PDB-8dc9: RNA ligase RtcB from Pyrococcus horikoshii in complex with Mn2+ a...

ID or keywords:

Entry

Database: PDB / ID: 8dc9

Title

RNA ligase RtcB from Pyrococcus horikoshii in complex with Mn2+ and GTP

Components

tRNA-splicing ligase RtcB

Keywords

LIGASE / RtcB / RNA ligase / tRNA splicing / RNA repair

Function / homology

Function and homology information

RNA splicing, via endonucleolytic cleavage and ligation / 3'-phosphate/5'-hydroxy nucleic acid ligase / : / tRNA-splicing ligase complex / GMP binding / RNA ligase (ATP) activity / intein-mediated protein splicing / intron homing / manganese ion binding / endonuclease activity ...
Similarity search - Function

Biological species

Pyrococcus horikoshii OT3 (archaea)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.47 Å

Authors

Jacewicz, A. / Dantuluri, S. / Shuman, S.

Funding support

United States, 2items

Organization	Grant number	Country
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	R35-GM126945	United States
National Institutes of Health/National Cancer Institute (NIH/NCI)	P30-CA008748	United States

Citation

Journal: Rna / Year: 2022
Title: Structures of RNA ligase RtcB in complexes with divalent cations and GTP.
Authors: Jacewicz, A. / Dantuluri, S. / Shuman, S.

History

Deposition	Jun 16, 2022	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 12, 2022	Provider: repository / Type: Initial release
Revision 1.1	Nov 9, 2022	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2	Oct 18, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	8dc9.cif.gz	472.5 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	8dc9_validation.pdf.gz	3 MB	Display	wwPDB validaton report
Full document	8dc9_full_validation.pdf.gz	3 MB	Display
Data in XML	8dc9_validation.xml.gz	35.8 KB	Display
Data in CIF	8dc9_validation.cif.gz	48.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/dc/8dc9 ftp://data.pdbj.org/pub/pdb/validation_reports/dc/8dc9	HTTPS FTP

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Related structure data

Related structure data	8dcaC 8dcbC 8dcdC 8dcfC 8dcgC 4isjS S: Starting model for refinement 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	#131 - Nov 2010 Inteins similarity (13) #219 - Mar 2018 Vacuolar ATPase similarity (13)

Deposited unit

A: tRNA-splicing ligase RtcB

B: tRNA-splicing ligase RtcB

hetero molecules

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

1

A: tRNA-splicing ligase RtcB

hetero molecules

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

2

B: tRNA-splicing ligase RtcB

hetero molecules

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

Unit cell

Length a, b, c (Å)	80.741, 137.284, 150.157
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁
Space group name Hall	P2ac2ab
Symmetry operation	#1: x,y,z #2: x+1/2,-y+1/2,-z #3: -x,y+1/2,-z+1/2 #4: -x+1/2,-y,z+1/2

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Protein / Sugars , 2 types, 4 molecules AB

#1: Protein

tRNA-splicing ligase RtcB / 3'-phosphate/5'-hydroxy nucleic acid ligase / tRNA ligase RtcB

Mass: 55753.781 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Pyrococcus horikoshii OT3 (archaea)
Strain: ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3
Gene: rtcB, PH1602 / Production host:

Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Codon Plus
References: UniProt: O59245, 3'-phosphate/5'-hydroxy nucleic acid ligase

#2: Polysaccharide

beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose

Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: sucrose

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Non-polymers , 5 types, 48 molecules

#3: Chemical	ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE Mass: 523.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₀H₁₆N₅O₁₄P₃ / Feature type: SUBJECT OF INVESTIGATION / Comment: GTP, energy-carrying molecule*YM
#4: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: SO₄
#5: Chemical	ChemComp-MN / MANGANESE (II) ION Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 20 / Source method: isolated from a natural source / Formula: H₂O

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Details

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: 3.73 Å³/Da / Density % sol: 67.04 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, sitting drop Details: apoenzyme crystals: 2.05 M ammonium sulfate, 0.2M lithium sulfate, 12 mM protein soak solution: 2.1 M ammonium sulfate, 0.2M lithium sulfate, 10 mM MnCl2, 10 mM GTP soak duration: 16-18h ...Details: apoenzyme crystals: 2.05 M ammonium sulfate, 0.2M lithium sulfate, 12 mM protein soak solution: 2.1 M ammonium sulfate, 0.2M lithium sulfate, 10 mM MnCl2, 10 mM GTP soak duration: 16-18h cryoprotectant: 2.0 M ammonium sulfate, 0.2 M lithium sulfate, 10 mM MnCl2, 5 mM GTP, 19.5 % sucrose

Crystal

Density Matthews: 3.73 Å³/Da / Density % sol: 67.04 %

Crystal grow

Temperature: 295 K / Method: vapor diffusion, sitting drop
Details: apoenzyme crystals: 2.05 M ammonium sulfate, 0.2M lithium sulfate, 12 mM protein soak solution: 2.1 M ammonium sulfate, 0.2M lithium sulfate, 10 mM MnCl2, 10 mM GTP soak duration: 16-18h ...

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 25, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9792 Å / Relative weight: 1
Reflection	Resolution: 2.47→49.39 Å / Num. obs: 60682 / % possible obs: 100 % / Redundancy: 13.8 % / B_iso Wilson estimate: 57 Å² / CC_1/2: 0.998 / R_pim(I) all: 0.035 / Net I/σ(I): 15.8
Reflection shell	Resolution: 2.47→2.53 Å / Redundancy: 12.8 % / Mean I/σ(I) obs: 2 / Num. unique obs: 4442 / CC_1/2: 0.763 / R_pim(I) all: 0.33 / % possible all: 100

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Processing

Software

Name	Version	Classification
PHENIX	1.20.1_4487	refinement
XDS		data reduction
XDS		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4ISJ

4isj

Resolution: 2.47→49.39 Å / SU ML: 0.3448 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.8671
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2182	5683	4.91 %
R_work	0.1832	109988	-
obs	0.1849	60613	99.99 %

Solvent computation

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

Displacement parameters

B_iso mean: 61.49 Å²

Refinement step

Cycle: LAST / Resolution: 2.47→49.39 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7534	0	212	20	7766

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0081	7880
X-RAY DIFFRACTION	f_angle_d	1.0163	10668
X-RAY DIFFRACTION	f_chiral_restr	0.0579	1128
X-RAY DIFFRACTION	f_plane_restr	0.0091	1370
X-RAY DIFFRACTION	f_dihedral_angle_d	14.8752	1128

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 (%)
2.47-2.5	0.3951	171	0.3051	3681	X-RAY DIFFRACTION	99.97
2.5-2.53	0.3189	198	0.292	3714	X-RAY DIFFRACTION	100
2.53-2.56	0.2744	194	0.2761	3605	X-RAY DIFFRACTION	100
2.56-2.59	0.3115	200	0.2504	3688	X-RAY DIFFRACTION	100
2.59-2.62	0.2658	186	0.2479	3673	X-RAY DIFFRACTION	100
2.62-2.66	0.307	219	0.2377	3631	X-RAY DIFFRACTION	100
2.66-2.7	0.2826	163	0.2364	3722	X-RAY DIFFRACTION	100
2.7-2.74	0.2678	171	0.2364	3651	X-RAY DIFFRACTION	100
2.74-2.78	0.3053	165	0.2566	3708	X-RAY DIFFRACTION	100
2.78-2.83	0.3134	217	0.2448	3625	X-RAY DIFFRACTION	100
2.83-2.88	0.3247	183	0.2323	3671	X-RAY DIFFRACTION	100
2.88-2.93	0.2409	214	0.2235	3597	X-RAY DIFFRACTION	99.97
2.93-2.98	0.2494	174	0.2038	3778	X-RAY DIFFRACTION	100
2.98-3.05	0.2214	186	0.1928	3592	X-RAY DIFFRACTION	100
3.05-3.11	0.2476	190	0.1999	3712	X-RAY DIFFRACTION	100
3.11-3.18	0.2784	207	0.1999	3634	X-RAY DIFFRACTION	100
3.18-3.26	0.218	178	0.1976	3670	X-RAY DIFFRACTION	99.97
3.26-3.35	0.2316	173	0.1932	3678	X-RAY DIFFRACTION	100
3.35-3.45	0.2167	170	0.2031	3655	X-RAY DIFFRACTION	100
3.45-3.56	0.264	183	0.1789	3701	X-RAY DIFFRACTION	99.97
3.56-3.69	0.2252	190	0.1736	3641	X-RAY DIFFRACTION	99.92
3.69-3.84	0.1952	178	0.1762	3700	X-RAY DIFFRACTION	100
3.84-4.01	0.2007	184	0.1686	3644	X-RAY DIFFRACTION	100
4.01-4.22	0.1977	207	0.1549	3663	X-RAY DIFFRACTION	100
4.22-4.49	0.1673	194	0.146	3701	X-RAY DIFFRACTION	100
4.49-4.83	0.1711	177	0.1412	3655	X-RAY DIFFRACTION	100
4.83-5.32	0.1806	209	0.1554	3668	X-RAY DIFFRACTION	100
5.32-6.09	0.1928	191	0.1784	3643	X-RAY DIFFRACTION	100
6.09-7.66	0.2085	185	0.1794	3655	X-RAY DIFFRACTION	99.92
7.67-49.39	0.2059	226	0.1727	3632	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	1.35633328524	0.221291190277	0.00912623790577	1.53214135996	-0.66728627056	2.56464764478	-0.0466996223391	-0.0300328880312	-0.387621871347	-0.170490903727	0.13626163942	0.127574072965	0.558885544536	-0.172511110849	-0.0836162087687	0.510623104835	-6.53886912262E-5	-0.0303251451877	0.391813298895	0.0496399282032	0.477151816222	5.23851423652	4.20341013369	18.8768789607
2	1.30206501625	0.238241766308	0.610759677554	1.38362044425	-0.450322382949	0.965813827396	0.105687419408	-0.346444594331	-0.157310443456	0.307335054659	-0.086078148067	-0.177069557131	-0.0950293767689	0.168816554488	-0.0288740633836	0.44871334124	-0.000716299442334	0.000232114534544	0.597032805409	0.0613532260404	0.401827475239	23.5637515717	20.7180805047	42.0373588434
3	2.18487004263	1.19787356249	-0.25308842359	1.81177916299	-0.261038212373	1.21289712213	0.0673102379125	-0.454163402015	-0.135556233272	0.15510905414	-0.0917532633689	0.000114060572354	0.0324138452874	-0.0607862174982	0.0268111642013	0.429298463507	0.0543402798944	0.00904902058125	0.521223799126	0.0715464680046	0.36646538412	12.3941410434	18.582637508	35.7645401808
4	1.81985659815	1.61714830505	0.0958717028519	1.53139924749	0.287258477439	2.1006773281	0.269428148191	-0.144211336712	-0.556094996282	-0.213346232817	-0.0552405344062	-0.400910055636	0.424259897015	0.226184687418	-0.183159952306	0.507525311177	0.0507990261842	-0.0111324743509	0.443231068375	0.100558594894	0.499764546981	25.6772290236	13.3153683164	24.0399451784
5	2.00527849171	0.46740710022	0.364010393662	3.20127419818	-0.000119451083657	1.81810168572	-0.0484039701932	0.643181983341	0.125087902587	-0.355257065536	-0.0568359573225	-0.149400708068	0.216169049647	0.328815759188	0.0900162244825	0.413179277408	0.0339612463213	0.00874335616602	0.462042678974	0.0993956217792	0.387454098177	54.8509608824	-15.0115005683	44.0600684749
6	2.0427358657	-0.634800451323	-0.0474551966308	0.383053016948	0.0840364221598	1.61775898954	0.0690843010101	0.196900631897	0.595028468447	0.0758726209131	-0.028731837275	0.022102484559	-0.288131391646	-0.0827326556332	-0.0510879170437	0.481536507915	0.0362682992326	0.00195865637377	0.415891794934	0.113666014977	0.592606797652	35.6775179164	7.29813673653	60.9480105271
7	2.18932775908	0.178363153576	-1.31041489936	1.3812343495	-0.431957283176	2.23096688743	0.00736724612798	0.0937159957065	0.364871817392	0.0723385489314	0.00613066329173	-0.0921553069912	-0.150369064243	0.106557439866	0.00506338953424	0.391632933641	-0.0323777657192	-0.10793801778	0.359988446442	0.102166456317	0.489905958063	47.462567968	1.78756940392	58.5811123025
8	1.75310250092	-0.94816255262	-1.66513123599	2.65586403998	0.0688865133284	1.85470746662	0.146815537733	0.788698349563	0.00552590122393	-0.370037781056	-0.206632324729	0.255120622432	0.0976568809351	-0.361846948785	0.0346217836324	0.542907790886	-0.0288755334618	-0.0671305083547	0.564636087426	0.0677547317711	0.468371892104	34.3196541084	-10.8546635801	54.1173433397

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 'A' and (resid 2 through 88 )	A	A	2 - 88	2 - 88
2	2	chain 'A' and (resid 89 through 157 )	A	A	89 - 157	89 - 157
3	3	chain 'A' and (resid 158 through 383 )	A	A	158 - 383	158 - 383
4	4	chain 'A' and (resid 384 through 481 )	A	A	384 - 481	384 - 481
5	5	chain 'B' and (resid 2 through 88 )	B	D	2 - 88	2 - 88
6	6	chain 'B' and (resid 89 through 158 )	B	D	89 - 158	89 - 158
7	7	chain 'B' and (resid 159 through 373 )	B	D	159 - 373	159 - 373
8	8	chain 'B' and (resid 374 through 481 )	B	D	374 - 481	374 - 481

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