PDB-6e3a: tRNA 2'-phosphotransferase

ID or keywords:

Entry

Database: PDB / ID: 6e3a

Title

tRNA 2'-phosphotransferase

Components

Probable RNA 2'-phosphotransferase

Keywords

TRANSFERASE / KptA / Tpt1 / TRPT1

Function / homology

Function and homology information

transferase activity, transferring phosphorus-containing groups /

Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor / tRNA splicing, via endonucleolytic cleavage and ligation /

NAD+ ADP-ribosyltransferase activity
Similarity search - Function

Biological species

Clostridium thermocellum (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.4 Å

Authors

Shuman, S. / Goldgur, Y. / Banerjee, A.

Funding support

United States, 1items

Citation

Journal: Nat Commun / Year: 2019
Title: Structure of tRNA splicing enzyme Tpt1 illuminates the mechanism of RNA 2'-PO4recognition and ADP-ribosylation.
Authors: Banerjee, A. / Munir, A. / Abdullahu, L. / Damha, M.J. / Goldgur, Y. / Shuman, S.

History

Deposition	Jul 13, 2018	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 20, 2019	Provider: repository / Type: Initial release
Revision 1.1	Dec 4, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2	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	6e3a.cif.gz	105.6 KB	Display	PDBx/mmCIF format
PDB format	pdb6e3a.ent.gz	79.2 KB	Display	PDB format
PDBx/mmJSON format	6e3a.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/e3/6e3a ftp://data.pdbj.org/pub/pdb/validation_reports/e3/6e3a	HTTPS FTP

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Related structure data

Related structure data	6edeC 1wfxS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	3s63-d 1oey-4 1ffw-2 4jof-d 2h5y-3 4nmo-d 1a0o-2 2rj2-d 7l7y-d 3gzg-1 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
Related items in Molecule of the Month	#146 - Feb 2012 Aminoglycoside Antibiotics similarity (1) #93 - Sep 2007 Citrate Synthase similarity (1) #154 - Oct 2012 Citric Acid Cycle similarity (1) #216 - Dec 2017 Biodegradable Plastic similarity (1) #39 - Mar 2003 lac Repressor similarity (1)

Deposited unit

A: Probable RNA 2'-phosphotransferase

hetero molecules

22.6 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)	53.367, 53.367, 308.903
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	178
Space group name H-M	P6₁22

Components on special symmetry positions

ID	Model	Components
1	1	A-434- HOH
2	1	A-438- HOH
3	1	A-468- HOH
4	1	A-472- HOH

#1: Protein	Probable RNA 2'-phosphotransferase Mass: 21149.461 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridium thermocellum (strain ATCC 27405 / DSM 1237 / NBRC 103400 / NCIMB 10682 / NRRL B-4536 / VPI 7372) (bacteria) Strain: ATCC 27405 / DSM 1237 / NBRC 103400 / NCIMB 10682 / NRRL B-4536 / VPI 7372 Gene: kptA, Cthe_3059 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: A3DJX6, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor
#2: Chemical	ChemComp-COA / COENZYME A / Coenzyme A Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂₁H₃₆N₇O₁₆P₃S
#3: Chemical	ChemComp-HQG / [[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{R},5~{R})-3,4-bis(oxidanyl)-5-phosphonooxy-oxolan-2-yl]methyl hydrogen phosphate Mass: 639.296 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₅H₂₄N₅O₁₇P₃
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 192 / 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: 3 Å³/Da / Density % sol: 59.03 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1M MES pH 6.0, 10 %MPD / PH range: 6

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1.2051 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 11, 2018
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.2051 Å / Relative weight: 1
Reflection	Resolution: 1.4→50 Å / Num. obs: 53083 / % possible obs: 99.8 % / Redundancy: 17.5 % / CC_1/2: 0.995 / R_pim(I) all: 0.016 / Χ²: 0.978 / Net I/σ(I): 24.1
Reflection shell	Resolution: 1.4→1.42 Å / Redundancy: 10.9 % / Num. unique obs: 2505 / CC_1/2: 0.83 / R_pim(I) all: 0.252 / Χ²: 0.842 / % possible all: 97.8

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Processing

Software

Name	Version	Classification
PHENIX	(1.12_2829)	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHASER		phasing
O		model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1WFX

1wfx

Resolution: 1.4→46.217 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.4

	R_factor	Num. reflection	% reflection
R_free	0.1857	3665	3.8 %
R_work	0.1616	-	-
obs	0.1625	52935	99.65 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.4→46.217 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1476	0	88	192	1756

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.015	1605
X-RAY DIFFRACTION	f_angle_d	1.467	2180
X-RAY DIFFRACTION	f_dihedral_angle_d	9.988	602
X-RAY DIFFRACTION	f_chiral_restr	0.098	230
X-RAY DIFFRACTION	f_plane_restr	0.01	260

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 (%)
1.4002-1.4186	0.2805	127	0.3062	3281	X-RAY DIFFRACTION	93
1.4186-1.4381	0.2581	146	0.2814	3638	X-RAY DIFFRACTION	99
1.4381-1.4586	0.298	140	0.2562	3504	X-RAY DIFFRACTION	100
1.4586-1.4804	0.2316	138	0.2335	3640	X-RAY DIFFRACTION	100
1.4804-1.5035	0.1988	142	0.2067	3532	X-RAY DIFFRACTION	100
1.5035-1.5282	0.2272	144	0.2021	3614	X-RAY DIFFRACTION	100
1.5282-1.5545	0.1706	139	0.1974	3540	X-RAY DIFFRACTION	100
1.5545-1.5828	0.2072	143	0.1832	3608	X-RAY DIFFRACTION	100
1.5828-1.6132	0.2229	135	0.185	3591	X-RAY DIFFRACTION	100
1.6132-1.6462	0.1742	144	0.1672	3565	X-RAY DIFFRACTION	100
1.6462-1.682	0.2213	140	0.1751	3597	X-RAY DIFFRACTION	100
1.682-1.7211	0.2019	143	0.1682	3641	X-RAY DIFFRACTION	100
1.7211-1.7641	0.2	138	0.1725	3525	X-RAY DIFFRACTION	100
1.7641-1.8118	0.1805	138	0.1682	3605	X-RAY DIFFRACTION	100
1.8118-1.8652	0.2142	144	0.1643	3544	X-RAY DIFFRACTION	100
1.8652-1.9254	0.1715	142	0.1589	3616	X-RAY DIFFRACTION	100
1.9254-1.9942	0.1892	144	0.1586	3559	X-RAY DIFFRACTION	100
1.9942-2.074	0.2105	144	0.1585	3594	X-RAY DIFFRACTION	100
2.074-2.1684	0.1839	144	0.1544	3580	X-RAY DIFFRACTION	100
2.1684-2.2827	0.1683	138	0.1597	3574	X-RAY DIFFRACTION	100
2.2827-2.4257	0.225	144	0.1661	3630	X-RAY DIFFRACTION	100
2.4257-2.613	0.1783	142	0.1689	3541	X-RAY DIFFRACTION	100
2.613-2.8759	0.1439	143	0.1564	3607	X-RAY DIFFRACTION	100
2.8759-3.292	0.201	142	0.1561	3570	X-RAY DIFFRACTION	100
3.292-4.1472	0.1773	143	0.1417	3597	X-RAY DIFFRACTION	100
4.1472-46.2424	0.1676	138	0.1572	3577	X-RAY DIFFRACTION	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	5.4714	-0.506	0.1616	4.4163	0.0352	5.1151	-0.0626	0.0837	0.2055	-0.2895	0.0234	0.2468	-0.327	-0.2572	0.0034	0.2846	0.037	-0.0266	0.1512	0.017	0.213	-17.8302	6.1242	10.3727
2	4.9203	-5.4273	3.3093	7.7623	-2.046	3.6513	-0.1141	0.1152	0.2774	-0.0198	-0.0722	0.0215	-0.6223	-0.1473	0.219	0.474	0.0584	-0.0152	0.2089	0.0017	0.2977	-17.1283	14.3023	14.0424
3	3.8648	-3.955	5.1646	4.2952	-5.8712	8.362	-0.0261	-0.2317	0.0178	-0.2757	0.0477	0.3862	-0.254	-0.5296	-0.1928	0.3859	0.1335	-0.0072	0.3586	0.0028	0.2933	-25.7607	9.2811	18.2393
4	3.6477	-1.0881	-2.171	4.46	2.1833	9.0139	-0.0602	-0.0489	-0.0071	-0.1402	0.1307	-0.1828	-0.2693	0.1909	-0.0547	0.2533	0.0297	-0.0364	0.1607	0.0327	0.2134	-11.8201	1.7942	15.8053
5	3.3224	0.5447	2.2457	3.0602	-1.1378	5.1903	0.1231	-0.0431	-0.0133	0.2872	-0.0641	-0.0443	0.2632	0.1826	-0.0809	0.2461	0.0737	0.0376	0.1876	-0.0058	0.1711	-5.2859	-13.5956	16.9645
6	1.9166	2.1244	0.0301	4.7109	0.1547	3.7906	-0.0787	0.3523	-0.1124	-0.3941	0.1101	-0.059	0.618	0.0057	-0.0409	0.4653	0.0314	-0.0278	0.2219	0.0006	0.2328	-11.3865	-21.5238	0.101
7	1.6468	-0.106	2.151	2.0291	-1.0961	3.7883	-0.0184	0.0404	0.0182	-0.1991	0.0035	-0.051	0.0445	0.0854	-0.0819	0.2871	0.0331	0.0112	0.1967	-0.0045	0.2281	-8.2985	-10.9511	9.0792
8	6.8301	-1.0142	6.3293	6.099	0.0092	7.7553	0.2498	-0.3905	-0.3362	0.0904	0.0613	0.448	0.6969	-0.7756	-0.2635	0.2687	-0.0555	-0.0035	0.269	0.0462	0.2655	-20.9154	-17.7554	10.9376
9	8.1902	0.0637	3.4605	2.4742	-0.1016	4.2843	0.3631	0.1521	-0.1758	0.0873	-0.0816	-0.2437	0.6265	0.3222	-0.2941	0.3764	0.0942	0.0002	0.2407	0.0097	0.2345	-2.2396	-20.8897	14.7635
10	4.4148	-4.508	-4.0098	5.9704	3.6248	3.7992	0.1311	-0.1574	0.3855	0.0047	0.0693	-0.3	0.0301	0.2259	-0.1637	0.264	0.053	-0.0155	0.2178	0.0256	0.2097	-4.9242	-9.881	17.1759
11	7.7974	-2.9754	1.4966	5.2928	3.9984	8.4513	0.2018	-0.1692	-0.7424	-0.2783	-0.1467	-0.2698	1.0119	0.2504	0.0297	0.4182	0.1181	-0.0013	0.2466	0.0207	0.2345	-3.4391	-22.3835	9.0904

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 3 through 32 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 33 through 45 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 46 through 63 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 64 through 88 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 89 through 104 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 105 through 114 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 115 through 129 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 130 through 144 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 145 through 157 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 158 through 171 )
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 172 through 182 )

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