PDB-6vt5: Naegleria gruberi RNA ligase R4a K121A mutant apo

ID or keywords:

Entry

Database: PDB / ID: 6vt5

Title

Naegleria gruberi RNA ligase R4a K121A mutant apo

Components

RNA Ligase

Keywords

LIGASE / RNA repair / adenylyltransferase

Function / homology

RNA ligase, DRB0094 / PHA02142 OB-fold domain / RNA ligase domain, REL/Rln2 / RNA ligase / ATP binding / metal ion binding / Predicted protein

Function and homology information

Biological species

Naegleria gruberi (eukaryote)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.8 Å

Authors

Unciuleac, M.C. / Goldgur, Y. / Shuman, S.

Funding support

United States, 1items

Citation

Journal: Nucleic Acids Res. / Year: 2020
Title: Caveat mutator: alanine substitutions for conserved amino acids in RNA ligase elicit unexpected rearrangements of the active site for lysine adenylylation.
Authors: Unciuleac, M.C. / Goldgur, Y. / Shuman, S.

History

Deposition	Feb 12, 2020	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 8, 2020	Provider: repository / Type: Initial release
Revision 1.1	May 6, 2020	Group: Database references / Category: citation Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2	Jun 10, 2020	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3	Oct 11, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	6vt5.cif.gz	159.1 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	6vt5_validation.pdf.gz	247.9 KB	Display	wwPDB validaton report
Full document	6vt5_full_validation.pdf.gz	247.8 KB	Display
Data in XML	6vt5_validation.xml.gz	1.1 KB	Display
Data in CIF	6vt5_validation.cif.gz	6.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/vt/6vt5 ftp://data.pdbj.org/pub/pdb/validation_reports/vt/6vt5	HTTPS FTP

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Related structure data

Related structure data	6vt0C 6vt1C 6vt3C 6vt4C 6vt6C 6vt8C 6vt9C 6vtbC 6vtdC 6vteC 6vtfC 6vtgC 5cotS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6vt1-1 6vtg-2 6vtg-3 6vte-d 4j31-1 3dqq-2 5cou-d 4k05-1 3qi7-1 5cov-d Search similar-shape structures by Omokage search (details) 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

Deposited unit

A: RNA Ligase

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	55.713, 55.713, 100.338
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	145
Space group name H-M	P3₂

#1: Protein	RNA Ligase Mass: 38517.613 Da / Num. of mol.: 1 / Mutation: R4A, K121A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Naegleria gruberi (eukaryote) / Gene: NAEGRDRAFT_82186 / Production host: Escherichia coli (E. coli) / References: UniProt: D2W2Z5
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 367 / 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: 2.33 Å³/Da / Density % sol: 47.3 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop Details: The NgrRnlR4A-K121A protein sample (10.2 mg/ml) was mixed with equal volume (1 ul) of 0.1 M HEPES pH 6.5, 30% PEG6000

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 24-ID-C / Wavelength: 0.9792 Å

Detector

Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 14, 2015

Radiation

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

Radiation wavelength

Wavelength: 0.9792 Å / Relative weight: 1

Reflection

Resolution: 1.8→30 Å / Num. obs: 58945 / % possible obs: 98.4 % / Redundancy: 3.9 % / R_merge(I) obs: 0.103 / R_pim(I) all: 0.064 / R_rim(I) all: 0.122 / Χ²: 3.524 / Net I/σ(I): 9.4

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all	Χ²	% possible all
1.8-1.83	4	0.515	1620	0.76	0.287	0.591	0.943	99.8
1.83-1.86	4.1	0.452	1618	0.777	0.25	0.518	1.113	99.8
1.86-1.9	4.2	0.422	1625	0.835	0.232	0.483	1.199	99.8
1.9-1.94	4.2	0.347	1610	0.869	0.191	0.397	1.378	99.8
1.94-1.98	4.1	0.328	1634	0.847	0.184	0.377	1.687	99.8
1.98-2.03	4.1	0.281	1607	0.901	0.158	0.324	1.993	99.4
2.03-2.08	3.6	0.236	1624	0.914	0.141	0.277	2.388	99.2
2.08-2.13	4.3	0.218	1606	0.933	0.121	0.25	2.64	99.8
2.13-2.2	4.3	0.198	1598	0.949	0.109	0.227	2.887	99.8
2.2-2.27	4.2	0.185	1645	0.939	0.104	0.213	3.078	99.6
2.27-2.35	4.1	0.17	1616	0.946	0.097	0.197	3.468	98.8
2.35-2.44	4	0.151	1598	0.956	0.089	0.176	3.794	99
2.44-2.55	3.6	0.139	1600	0.959	0.086	0.164	4.17	98
2.55-2.69	4.1	0.129	1601	0.968	0.075	0.15	4.693	98.8
2.69-2.86	4	0.115	1571	0.975	0.068	0.134	4.967	98.6
2.86-3.08	3.7	0.104	1599	0.968	0.064	0.123	5.872	97.1
3.08-3.39	3.3	0.092	1518	0.977	0.06	0.11	7.067	94.1
3.39-3.88	3.5	0.088	1586	0.964	0.057	0.105	7.66	96.6
3.88-4.88	3.2	0.08	1500	0.976	0.054	0.097	7.847	93.2
4.88-30	3.5	0.075	1587	0.973	0.048	0.09	6.247	96.5

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Processing

Software

Name	Version	Classification
SCALEPACK		data scaling
PHENIX	1.17.1_3660	refinement
PDB_EXTRACT	3.25	data extraction
HKL-2000		data reduction
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5COT

5cot

Resolution: 1.8→27.49 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.99 / Phase error: 24.97

	R_factor	Num. reflection	% reflection
R_free	0.2291	3706	6.29 %
R_work	0.1943	-	-
obs	0.1965	58945	90.66 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Displacement parameters

B_iso max: 111.61 Å² / B_iso mean: 38.7682 Å² / B_iso min: 18.63 Å²

Refinement step

Cycle: final / Resolution: 1.8→27.49 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2689	0	0	367	3056
B_iso mean	-	-	-	43.87	-
Num. residues	-	-	-	-	337

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / Total num. of bins used: 26

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.8-1.82	0.4339	136	0.3152	2116	2252	91
1.82-1.84	0.3218	151	0.285	2242	2393	95
1.84-1.87	0.332	141	0.2714	2166	2307	95
1.87-1.9	0.3026	149	0.2716	2254	2403	95
1.9-1.93	0.2869	149	0.2483	2220	2369	95
1.93-1.96	0.2912	145	0.2555	2254	2399	95
1.96-1.99	0.2963	157	0.2486	2245	2402	95
1.99-2.03	0.2759	139	0.257	2119	2258	93
2.03-2.07	0.2929	151	0.257	2184	2335	91
2.07-2.11	0.3132	151	0.2414	2155	2306	94
2.11-2.16	0.275	149	0.2296	2196	2345	95
2.16-2.21	0.291	151	0.2239	2282	2433	94
2.21-2.26	0.2994	134	0.2249	2180	2314	93
2.26-2.32	0.268	150	0.2236	2184	2334	93
2.32-2.39	0.3143	143	0.2189	2162	2305	92
2.39-2.47	0.2676	141	0.221	2121	2262	91
2.47-2.56	0.2609	150	0.22	2068	2218	89
2.56-2.66	0.2949	161	0.202	2170	2331	92
2.66-2.78	0.2605	147	0.209	2139	2286	90
2.78-2.93	0.2285	131	0.1928	2082	2213	89
2.93-3.11	0.2547	127	0.1897	2033	2160	86
3.11-3.35	0.209	121	0.1898	1890	2011	81
3.35-3.68	0.189	136	0.1721	1977	2113	85
3.69-4.22	0.1545	127	0.1609	1934	2061	82
4.22-5.31	0.1463	129	0.1396	1855	1984	80
5.32-27.49	0.1733	140	0.1525	2011	2151	85

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	2.6796	-0.4939	0.5919	2.2793	-0.4274	1.0948	-0.2186	0.1146	0.3454	0.2584	-0.0031	-0.1355	-0.2412	0.0848	0.1658	0.3136	-0.023	-0.0579	0.1968	0.0192	0.2637	12.8287	15.1631	16.0231
2	0.0887	0.0736	-0.0858	1.175	0.9875	1.4087	-0.0231	0.0409	-0.0204	-0.1991	0.0271	-0.0167	-0.081	0.1357	-0.0203	0.257	-0.0091	-0.0248	0.2382	0.0321	0.2394	11.9172	-4.431	5.5399
3	0.8202	-0.4312	-0.6533	1.7011	1.3071	1.9769	-0.0225	0.0009	-0.1245	-0.0224	-0.009	0.0657	0.0335	0.0718	0.0191	0.2362	-0.0311	-0.0257	0.1848	0.025	0.2211	11.4066	-15.1508	5.5739

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 3 through 117 )	A	3 - 117
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 118 through 173 )	A	118 - 173
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 174 through 339 )	A	174 - 339

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