D' and resid 1 through 75)
5	X-RAY DIFFRACTION	5	(chain 'E' and resid 28 through 260)
6	X-RAY DIFFRACTION	6	(chain 'F' and resid 1 through 75)
7	X-RAY DIFFRACTION	7	(chain 'G' and resid 26 through 260)
8	X-RAY DIFFRACTION	8	(chain 'H' and resid 1 through 75)
9	X-RAY DIFFRACTION	9	(chain 'I' and resid 28 through 260)
10	X-RAY DIFFRACTION	10	(chain 'J' and resid 1 through 75)
11	X-RAY DIFFRACTION	11	(chain 'K' and resid 28 through 261)
12	X-RAY DIFFRACTION	12	(chain 'L' and resid 1 through 75)
13	X-RAY DIFFRACTION	13	(chain 'M' and resid 26 through 259)
14	X-RAY DIFFRACTION	14	(chain 'N' and resid 1 through 75)
15	X-RAY DIFFRACTION	15	(chain 'O' and resid 28 through 262)
16	X-RAY DIFFRACTION	16	(chain 'P' and resid 1 through 75)
17	X-RAY DIFFRACTION	17	(chain 'Q' and resid 26 through 259)
18	X-RAY DIFFRACTION	18	(chain 'R' and resid 1 through 75)
19	X-RAY DIFFRACTION	19	(chain 'S' and resid 26 through 260)
20	X-RAY DIFFRACTION	20	(chain 'T' and resid 1 through 75)
21	X-RAY DIFFRACTION	21	(chain 'U' and resid 25 through 259)
22	X-RAY DIFFRACTION	22	(chain 'V' and resid 1 through 75)
23	X-RAY DIFFRACTION	23	(chain 'W' and resid 26 through 258)
24	X-RAY DIFFRACTION	24	(chain 'X' and resid 1 through 75)

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