PDB-6vtg: Naegleria gruberi RNA ligase E227A mutant apo

ID or keywords:

Entry

Database: PDB / ID: 6vtg

Title

Naegleria gruberi RNA ligase E227A 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: 2.49 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 / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6vtg.cif.gz	556 KB	Display	PDBx/mmCIF format
PDB format	pdb6vtg.ent.gz	464.7 KB	Display	PDB format
PDBx/mmJSON format	6vtg.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6vtg_validation.pdf.gz	252 KB	Display	wwPDB validaton report
Full document	6vtg_full_validation.pdf.gz	251.9 KB	Display
Data in XML	6vtg_validation.xml.gz	1.6 KB	Display
Data in CIF	6vtg_validation.cif.gz	13.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/vt/6vtg ftp://data.pdbj.org/pub/pdb/validation_reports/vt/6vtg	HTTPS FTP

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Related structure data

Related structure data	6vt0C 6vt1C 6vt3C 6vt4C 6vt5C 6vt6C 6vt8C 6vt9C 6vtbC 6vtdC 6vteC 6vtfC 5cotS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6vt1-2 6vtf-2 6vt9-d 6vt8-d 6vte-d 5cou-d 6vtf-1 6vt1-1 6vt6-d 4hb9-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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

Related structure data

S: Starting model for refinement

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: RNA ligase

B: RNA ligase

C: RNA ligase

D: RNA ligase

154 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: RNA ligase

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

2

B: RNA ligase

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

3

C: RNA ligase

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

4

D: RNA ligase

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

Unit cell

Length a, b, c (Å)	124.101, 104.037, 119.974
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	18
Space group name H-M	P2₁2₁2

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	chain A
2	1	chain B
3	1	chain C
4	1	chain D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: ARG / End label comp-ID: ARG / Auth seq-ID: 0 - 339 / Label seq-ID: 1 - 340

Dom-ID	Selection details	Auth asym-ID	Label asym-ID
1	chain A	A	A
2	chain B	B	B
3	chain C	C	C
4	chain D	D	D

#1: Protein	RNA ligase Mass: 38603.797 Da / Num. of mol.: 4 / Mutation: E227A 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.: 92 / 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: 2.51 Å³/Da / Density % sol: 50.95 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop Details: The NgrRnlE227A protein sample (12 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: 0.9795 Å

Detector

Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 25, 2015

Radiation

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

Radiation wavelength

Wavelength: 0.9795 Å / Relative weight: 1

Reflection

Resolution: 2.49→30 Å / Num. obs: 102490 / % possible obs: 99.3 % / Redundancy: 5.6 % / R_merge(I) obs: 0.111 / R_pim(I) all: 0.053 / R_rim(I) all: 0.124 / Χ²: 2.371 / Net I/σ(I): 7.4

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
2.49-2.54	5.5	0.813	2709	0.668	0.376	0.898	0.855	99.8
2.54-2.59	5.3	0.7	2692	0.737	0.327	0.776	0.905	99.9
2.59-2.64	6.1	0.624	2679	0.8	0.274	0.683	0.92	99.9
2.64-2.69	6.1	0.556	2703	0.835	0.244	0.609	0.993	100
2.69-2.75	6.1	0.465	2685	0.854	0.203	0.508	1.19	99.7
2.75-2.82	6	0.415	2727	0.873	0.183	0.454	1.297	100
2.82-2.89	6	0.365	2713	0.884	0.162	0.4	1.525	99.9
2.89-2.96	5.9	0.305	2680	0.928	0.137	0.336	1.687	99.7
2.96-3.05	5.7	0.267	2716	0.926	0.123	0.295	1.981	99.9
3.05-3.15	5.2	0.228	2712	0.945	0.11	0.254	2.127	99.2
3.15-3.26	5.8	0.196	2709	0.96	0.09	0.217	2.314	99.7
3.26-3.39	5.9	0.163	2698	0.974	0.074	0.179	2.553	99.9
3.39-3.55	5.8	0.142	2732	0.977	0.066	0.158	2.949	99.7
3.55-3.73	5.7	0.126	2702	0.973	0.059	0.139	3.178	99.3
3.73-3.97	5.5	0.113	2731	0.981	0.054	0.126	3.467	99.3
3.97-4.27	5.1	0.102	2700	0.974	0.051	0.115	4.351	98.1
4.27-4.7	5.5	0.092	2732	0.981	0.044	0.102	4.588	98.8
4.7-5.38	5.3	0.092	2735	0.986	0.045	0.103	5.183	98.7
5.38-6.76	5.2	0.077	2755	0.984	0.038	0.086	4.13	97.5
6.76-30	5.5	0.049	2870	0.997	0.023	0.054	2.168	97.3

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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: 2.49→29.73 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31

	R_factor	Num. reflection	% reflection
R_free	0.2732	3777	3.71 %
R_work	0.215	-	-
obs	0.2172	102490	97.79 %

Solvent computation

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

Displacement parameters

B_iso max: 178.11 Å² / B_iso mean: 82.0559 Å² / B_iso min: 25.8 Å²

Refinement step

Cycle: final / Resolution: 2.49→29.73 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10852	0	0	92	10944
B_iso mean	-	-	-	55.89	-
Num. residues	-	-	-	-	1360

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Number	Refine-ID	Rms	Type
1	1	A	4148	X-RAY DIFFRACTION	10.833	TORSIONAL
1	2	B	4148	X-RAY DIFFRACTION	10.833	TORSIONAL
1	3	C	4148	X-RAY DIFFRACTION	10.833	TORSIONAL
1	4	D	4148	X-RAY DIFFRACTION	10.833	TORSIONAL

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / Total num. of bins used: 27

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
2.49-2.52	0.3401	115	0.3051	3367	3482	90
2.52-2.56	0.3626	146	0.3081	3667	3813	98
2.56-2.59	0.4006	147	0.3143	3640	3787	98
2.59-2.63	0.356	125	0.2993	3727	3852	100
2.63-2.67	0.3034	163	0.2888	3757	3920	100
2.67-2.71	0.3377	139	0.2837	3683	3822	100
2.71-2.75	0.3036	141	0.2641	3793	3934	100
2.75-2.8	0.4206	159	0.2792	3690	3849	100
2.8-2.85	0.3268	131	0.2754	3733	3864	100
2.85-2.91	0.328	145	0.2647	3730	3875	100
2.91-2.97	0.3238	146	0.2489	3733	3879	99
2.97-3.03	0.2877	142	0.2547	3699	3841	99
3.03-3.1	0.3207	142	0.2539	3749	3891	99
3.1-3.18	0.321	145	0.2346	3593	3738	96
3.18-3.26	0.3241	141	0.2445	3672	3813	99
3.26-3.36	0.3034	120	0.2364	3746	3866	99
3.36-3.47	0.3197	156	0.2234	3683	3839	99
3.47-3.59	0.3363	128	0.2308	3676	3804	98
3.59-3.74	0.3066	146	0.234	3604	3750	97
3.74-3.91	0.2768	143	0.2234	3633	3776	97
3.91-4.11	0.2514	130	0.1989	3554	3684	95
4.11-4.37	0.2208	147	0.1723	3562	3709	95
4.37-4.7	0.1965	145	0.1644	3585	3730	96
4.7-5.17	0.2269	134	0.18	3648	3782	96
5.17-5.92	0.2811	136	0.2006	3603	3739	96
5.92-7.44	0.2343	148	0.2059	3567	3715	96
7.44-29.73	0.212	142	0.1666	3594	3736	96

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	4.4848	0.3235	-1.5372	6.6495	1.3305	4.9463	-0.0086	-0.212	0.3888	-0.0845	0.3809	0.8141	0.3169	-0.4751	-0.2735	0.6213	-0.0195	-0.0481	0.8215	0.1184	0.7281	-42.5806	1.2739	-8.0345
2	-0.0161	-0.2068	0.0221	2.1358	-1.2971	3.9789	-0.1966	0.0469	0.0477	-0.6145	0.3791	0.8004	0.5209	-1.0273	-0.1353	0.7664	-0.174	-0.2085	0.8625	0.1408	0.843	-45.1673	7.074	-25.3281
3	1.1039	-1.4564	0.9553	2.735	-2.5126	6.0616	0.3489	-0.2761	-0.1637	-0.383	-0.0089	0.0866	1.5557	-0.5193	-0.2386	0.7928	-0.1271	-0.1124	0.5157	-0.007	0.5099	-36.2056	5.3431	-39.3419
4	4.1375	-1.5011	0.1123	5.4646	0.5311	1.6784	-0.0173	0.151	-0.0812	0.0936	0.0054	0.1894	-0.0617	-0.0433	-0.0009	0.2498	-0.0027	0.0354	0.3526	0.0229	0.3509	-46.1007	49.2012	-53.6985
5	1.0612	0.2856	1.7921	1.8311	-1.0916	5.3831	0.1366	-0.5032	-0.0482	0.5377	-0.1531	-0.0577	-0.16	-0.6368	0.019	0.655	-0.0865	0.0055	0.5966	0.0457	0.4255	-38.8137	47.0253	-25.4331
6	1.8176	0.6582	0.5976	5.8257	-0.2908	5.1714	-0.0564	0.0998	-0.189	-0.3485	-0.0073	-0.2634	0.6635	0.0062	0.0584	0.3954	-0.0492	0.0863	0.3899	-0.0305	0.3463	-42.5498	22.1098	-75.2942
7	5.8812	1.359	-0.4488	1.8339	-0.1161	0.8715	0.0462	-0.4565	-0.2537	0.0922	-0.0563	-0.1019	-0.0305	0.1465	0.0312	0.3221	-0.0327	0.0174	0.4414	-0.0127	0.4107	-69.544	20.6881	-65.5919
8	3.1727	1.0368	-0.0364	6.0831	0.4614	5.3649	-0.1842	0.078	-0.2368	0.0101	-0.1186	-0.0368	-0.0067	0.3531	0.272	0.6379	-0.0009	0.1051	0.5637	0.0313	0.4665	-40.842	28.1637	11.6232
9	3.6003	-0.3726	1.7807	1.1543	0.2796	1.434	-0.2249	0.0936	0.2227	-0.2198	-0.1845	0.6852	-0.2336	-0.3187	0.3456	0.8215	-0.0711	-0.003	0.784	-0.1473	0.9137	-67.1306	31.883	6.582

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 0 through 100 )	A	0 - 100
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 101 through 173 )	A	101 - 173
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 174 through 339 )	A	174 - 339
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 0 through 119 )	B	0 - 119
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 120 through 339 )	B	120 - 339
6	X-RAY DIFFRACTION	6	chain 'C' and (resid 0 through 119 )	C	0 - 119
7	X-RAY DIFFRACTION	7	chain 'C' and (resid 120 through 339 )	C	120 - 339
8	X-RAY DIFFRACTION	8	chain 'D' and (resid 0 through 100 )	D	0 - 100
9	X-RAY DIFFRACTION	9	chain 'D' and (resid 101 through 339 )	D	101 - 339

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