PDB-8adc: Viral tegument-like DUBs

ID or keywords:

Entry

Database: PDB / ID: 8adc

Title

Viral tegument-like DUBs

Components

Viral deubiquitinating enzyme

Keywords

HYDROLASE / DUBs / deubiquitinating enzymes / ubiquitin / tegument

Function / homology

Papain-like cysteine peptidase superfamily / membrane / PPM-type phosphatase domain-containing protein

Function and homology information

Biological species

Waddlia chondrophila (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SIR / Resolution: 1.7 Å

Authors

Erven, I. / Abraham, E.T. / Hermanns, T. / Baumann, U. / Hofmann, K.

Funding support

Germany, 2items

Citation

Journal: Nat Commun / Year: 2022
Title: A widely distributed family of eukaryotic and bacterial deubiquitinases related to herpesviral large tegument proteins.
Authors: Erven, I. / Abraham, E. / Hermanns, T. / Baumann, U. / Hofmann, K.

History

Deposition	Jul 8, 2022	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Feb 15, 2023	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	8adc.cif.gz	298.3 KB	Display	PDBx/mmCIF format
PDB format	pdb8adc.ent.gz	207.1 KB	Display	PDB format
PDBx/mmJSON format	8adc.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8adc_validation.pdf.gz	437.7 KB	Display	wwPDB validaton report
Full document	8adc_full_validation.pdf.gz	443.4 KB	Display
Data in XML	8adc_validation.xml.gz	20.7 KB	Display
Data in CIF	8adc_validation.cif.gz	27.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ad/8adc ftp://data.pdbj.org/pub/pdb/validation_reports/ad/8adc	HTTPS FTP

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Related structure data

Related structure data	8adbC 8addC 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	#60 - Dec 2004 Ubiquitin similarity (1)

Deposited unit

B: Viral deubiquitinating enzyme

A: Viral deubiquitinating enzyme

48.6 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

B: Viral deubiquitinating enzyme

defined by author
Evidence: gel filtration
24.3 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

A: Viral deubiquitinating enzyme

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

Unit cell

Length a, b, c (Å)	37.121, 70.295, 75.890
Angle α, β, γ (deg.)	90.000, 101.840, 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

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
d_1	ens_1	(chain "A" and ((resid 284 and (name N or name...
d_2	ens_1	(chain "B" and ((resid 284 and (name N or name...

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Beg label comp-ID	End label comp-ID	Label asym-ID	Label seq-ID
d_1	1	ens_1	GLU	ALA	B	1 - 29
d_1	2	ens_1	THR	TYR	B	31 - 75
d_1	3	ens_1	LEU	ASP	B	77 - 106
d_1	4	ens_1	PHE	ARG	B	108 - 203
d_2	1	ens_1	GLU	ALA	A	2 - 30
d_2	2	ens_1	THR	LYS	A	32 - 70
d_2	3	ens_1	THR	TYR	A	74 - 79
d_2	4	ens_1	LEU	ASP	A	81 - 110
d_2	5	ens_1	PHE	ARG	A	112 - 207

NCS oper: (Code: givenMatrix: (0.934260764915, 0.00337908583771, 0.356574543285), (0.00444118042566, -0.999987805235, -0.00215992982546), (0.356562896354, 0.00360154957283, -0.934264378955)Vector: -7. ...

#1: Protein	Viral deubiquitinating enzyme Mass: 24281.262 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Waddlia chondrophila (bacteria) / Strain: ATCC VR-1470 / WSU 86-1044 / Gene: wcw_1294 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Rosetta (DE3) pLysS / References: UniProt: D6YWY5
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 161 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	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 Å³/Da / Density % sol: 38.48 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.2 M sodium chloride, 0.1 M BisTris pH 5.5, 25 % w/v PEG 3350

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9762 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 24, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9762 Å / Relative weight: 1
Reflection	Resolution: 1.7→80 Å / Num. obs: 81659 / % possible obs: 98.8 % / Redundancy: 3.4 % / B_iso Wilson estimate: 25.86 Å² / CC_1/2: 0.997 / R_merge(I) obs: 0.079 / R_rim(I) all: 0.08 / Net I/σ(I): 8.5
Reflection shell	Resolution: 1.7→1.8 Å / Redundancy: 3.1 % / R_merge(I) obs: 1.18 / Mean I/σ(I) obs: 1 / Num. unique obs: 13147 / CC_1/2: 0.535 / R_rim(I) all: 1.41 / % possible all: 98.3

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Processing

Software

Name	Version	Classification
PHENIX	1.20_4478	refinement
PHENIX	1.20_4478	refinement
XDS		data reduction
XDS		data scaling
SHELXDE		phasing

Refinement

Method to determine structure:

SIR / Resolution: 1.7→51.06 Å / SU ML: 0.2741 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.2442
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2351	4045	4.96 %
R_work	0.1975	77461	-
obs	0.1993	81506	98.74 %

Solvent computation

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

Displacement parameters

B_iso mean: 44.45 Å²

Refinement step

Cycle: LAST / Resolution: 1.7→51.06 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3211	0	0	161	3372

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	3289
X-RAY DIFFRACTION	f_angle_d	0.8363	4453
X-RAY DIFFRACTION	f_chiral_restr	0.0497	493
X-RAY DIFFRACTION	f_plane_restr	0.006	588
X-RAY DIFFRACTION	f_dihedral_angle_d	10.7855	1241

Refine LS restraints NCS

Type: Torsion NCS / Rms dev position: 0.622424792894 Å

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 (%)
1.7-1.72	0.4495	129	0.4119	2602	X-RAY DIFFRACTION	95.93
1.72-1.74	0.3914	144	0.3771	2655	X-RAY DIFFRACTION	98.56
1.74-1.76	0.3438	150	0.356	2711	X-RAY DIFFRACTION	98.11
1.76-1.79	0.3667	142	0.3242	2611	X-RAY DIFFRACTION	98.78
1.79-1.81	0.3227	136	0.3196	2640	X-RAY DIFFRACTION	98.09
1.81-1.84	0.2914	111	0.2928	2714	X-RAY DIFFRACTION	98.74
1.84-1.86	0.3039	167	0.2898	2652	X-RAY DIFFRACTION	98.15
1.86-1.89	0.3073	121	0.274	2694	X-RAY DIFFRACTION	98.74
1.89-1.92	0.3285	141	0.2551	2629	X-RAY DIFFRACTION	98.61
1.92-1.96	0.284	152	0.2632	2672	X-RAY DIFFRACTION	98.36
1.96-1.99	0.2814	128	0.2398	2704	X-RAY DIFFRACTION	99.26
1.99-2.03	0.2832	127	0.2254	2658	X-RAY DIFFRACTION	98.38
2.03-2.07	0.2262	162	0.2161	2633	X-RAY DIFFRACTION	98.45
2.07-2.12	0.254	129	0.2018	2683	X-RAY DIFFRACTION	99.4
2.12-2.17	0.256	131	0.2013	2721	X-RAY DIFFRACTION	98.96
2.17-2.22	0.2282	142	0.1975	2671	X-RAY DIFFRACTION	99.08
2.22-2.28	0.275	156	0.197	2641	X-RAY DIFFRACTION	99.04
2.28-2.35	0.2124	131	0.2066	2698	X-RAY DIFFRACTION	98.67
2.35-2.43	0.2524	149	0.1899	2684	X-RAY DIFFRACTION	99.16
2.43-2.51	0.196	138	0.1994	2665	X-RAY DIFFRACTION	99.12
2.51-2.61	0.2165	144	0.1858	2688	X-RAY DIFFRACTION	98.71
2.61-2.73	0.2811	132	0.1965	2641	X-RAY DIFFRACTION	99.57
2.73-2.88	0.2246	148	0.1868	2727	X-RAY DIFFRACTION	99.48
2.88-3.05	0.2281	144	0.1909	2684	X-RAY DIFFRACTION	99.37
3.06-3.29	0.2593	131	0.1807	2683	X-RAY DIFFRACTION	99.47
3.29-3.62	0.2298	150	0.1732	2669	X-RAY DIFFRACTION	99.16
3.62-4.15	0.193	139	0.1627	2717	X-RAY DIFFRACTION	99.41
4.15-5.22	0.1657	136	0.1446	2647	X-RAY DIFFRACTION	98.17
5.22-51.06	0.2169	135	0.201	2667	X-RAY DIFFRACTION	98.73

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	1.10034929373	-1.27675007177	-0.0449883167615	3.52805116057	-0.479428839312	0.371991779863	0.0662940320299	-0.0640649529152	0.12036022115	-0.341698028614	-0.116508418512	0.26931227789	-0.065829796421	-0.0739678460662	0.00112625392666	0.25131182992	0.00102812251873	-0.0262663297959	0.242797164247	-0.00507892400553	0.267173540238	-11.5133390419	38.7169277133	34.0248837549
2	0.438228439075	0.781961507998	0.227623360595	1.98048268265	0.17766661364	0.208208012164	0.0628810790799	0.227724388668	0.194041662472	0.0232609817124	-0.00723067161262	-1.09069623793	0.00864881903781	0.112404920379	0.246600674412	0.227818132417	0.0333115858823	0.0222177371655	0.357200887459	0.0261794759168	0.620962109469	6.88794189487	29.0449315372	37.9140894531
3	0.364561572398	0.0243103520075	-0.332227288818	3.56876351903	0.0504328585487	0.318235721573	0.00893597211982	-0.050028128167	-0.10028915911	-0.144421562861	-0.11007184176	0.021255075262	0.092229853404	-0.0225254400337	-0.00867977009688	0.193678309636	0.0145056784539	-0.0246250780852	0.243968065676	-0.0201466602513	0.222438237662	-5.99935362962	21.6748263434	35.9396578513
4	0.970313278118	0.481643628693	0.0115489140839	3.23166906159	0.809287409589	0.632267272735	0.236617777427	0.128369443389	-0.0298332991002	0.751436944223	-0.111421008378	0.0267871658938	0.215132292264	0.0866317960852	0.0423744464559	0.563993633793	-0.0317633565121	0.0504550631763	0.267768694053	0.00337017581649	0.274093875098	1.90941025593	36.1583171038	2.41445383355
5	0.963526297792	0.173063911512	0.120240556825	1.44015887039	0.311784598837	0.38852434998	0.120476570061	0.0444202619874	0.176818587804	0.0926684899552	-0.012984983836	-0.113492534607	-0.0927908249668	0.0397247092611	1.2489774473E-5	0.478067632878	-0.00238076196394	0.0845824865118	0.307818866897	-0.0094488523635	0.294153331504	4.01523163645	48.000442393	-2.15788378105
6	0.762482430879	0.362598365745	-0.332940385125	1.84649743143	0.0116066401114	1.02214508607	0.0522149941124	-0.00661966132704	-0.117272780868	0.672802980227	-0.112401826855	0.42049627229	0.00416850858583	-0.115658969253	0.172016761746	0.608504232094	0.0086087757504	0.143743593788	0.313213276779	-0.0559594582312	0.356631192615	-1.41362014306	50.9713349857	5.85362147708

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 'B' and (resid 283 through 351 )	B	A	283 - 351	1 - 69
2	2	chain 'B' and (resid 352 through 390)	B	A	352 - 390	70 - 104
3	3	chain 'B' and (resid 391 through 493 )	B	A	391 - 493	105 - 207
4	4	chain 'A' and (resid 284 through 390 )	A	B	284 - 390	1 - 100
5	5	chain 'A' and (resid 391 through 440 )	A	B	391 - 440	101 - 150
6	6	chain 'A' and (resid 441 through 493 )	A	B	441 - 493	151 - 203

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