PDB-5v0r: Crystal structure of ubiquitin-conjugating enzyme from Naegleria ...

ID or keywords:

Entry

Database: PDB / ID: 5v0r

Title

Crystal structure of ubiquitin-conjugating enzyme from Naegleria fowleri with modified Cys99

Components

Ubiquitin-conjugating enzyme

Keywords

LIGASE / SSGCID /

Naegleria fowleri /

ubiquitin-conjugating enzyme / e2 /

Structural Genomics / Seattle Structural Genomics Center for Infectious Disease

Function / homology

Function and homology information

transferase activity /

Biological species

Naegleria fowleri (brain-eating amoeba)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.55 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Citation

Journal: to be published
Title: Crystal structure of ubiquitin-conjugating enzyme from Naegleria fowleri with modified Cys99
Authors: Irwin, R.M. / Mayclin, S.J. / Lorimer, D.D. / Edwards, T.E.

History

Deposition	Feb 28, 2017	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 29, 2017	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	5v0r.cif.gz	74.9 KB	Display	PDBx/mmCIF format
PDB format	pdb5v0r.ent.gz	58.3 KB	Display	PDB format
PDBx/mmJSON format	5v0r.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/v0/5v0r ftp://data.pdbj.org/pub/pdb/validation_reports/v0/5v0r	HTTPS FTP

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Related structure data

Similar structure data	1ea4-2 4lad-d 2dvw-d 3iee-d 3aji-1 4lmo-2 1p69-d 2dwz-1 4ive-d 2dzn-3 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Other databases	TargetTrack: SSGCID-NafoA.00601.c

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#234 - Jun 2019 MDM2 and Cancer similarity (6) #60 - Dec 2004 Ubiquitin similarity (6)

Deposited unit

A: Ubiquitin-conjugating enzyme

hetero molecules

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

1

A: Ubiquitin-conjugating enzyme

hetero molecules

A: Ubiquitin-conjugating enzyme

hetero molecules

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

Unit cell

Length a, b, c (Å)	52.360, 85.240, 33.850
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	18
Space group name H-M	P2₁2₁2

Components on special symmetry positions

ID	Model	Components
1	1	A-446- HOH
2	1	A-448- HOH
3	1	A-463- HOH

#1: Protein	Ubiquitin-conjugating enzyme / / NafoA.00601.c Mass: 19401.043 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Naegleria fowleri (brain-eating amoeba) Strain: ATCC 30863 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A1W2VMZ9*PLUS
#2: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical	ChemComp-CL / CHLORIDE ION / Chloride Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 239 / Source method: isolated from a natural source / Formula: H₂O

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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: 40.46 %
Crystal grow	Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: Top96 C9 (100 mM Tris-HCl pH 8.5, 200 mM MgCl2, 25 % PEG 3350), cryo 15% ethylene glycol, apo, tray 286982 puck vxx6-11

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å

Detector

Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Jan 27, 2016

Radiation

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

Radiation wavelength

Wavelength: 1.5418 Å / Relative weight: 1

Reflection

Resolution: 1.55→42.62 Å / Num. obs: 22634 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 10.822 % / B_iso Wilson estimate: 15.26 Å² / CC_1/2: 1 / R_merge(I) obs: 0.027 / R_rim(I) all: 0.028 / Χ²: 1.046 / Net I/σ(I): 48.14 / Num. measured all: 244943 / Scaling rejects: 80

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. possible	Num. unique obs	CC_1/2	R_rim(I) all	% possible all
1.55-1.59	4.035	0.198	6.26	6428	1636	1593	0.966	0.227	97.4
1.59-1.63	6.966	0.187	9.41	11104	1608	1594	0.988	0.201	99.1
1.63-1.68	7.708	0.159	11.18	11994	1564	1556	0.993	0.17	99.5
1.68-1.73	7.945	0.128	14.15	12124	1527	1526	0.995	0.137	99.9
1.73-1.79	8.35	0.109	16.97	12367	1481	1481	0.996	0.116	100
1.79-1.85	8.686	0.091	20.96	12404	1428	1428	0.998	0.096	100
1.85-1.92	9.167	0.07	26.89	12504	1364	1364	0.998	0.074	100
1.92-2	9.51	0.055	34.39	12877	1354	1354	0.999	0.058	100
2-2.09	9.93	0.047	42	12711	1280	1280	0.999	0.049	100
2.09-2.19	10.252	0.042	51.13	12477	1217	1217	0.999	0.044	100
2.19-2.31	11.416	0.036	59.95	13414	1176	1175	1	0.038	99.9
2.31-2.45	12.742	0.034	70.27	14207	1116	1115	1	0.035	99.9
2.45-2.62	13.341	0.031	75.01	14035	1052	1052	1	0.033	100
2.62-2.83	14.222	0.029	83.11	13895	977	977	1	0.03	100
2.83-3.1	15.485	0.026	96.28	14122	912	912	1	0.027	100
3.1-3.47	18.718	0.024	114.25	15424	824	824	1	0.025	100
3.47-4	20.208	0.021	129.61	14873	736	736	1	0.021	100
4-4.9	19.923	0.019	130.21	12711	638	638	1	0.019	100
4.9-6.93	19.598	0.019	127.22	9897	506	505	1	0.02	99.8
6.93-42.62	17.508	0.016	123.36	5375	308	307	1	0.016	99.7

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
PHENIX		refinement
XSCALE		data scaling
PDB_EXTRACT	3.22	data extraction
XDS		data reduction
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.55→42.62 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.02 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.191	2106	9.3 %
R_work	0.1561	20528	-
obs	0.1592	22634	99.68 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso max: 65.07 Å² / B_iso mean: 20.3808 Å² / B_iso min: 9.09 Å²

Refinement step

Cycle: final / Resolution: 1.55→42.62 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1142	0	2	246	1390
B_iso mean	-	-	15.79	32.44	-
Num. residues	-	-	-	-	146

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.005	1205
X-RAY DIFFRACTION	f_angle_d	0.889	1655
X-RAY DIFFRACTION	f_chiral_restr	0.052	186
X-RAY DIFFRACTION	f_plane_restr	0.007	216
X-RAY DIFFRACTION	f_dihedral_angle_d	14.311	742

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / Total num. of bins used: 15

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.5499-1.586	0.2381	131	0.1964	1295	1426	97
1.586-1.6256	0.2309	117	0.179	1346	1463	99
1.6256-1.6696	0.202	147	0.1716	1338	1485	99
1.6696-1.7187	0.1863	153	0.1692	1329	1482	100
1.7187-1.7742	0.1948	146	0.164	1352	1498	100
1.7742-1.8376	0.235	158	0.1753	1331	1489	100
1.8376-1.9112	0.1794	127	0.1688	1362	1489	100
1.9112-1.9982	0.2029	140	0.1624	1369	1509	100
1.9982-2.1035	0.1833	149	0.1497	1349	1498	100
2.1035-2.2353	0.179	154	0.1472	1366	1520	100
2.2353-2.4079	0.1858	137	0.1455	1376	1513	100
2.4079-2.6502	0.185	131	0.1567	1379	1510	100
2.6502-3.0336	0.1722	137	0.1549	1408	1545	100
3.0336-3.8216	0.1742	129	0.1456	1420	1549	100
3.8216-42.6361	0.2077	150	0.1544	1508	1658	100

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	7.7442	-0.9559	1.2741	2.9808	-0.9067	3.6356	0.0268	0.4518	0.292	-0.3356	-0.1521	-0.1426	0.0244	0.1837	0.1208	0.1484	0.0179	0.0116	0.0862	0.011	0.1115	5.0225	-2.2217	-16.3882
2	2.0014	0.5808	-0.0556	3.2162	-0.3064	1.0329	-0.1228	0.0768	0.0068	-0.2681	0.0654	0.0436	-0.0748	-0.0502	0.0761	0.0962	0.0089	0.0114	0.0628	0.0018	0.0969	-2.198	-6.5492	-9.2561
3	3.4427	0.3621	0.2683	2.9146	0.2988	1.1531	-0.1328	-0.0531	-0.1954	-0.092	-0.0523	0.108	0.0038	-0.0747	0.1921	0.1085	0.0016	0.0125	0.0976	0.0015	0.1163	-3.0621	-8.6497	-5.7289
4	2.6354	1.092	-0.371	1.7069	0.3405	0.4169	0.0214	-0.1622	0.0788	0.2024	-0.0572	0.095	0.1089	0.042	0.0326	0.1239	-0.0034	0.0008	0.0992	0.0282	0.102	1.2288	-15.834	-3.2418
5	4.2679	2.5747	-4.8656	3.1293	-2.0528	6.0387	-0.0371	0.0815	-0.0807	-0.0623	0.0862	-0.0175	0.348	-0.2225	-0.0487	0.1228	-0.0109	0.0015	0.1348	0.0217	0.1396	3.971	-21.4148	-7.7198
6	2.2926	0.6801	1.5477	2.9137	-0.1602	2.0047	-0.1468	-0.0689	-0.0006	0.105	0.1123	0.0116	-0.1126	-0.0799	0.0438	0.1098	0.0326	0.0223	0.1227	0.0165	0.1039	8.0933	-13.2433	-13.2355
7	4.0262	3.946	-0.0501	7.7352	-2.9363	6.4044	-0.0167	0.3029	-0.0964	-0.6778	0.0493	-0.105	0.4228	0.3762	-0.076	0.1211	0.0325	0.0217	0.1756	0.0005	0.1925	-4.8268	-22.706	-13.4517
8	8.3303	-0.3058	1.141	2.1222	2.4359	5.2026	0.2075	-0.0524	0.1372	-0.0394	-0.1075	0.047	0.0517	-0.3726	-0.0997	0.0968	-0.0293	0.0173	0.1227	0.0306	0.1091	-17.2789	-24.9977	-9.5279
9	3.7869	4.1663	2.7455	4.7499	3.3411	2.6084	0.2631	-1.1753	1.0493	0.0278	-0.2302	0.0494	-0.3553	-0.2712	-0.0129	0.2815	-0.0195	0.0925	0.3183	-0.1173	0.3378	-17.6477	-15.6256	-4.2937

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 21 through 36 )	A	21 - 36
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 37 through 60 )	A	37 - 60
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 61 through 70 )	A	61 - 70
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 71 through 96 )	A	71 - 96
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 97 through 106 )	A	97 - 106
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 107 through 120 )	A	107 - 120
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 121 through 133 )	A	121 - 133
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 134 through 151 )	A	134 - 151
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 152 through 155 )	A	152 - 163

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