PDB-8dcd: RNA ligase RtcB from Pyrococcus horikoshii in complex with Zn2+ a...

ID or keywords:

Entry

Database: PDB / ID: 8dcd

Title

RNA ligase RtcB from Pyrococcus horikoshii in complex with Zn2+ 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 / RNA ligase (GTP) activity / RNA ligase (ATP) activity / intron homing / intein-mediated protein splicing / tRNA processing / GMP binding / manganese ion binding / endonuclease activity ...
Similarity search - Function

Biological species

Pyrococcus horikoshii OT3 (archaea)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.22 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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Download

PDBx/mmCIF format	8dcd.cif.gz	477.3 KB	Display	PDBx/mmCIF format
PDB format	pdb8dcd.ent.gz	323.7 KB	Display	PDB format
PDBx/mmJSON format	8dcd.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8dcd_validation.pdf.gz	3.1 MB	Display	wwPDB validaton report
Full document	8dcd_full_validation.pdf.gz	3.1 MB	Display
Data in XML	8dcd_validation.xml.gz	37.1 KB	Display
Data in CIF	8dcd_validation.cif.gz	51.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/dc/8dcd ftp://data.pdbj.org/pub/pdb/validation_reports/dc/8dcd	HTTPS FTP

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Related structure data

Related structure data	8dc9C 8dcaC 8dcbC 8dcfC 8dcgC 4iszS C: citing same article (ref.) S: Starting model for refinement
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
57.9 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
57.4 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	80.910, 136.473, 150.065
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 , 6 types, 186 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: SO₄
#6: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#8: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 160 / 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: 3.72 Å³/Da / Density % sol: 66.89 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, sitting drop Details: apoenzyme: 0.12 mM protein, 2.1 M ammonium sulfate, 0.2 M lithium sulfate soak: 2.1 M ammonium sulfate, 0.2 M lithium sulfate, 2 mM ZnCl2, 10 mM GTP soak duration: 60 min cryoprotectant: 2.0 ...Details: apoenzyme: 0.12 mM protein, 2.1 M ammonium sulfate, 0.2 M lithium sulfate soak: 2.1 M ammonium sulfate, 0.2 M lithium sulfate, 2 mM ZnCl2, 10 mM GTP soak duration: 60 min cryoprotectant: 2.0 M ammonium sulfate, 0.2 M lithium sulfate, 2 mM ZnCl2, 8 mM GTP, 20 % (w/v) sucrose

Crystal

Density Matthews: 3.72 Å³/Da / Density % sol: 66.89 %

Crystal grow

Temperature: 295 K / Method: vapor diffusion, sitting drop
Details: apoenzyme: 0.12 mM protein, 2.1 M ammonium sulfate, 0.2 M lithium sulfate soak: 2.1 M ammonium sulfate, 0.2 M lithium sulfate, 2 mM ZnCl2, 10 mM GTP soak duration: 60 min cryoprotectant: 2.0 ...

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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: 1.2822 Å
Detector	Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Oct 31, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.2822 Å / Relative weight: 1
Reflection	Resolution: 2.22→49.27 Å / Num. obs: 82379 / % possible obs: 99.6 % / Redundancy: 14.2 % / B_iso Wilson estimate: 44.2 Å² / CC_1/2: 0.998 / R_pim(I) all: 0.039 / Net I/σ(I): 15.7
Reflection shell	Resolution: 2.22→2.26 Å / Redundancy: 13.8 % / Mean I/σ(I) obs: 2 / Num. unique obs: 4437 / CC_1/2: 0.737 / R_pim(I) all: 0.443 / % possible all: 98.7

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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: 4ISZ

4isz

Resolution: 2.22→49.27 Å / SU ML: 0.2664 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.6709
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.1971	4041	4.91 %
R_work	0.1697	78262	-
obs	0.171	82303	99.47 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 50.21 Å²

Refinement step

Cycle: LAST / Resolution: 2.22→49.27 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7533	0	208	160	7901

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0075	7902
X-RAY DIFFRACTION	f_angle_d	0.9543	10696
X-RAY DIFFRACTION	f_chiral_restr	0.0566	1131
X-RAY DIFFRACTION	f_plane_restr	0.0081	1374
X-RAY DIFFRACTION	f_dihedral_angle_d	14.1372	1135

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 (%)
2.22-2.25	0.2783	146	0.2544	2655	X-RAY DIFFRACTION	98.11
2.25-2.27	0.3163	132	0.2379	2689	X-RAY DIFFRACTION	99.68
2.27-2.3	0.2715	120	0.2342	2632	X-RAY DIFFRACTION	98.67
2.3-2.33	0.2647	131	0.229	2624	X-RAY DIFFRACTION	98.39
2.33-2.36	0.3042	116	0.2362	2693	X-RAY DIFFRACTION	99.68
2.36-2.4	0.2999	132	0.2315	2678	X-RAY DIFFRACTION	98.8
2.4-2.43	0.2716	152	0.2248	2648	X-RAY DIFFRACTION	99.75
2.43-2.47	0.2796	148	0.2147	2646	X-RAY DIFFRACTION	98.9
2.47-2.51	0.2472	137	0.2074	2693	X-RAY DIFFRACTION	99.79
2.51-2.56	0.2511	129	0.2009	2645	X-RAY DIFFRACTION	99.07
2.56-2.6	0.2336	139	0.1957	2684	X-RAY DIFFRACTION	99.68
2.6-2.65	0.2423	140	0.1948	2653	X-RAY DIFFRACTION	99.5
2.65-2.71	0.2373	147	0.194	2697	X-RAY DIFFRACTION	99.37
2.71-2.77	0.2067	132	0.1903	2676	X-RAY DIFFRACTION	100
2.77-2.83	0.2542	131	0.1986	2707	X-RAY DIFFRACTION	99.51
2.83-2.9	0.2216	141	0.2062	2726	X-RAY DIFFRACTION	99.58
2.9-2.98	0.2617	163	0.1986	2636	X-RAY DIFFRACTION	99.82
2.98-3.07	0.2205	156	0.2053	2643	X-RAY DIFFRACTION	99.22
3.07-3.17	0.2599	135	0.1977	2731	X-RAY DIFFRACTION	99.72
3.17-3.28	0.2194	133	0.1887	2667	X-RAY DIFFRACTION	98.73
3.28-3.41	0.204	138	0.1754	2724	X-RAY DIFFRACTION	99.69
3.41-3.57	0.1867	142	0.1689	2695	X-RAY DIFFRACTION	100
3.57-3.75	0.1884	126	0.1563	2746	X-RAY DIFFRACTION	100
3.75-3.99	0.1832	140	0.1429	2722	X-RAY DIFFRACTION	100
3.99-4.3	0.146	153	0.1285	2738	X-RAY DIFFRACTION	100
4.3-4.73	0.1311	151	0.1158	2745	X-RAY DIFFRACTION	100
4.73-5.41	0.1634	151	0.131	2755	X-RAY DIFFRACTION	99.97
5.41-6.81	0.1744	127	0.1634	2799	X-RAY DIFFRACTION	98.95
6.82-49.27	0.1663	153	0.17	2915	X-RAY DIFFRACTION	99.87

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	2.49622503093	-0.0590906150579	-0.651612134696	1.35213426722	0.158291432972	4.59123517038	0.0331722253482	-0.0312945137292	-0.426759970824	-0.100501891871	0.0497296898809	0.101673240367	0.471086855811	-0.303212861946	-0.0524782998774	0.371380583848	-0.0388309742157	-0.0371792717265	0.282431011275	0.0317994058397	0.331754595343	5.32314034482	3.90142865324	18.7294201356
2	1.30480425842	0.489465035393	0.718017588559	2.10072215378	-0.330105573386	1.20479994491	-0.00181964117581	-0.315037298927	-0.0836705355439	0.250386366295	-0.0539680557466	-0.146900172893	-0.0700310923216	-0.0733789534168	0.0560563727223	0.356514046418	0.0183087294796	-0.0106671432184	0.423420175244	0.0269232516327	0.312983105295	23.7486299305	20.6008301294	41.7792935676
3	2.16911814538	0.462027509014	-0.418640990331	2.66939185649	-1.04489507767	2.26033590317	-0.036348286155	-0.330493579733	-0.02514086605	0.0843421514982	0.021355184895	0.0588829819752	-0.0063636308942	-0.0882763600367	0.0119670610759	0.304796008212	0.0127836787626	-0.0229611770349	0.354660146246	0.0187454414451	0.291583895459	18.3329313311	22.3338523219	36.5716318106
4	3.12662411364	1.23398761424	0.144103291871	1.89265769481	-0.110869367796	1.38608282653	0.112346012816	-0.444691782292	-0.328378994336	0.143552148342	-0.14831269749	0.037229629969	0.174717631949	-0.223257538373	0.0375594115249	0.359077829657	0.0141751944044	0.010090316924	0.470770016409	0.104690103886	0.325220999729	8.68514361759	9.60079895541	40.4964620954
5	2.43097961339	0.992673216572	0.515454443511	1.23636405248	0.00202877612786	1.54756661435	-0.0103915764039	-0.0463783681419	-0.197780938243	-0.074784189973	0.0319666920694	-0.0911359947194	0.0643730385788	0.0403711396036	-0.0140016055049	0.365354176347	0.00597197063613	0.0038675796631	0.323124107843	0.0563604241872	0.293971122093	19.2531380296	17.9189885292	25.8532768142
6	2.31344476169	0.920557359629	0.285687456613	3.98186743884	0.183708452178	1.41835935129	-0.0697752316594	0.403262018134	0.100411990525	-0.313946736415	-0.0303208281996	-0.0972860288232	0.0774851831726	0.198390463939	0.0942026672597	0.319477374326	0.0500812623071	-0.00388748390513	0.351434068683	0.0624950510006	0.292460795165	54.9231403569	-14.915886027	43.6840066587
7	2.48795804407	-0.345703135215	-0.733754413658	1.06522645863	-0.339930884158	1.64872947027	0.0875018224112	0.112441454779	0.414676549475	0.0986193047302	-0.0304320804467	0.036971233969	-0.287675360153	-0.145687683007	-0.0674381339161	0.361123573578	0.0187085527992	-0.0266221198757	0.345060786875	0.0684565110386	0.419985750019	35.7139083519	7.16189304165	60.5957326655
8	2.00925595836	0.89026683461	-0.918887127662	2.43699567922	-0.909024419559	2.19365340301	-0.0303396622856	-0.00666923555775	0.323519401698	-0.0177726074306	-0.0292976912917	-0.0573905555531	-0.0975637333235	0.0262659673663	0.0678702228523	0.301624179099	0.0125196920699	-0.0465242330323	0.317266301046	0.0551763060032	0.334973059563	41.4231051205	2.14174018406	62.4878142583
9	3.3359278343	-1.09435801361	-1.36239082494	1.66784347932	1.58016178593	1.67600392982	0.0812291764807	0.409141474638	0.291116454939	-0.339546164308	-0.0405879102407	-0.0941216037428	-0.294795531152	-0.0437956309586	-0.079093967512	0.464020446425	-0.0510196107678	-0.0105600388561	0.530403494831	0.223141041782	0.589728528838	57.3446907132	5.12352329156	39.4396709705
10	3.10566340263	0.0613550203642	-1.79360620663	0.758237808028	-0.0804134242519	2.53683107501	0.104865451931	0.026372761652	0.357042401625	0.119928778573	0.0244477160702	-0.0185172096968	-0.241776211042	0.0113870750996	-0.152043288916	0.367107332472	-0.0328228376359	-0.0597235350608	0.270448608724	0.0468649109249	0.380604306711	44.6522660353	3.99379395474	62.3854202128
11	2.8627517827	-0.406074719445	-1.53778682975	1.37618240834	0.3434443528	1.39696807839	0.013369012781	-0.0429648393177	0.0848143084647	0.147099848229	-0.0448199211216	-0.193556109708	0.141656931279	0.0813516236658	0.0403562295814	0.376210545503	-0.00161945792683	-0.0516553753569	0.3474008875	0.0772820073086	0.359533810119	50.2851312048	-9.46596751969	60.2964701694
12	2.99433144885	-0.911015611271	-0.816417583319	2.28275093409	0.121935809361	2.69217806561	0.125174752716	0.478168896632	-0.145349637396	-0.374062360319	-0.10609292938	0.426130703141	0.158674938053	-0.684112905468	-0.0119849635565	0.411579518522	-0.0543010227511	-0.0335313279663	0.467689967885	0.0220389021568	0.418041081765	29.5454229964	-10.2998763568	52.441685662

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 1 through 88 )	A	A	1 - 88	1 - 88
2	2	chain 'A' and (resid 89 through 157 )	A	A	89 - 157	89 - 157
3	3	chain 'A' and (resid 158 through 237 )	A	A	158 - 237	158 - 237
4	4	chain 'A' and (resid 238 through 311 )	A	A	238 - 311	238 - 311
5	5	chain 'A' and (resid 312 through 481 )	A	A	312 - 481	312 - 481
6	6	chain 'B' and (resid 1 through 88 )	B	E	1 - 88	1 - 88
7	7	chain 'B' and (resid 89 through 157 )	B	E	89 - 157	89 - 157
8	8	chain 'B' and (resid 158 through 237 )	B	E	158 - 237	158 - 237
9	9	chain 'B' and (resid 238 through 275 )	B	E	238 - 275	238 - 275
10	10	chain 'B' and (resid 276 through 341 )	B	E	276 - 341	276 - 341
11	11	chain 'B' and (resid 342 through 411 )	B	E	342 - 411	342 - 411
12	12	chain 'B' and (resid 412 through 481 )	B	E	412 - 481	412 - 481

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Protein / Sugars , 2 types, 4 molecules AB

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Non-polymers , 6 types, 186 molecules

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-Protein / Sugars , 2 types, 4 molecules AB

-Non-polymers , 6 types, 186 molecules

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+About Yorodumi

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-Feb 9, 2022. New format data for meta-information of EMDB entries

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Protein / Sugars , 2 types, 4 molecules AB

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Non-polymers , 6 types, 186 molecules

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