PDB-9fpa: DUBS Parachlamydia sp. PcJOS orthorhombic crystal form

ID or keywords:

Entry

Database: PDB / ID: 9fpa

Title

DUBS Parachlamydia sp. PcJOS orthorhombic crystal form

Components

Peptidase C39-like domain-containing protein
Ubiquitin

Keywords

HYDROLASE / Debiquitinylating enzyme

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 / membrane
Similarity search - Function

Biological species

Homo sapiens (human)

Parachlamydia sp. (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.18 Å

Authors

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

Funding support

Germany, 2items

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	Jun 13, 2024	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Apr 23, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	9fpa.cif.gz	354.1 KB	Display	PDBx/mmCIF format
PDB format	pdb9fpa.ent.gz	293.2 KB	Display	PDB format
PDBx/mmJSON format	9fpa.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	9fpa_validation.pdf.gz	1.2 MB	Display	wwPDB validaton report
Full document	9fpa_full_validation.pdf.gz	1.2 MB	Display
Data in XML	9fpa_validation.xml.gz	28.8 KB	Display
Data in CIF	9fpa_validation.cif.gz	38.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/fp/9fpa ftp://data.pdbj.org/pub/pdb/validation_reports/fp/9fpa	HTTPS FTP

-
Related structure data

Related structure data	9f5tC 9fn4C 9g7gC 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	#234 - Jun 2019 MDM2 and Cancer similarity (1)

Deposited unit

B: Ubiquitin

C: Peptidase C39-like domain-containing protein

A: Peptidase C39-like domain-containing protein

hetero molecules

73.9 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: 2 PcJOS:1 diubioquitin

Unit cell

Length a, b, c (Å)	54.220, 108.180, 149.610
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Ubiquitin Mass: 17135.654 Da / Num. of mol.: 1 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
#2: Protein	Peptidase C39-like domain-containing protein Mass: 28170.064 Da / Num. of mol.: 2 / Mutation: C162A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Parachlamydia sp. (bacteria) / Gene: CK425_03690 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2H9SU66
#3: Chemical	ChemComp-CIT / CITRIC ACID Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₆H₈O₇ / Feature type: SUBJECT OF INVESTIGATION
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 230 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	N

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.99 Å³/Da / Density % sol: 58.81 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop Details: Midas G6. 35 % v/v glycerol ethoxylate, 0.2 M lithium citrate

-
Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

ESRF

/ Beamline: ID23-2 / Wavelength: 0.873128 Å

Detector

Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Apr 11, 2021

Radiation

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

Radiation wavelength

Wavelength: 0.873128 Å / Relative weight: 1

Reflection

Resolution: 2.18→50 Å / Num. obs: 46803 / % possible obs: 99.9 % / Redundancy: 7.7 % / CC_1/2: 0.997 / R_merge(I) obs: 0.137 / R_rim(I) all: 0.143 / Net I/σ(I): 10.03

Reflection shell

Resolution (Å)	R_merge(I) obs	Mean I/σ(I) obs	Num. unique obs	CC_1/2	R_rim(I) all	Diffraction-ID
2.18-2.24	1.329	1.37	3382	0.613	1.443	1
2.24-2.3	1.099		3316	0.751	1.174	1
2.3-2.36	0.863		3257	0.822	0.922	1
2.36-2.44	0.761		3135	0.854	0.813	1
2.44-2.52	0.628		3053	0.895	0.672	1
2.52-2.61	0.52		2967	0.924	0.556	1
2.61-2.7	0.408		2857	0.948	0.436	1
2.7-2.81	0.322		2739	0.966	0.345	1
2.81-2.94	0.254		2652	0.978	0.272	1
2.94-3.08	0.199		2526	0.986	0.213	1
3.08-3.25	0.154		2434	0.993	0.165	1
3.25-3.45	0.123		2284	0.993	0.132	1
3.45-3.68	0.102		2161	0.995	0.109	1
3.68-3.98	0.093		2024	0.995	0.1	1
3.98-4.36	0.08		1865	0.996	0.086	1
4.36-4.87	0.072		1704	0.996	0.078	1
4.87-5.63	0.069		1506	0.996	0.074	1
5.63-6.89	0.064		1312	0.997	0.069	1
6.89-9.75	0.049		1029	0.998	0.053	1
9.75-50	0.039		600	0.998	0.042	1

-
Processing

Software

Name	Version	Classification
PHENIX	(1.21.1_5286: ???)	refinement
XSCALE		data scaling
XDS		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.18→43.9 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.03 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2123	2263	4.84 %
R_work	0.1844	-	-
obs	0.1857	46730	99.88 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.18→43.9 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4684	0	26	230	4940

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	4784
X-RAY DIFFRACTION	f_angle_d	0.915	6482
X-RAY DIFFRACTION	f_dihedral_angle_d	13.9	1796
X-RAY DIFFRACTION	f_chiral_restr	0.053	745
X-RAY DIFFRACTION	f_plane_restr	0.009	845

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 (%)
2.18-2.23	0.3228	136	0.2817	2697	X-RAY DIFFRACTION	99
2.23-2.28	0.2638	140	0.2575	2759	X-RAY DIFFRACTION	100
2.28-2.34	0.2678	135	0.237	2734	X-RAY DIFFRACTION	100
2.34-2.4	0.2443	142	0.2281	2743	X-RAY DIFFRACTION	100
2.4-2.47	0.2547	148	0.2108	2761	X-RAY DIFFRACTION	100
2.47-2.55	0.232	130	0.2015	2716	X-RAY DIFFRACTION	100
2.55-2.64	0.223	146	0.1962	2771	X-RAY DIFFRACTION	100
2.64-2.75	0.2338	147	0.1948	2749	X-RAY DIFFRACTION	100
2.75-2.87	0.2432	126	0.1988	2781	X-RAY DIFFRACTION	100
2.87-3.02	0.2481	143	0.2115	2777	X-RAY DIFFRACTION	100
3.02-3.21	0.2453	150	0.1982	2746	X-RAY DIFFRACTION	100
3.21-3.46	0.2341	137	0.2	2793	X-RAY DIFFRACTION	100
3.46-3.81	0.2123	142	0.1889	2792	X-RAY DIFFRACTION	100
3.81-4.36	0.1814	146	0.158	2815	X-RAY DIFFRACTION	100
4.36-5.49	0.1617	146	0.1404	2872	X-RAY DIFFRACTION	100
5.49-43.9	0.1816	149	0.1627	2961	X-RAY DIFFRACTION	99

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	4.8187	0.9742	-0.2677	2.6803	-0.6831	3.8391	0.3887	-0.4196	-0.1732	0.4627	-0.2671	-0.0558	0.05	-0.0312	-0.1444	0.4287	-0.0721	-0.0214	0.561	0.102	0.3495	19.4704	11.9741	34.9543
2	3.7165	-1.1341	-0.7325	3.4446	-0.2777	4.1664	0.0106	-0.1533	-0.2532	0.2031	0.0779	-0.0674	0.4483	0.0527	-0.1197	0.4933	0.0406	-0.0699	0.3783	-0.0102	0.4189	21.5229	-4.3496	-1.1145
3	4.2831	0.812	-0.5207	3.1298	-0.2162	4.3712	-0.39	0.6527	-0.0238	-0.4077	0.3559	0.1226	-0.1565	-0.3298	0.0475	0.4723	-0.1134	-0.0091	0.5964	-0.0699	0.296	20.8196	7.5402	-36.2196
4	0.9557	-1.0727	1.3096	1.9257	-0.2916	7.7347	-0.0194	0.0643	-0.6199	-0.021	0.2099	-0.3637	1.6643	0.3141	-0.0823	0.7402	0.0844	0.0058	0.4308	-0.1211	0.7964	30.0798	-16.7483	-16.9699
5	2.0101	0.7282	0.344	2.69	0.08	3.5368	-0.1915	0.2322	-0.1709	-0.056	0.155	-0.4445	0.0955	0.2833	0.0572	0.3758	-0.031	0.0102	0.5257	-0.1201	0.4525	31.373	1.2089	-26.4844
6	3.0338	0.618	0.6216	1.8671	-0.023	2.2045	0.0937	0.1089	-0.153	-0.1048	-0.0243	0.0633	0.2563	-0.018	-0.0673	0.3282	0.0135	0.0012	0.3044	0.012	0.2917	11.0139	14.411	2.9999
7	1.856	1.2832	0.5726	3.9234	-2.7194	6.9816	0.2068	-0.5456	0.0004	0.6888	-0.5044	-0.2342	-0.1031	1.0152	0.2946	0.3636	-0.0643	-0.0111	0.643	0.0689	0.3482	34.8796	18.9555	24.3684
8	3.6171	0.557	-0.9002	7.8163	-2.1483	3.8278	0.019	-0.1037	-0.0757	0.5226	-0.0445	-0.2944	0.034	0.4382	0.0204	0.3226	-0.0104	-0.0359	0.4906	-0.0062	0.2909	27.3444	21.1827	19.4934
9	1.8593	-0.2384	0.34	1.5927	-0.0062	3.2891	0.0439	-0.0531	0.0064	0.0809	-0.0636	-0.002	0.07	-0.0884	-0.0003	0.2543	-0.0113	0.0036	0.3338	0.0227	0.2997	11.5433	21.5777	8.6805

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'B' and (resid 1 through 76)
2	X-RAY DIFFRACTION	2	chain 'B' and (resid 77 through 150 )
3	X-RAY DIFFRACTION	3	chain 'C' and (resid 98 through 161 )
4	X-RAY DIFFRACTION	4	chain 'C' and (resid 162 through 213 )
5	X-RAY DIFFRACTION	5	chain 'C' and (resid 214 through 324 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 98 through 177)
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 178 through 205 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 206 through 225 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 226 through 324 )

-
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