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- PDB-8dcb: RNA ligase RtcB from Pyrococcus horikoshii in complex with Ni2+ a... -

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Basic information

Entry
Database: PDB / ID: 8dcb
TitleRNA ligase RtcB from Pyrococcus horikoshii in complex with Ni2+ and GTP
ComponentstRNA-splicing ligase RtcB
KeywordsLIGASE / 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 / GMP binding / RNA ligase (ATP) activity / intein-mediated protein splicing / intron homing / tRNA processing / manganese ion binding / endonuclease activity ...RNA splicing, via endonucleolytic cleavage and ligation / 3'-phosphate/5'-hydroxy nucleic acid ligase / RNA ligase (GTP) activity / GMP binding / RNA ligase (ATP) activity / intein-mediated protein splicing / intron homing / tRNA processing / manganese ion binding / endonuclease activity / Hydrolases; Acting on ester bonds / GTP binding / DNA binding
Similarity search - Function
RNA-splicing ligase, RtcB / tRNA-splicing ligase RtcB-like superfamily / tRNA-splicing ligase RtcB / LAGLIDADG-like domain / Intein splicing domain / Intein / Intein DOD homing endonuclease / Intein DOD-type homing endonuclease domain profile. / Homing endonuclease, LAGLIDADG / Intein C-terminal splicing region ...RNA-splicing ligase, RtcB / tRNA-splicing ligase RtcB-like superfamily / tRNA-splicing ligase RtcB / LAGLIDADG-like domain / Intein splicing domain / Intein / Intein DOD homing endonuclease / Intein DOD-type homing endonuclease domain profile. / Homing endonuclease, LAGLIDADG / Intein C-terminal splicing region / Intein C-terminal splicing motif profile. / Hint domain C-terminal / Hint (Hedgehog/Intein) domain C-terminal region / Intein N-terminal splicing region / Intein N-terminal splicing motif profile. / Hint domain N-terminal / Hint (Hedgehog/Intein) domain N-terminal region / Homing endonuclease / Hint domain superfamily
Similarity search - Domain/homology
sucrose / GUANOSINE-5'-TRIPHOSPHATE / NICKEL (II) ION / tRNA-splicing ligase RtcB
Similarity search - Component
Biological speciesPyrococcus horikoshii OT3 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsJacewicz, A. / Dantuluri, S. / Shuman, S.
Funding support United States, 2items
OrganizationGrant numberCountry
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
CitationJournal: Rna / Year: 2022
Title: Structures of RNA ligase RtcB in complexes with divalent cations and GTP.
Authors: Jacewicz, A. / Dantuluri, S. / Shuman, S.
History
DepositionJun 16, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 9, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: tRNA-splicing ligase RtcB
B: tRNA-splicing ligase RtcB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,65624
Polymers111,5082
Non-polymers3,14822
Water30617
1
A: tRNA-splicing ligase RtcB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,34512
Polymers55,7541
Non-polymers1,59111
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: tRNA-splicing ligase RtcB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,31112
Polymers55,7541
Non-polymers1,55711
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.241, 137.492, 149.559
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
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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Components

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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
DescriptorTypeProgram
DFrufb2-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[ha122h-2b_2-5][a2122h-1a_1-5]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][b-D-Fruf]{[(2+1)][a-D-Glcp]{}}LINUCSPDB-CARE

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Non-polymers , 6 types, 37 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.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ni / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#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.: 17 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.75 Å3/Da / Density % sol: 67.16 %
Crystal growTemperature: 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, 10 mM NiCl2, 10 mM GTP soak duration: 60 min cryoprotectant: 2. ...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, 10 mM NiCl2, 10 mM GTP soak duration: 60 min cryoprotectant: 2.0 M ammonium sulfate, 0.2 M lithium sulfate, 5 mM NiCl2, 5 mM GTP, 20 %(w/v) sucrose

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1.4857 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Oct 31, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.4857 Å / Relative weight: 1
ReflectionResolution: 2.6→49.85 Å / Num. obs: 52086 / % possible obs: 99.6 % / Redundancy: 12.9 % / Biso Wilson estimate: 53.1 Å2 / CC1/2: 0.998 / Rpim(I) all: 0.047 / Net I/σ(I): 15.9
Reflection shellResolution: 2.6→2.68 Å / Redundancy: 13.9 % / Mean I/σ(I) obs: 2.1 / Num. unique obs: 4421 / CC1/2: 0.762 / Rpim(I) all: 0.326 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ISZ

4isz


Resolution: 2.6→49.52 Å / SU ML: 0.3434 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.4527
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2086 4919 4.97 %
Rwork0.1704 94092 -
obs0.1723 52016 99.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 67.94 Å2
Refinement stepCycle: LAST / Resolution: 2.6→49.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7534 0 173 17 7724
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087849
X-RAY DIFFRACTIONf_angle_d0.968810619
X-RAY DIFFRACTIONf_chiral_restr0.05661128
X-RAY DIFFRACTIONf_plane_restr0.00921370
X-RAY DIFFRACTIONf_dihedral_angle_d15.09461130
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.630.32651760.26543115X-RAY DIFFRACTION97.98
2.63-2.660.27881270.25093177X-RAY DIFFRACTION99.91
2.66-2.690.32041860.25883088X-RAY DIFFRACTION99
2.69-2.730.26311600.25723062X-RAY DIFFRACTION98.44
2.73-2.760.33311670.28473154X-RAY DIFFRACTION99.85
2.76-2.80.35751900.29763151X-RAY DIFFRACTION98.53
2.8-2.840.31521620.26333122X-RAY DIFFRACTION99.94
2.84-2.880.3331750.26843132X-RAY DIFFRACTION99.85
2.88-2.930.24961310.24123119X-RAY DIFFRACTION98.9
2.93-2.980.2821610.20993138X-RAY DIFFRACTION99.94
2.98-3.030.22861530.20383151X-RAY DIFFRACTION99.25
3.03-3.080.2541620.21193172X-RAY DIFFRACTION100
3.08-3.140.24741800.20963129X-RAY DIFFRACTION99.19
3.14-3.210.26611970.21753114X-RAY DIFFRACTION99.94
3.21-3.280.28021430.20533148X-RAY DIFFRACTION99.64
3.28-3.350.25761680.21433124X-RAY DIFFRACTION99.94
3.35-3.440.28191880.20763118X-RAY DIFFRACTION99.64
3.44-3.530.26211640.17973184X-RAY DIFFRACTION99.55
3.53-3.630.21671520.16793075X-RAY DIFFRACTION98.09
3.63-3.750.21251580.15693113X-RAY DIFFRACTION99.21
3.75-3.880.21191760.15343176X-RAY DIFFRACTION99.97
3.88-4.040.18631770.14483124X-RAY DIFFRACTION100
4.04-4.220.22451450.13253160X-RAY DIFFRACTION99.97
4.22-4.450.12021420.12723173X-RAY DIFFRACTION100
4.45-4.720.15451810.11873165X-RAY DIFFRACTION99.91
4.72-5.090.14631790.13213133X-RAY DIFFRACTION99.94
5.09-5.60.19661730.14853120X-RAY DIFFRACTION100
5.6-6.410.19731770.16383144X-RAY DIFFRACTION99.97
6.41-8.070.16751360.1493151X-RAY DIFFRACTION98.68
8.07-49.520.13161330.15413160X-RAY DIFFRACTION99.43
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
12.570208042060.982773836136-1.028772539681.79899731522-0.2300548816084.026377339440.125920817467-0.17059857136-0.635638172384-0.1343461975710.00333969260427-0.01043361312750.562094934848-0.154465538692-0.1150373281840.5396199724320.000781111814104-0.09091526680730.3976111694310.1080237099860.5080217738685.188496036184.1817793039618.8009085787
21.455920847140.5174892960180.513494818481.652982344340.0565135175751.212760454350.240237117291-0.888359451302-0.23058647250.43571821234-0.201574146883-0.1562114058890.10582374062-0.0314362729117-0.0001589598253590.497756938504-0.0604394391568-0.07498404263270.7088446266750.1289287083280.39931831684523.475575181320.979734146141.8780738181
32.477954665621.350887965670.1579495687161.998319638930.2122137141011.331103141020.17846336455-0.638286863377-0.168453242990.197552818909-0.1984861843810.03913366990680.12094147371-0.1906418170040.02394254319510.4716205256450.0190843546667-0.01817700889920.571658771510.1510064767560.35576989991212.292815852318.84376488735.6175605956
42.748445255861.761375993790.106801566791.556763439980.9514674112692.05001521960.103748303998-0.255742877764-0.861522919223-0.06494014347270.130414003283-0.4748140966720.4287635416450.266197940313-0.2440764185520.5683521791220.05043309429560.001093459232740.5187423829150.1546645936120.60752767558725.612839099913.480277577423.8800607016
53.391936893941.29070882724-0.3528904717184.82520861024-0.1966488132792.51011384049-0.120790205760.7838759012240.066706016879-0.5154362826820.0319961346305-0.03636751593150.2500536817060.2423531001160.09904874853980.4258870910380.0353544654873-0.03122580960230.5213387570170.06232627505430.37443615613155.2378923684-14.9151599943.6549978503
62.20257610820.118167934101-0.9280942186870.834802451019-0.1132434428931.775131063230.2009496695550.4006440460041.007214486080.1027518840720.08164500643250.335782446219-0.524650761832-0.279649642709-0.2956755573490.5971445992060.05912595081470.01601891610460.4943860687360.1683103774610.78954031663135.88609541077.2372390471860.6581176285
73.068593682620.447668100368-1.629734676391.51891013666-0.3132957433052.453255948250.0278363280920.2620155654290.5751336263960.06726133365590.06787346077420.0286279972284-0.220915969295-0.0222342719611-0.0816787224410.433858288518-0.015121539819-0.1048361664480.3683783978420.1110088388280.48048253324747.24426706971.358565788958.2907214899
82.34911474883-0.511417198276-2.099975457292.16324552890.2790976622551.90773497501-0.01599051855481.054276911070.0897016542825-0.268487046659-0.04802773815110.3506326391460.273247483007-0.629374527820.0646462366850.567064316372-0.070525798345-0.08518603450940.6495658059540.09742082320220.49460951659934.4634382373-11.048972779353.342878578
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 88 )AA1 - 881 - 88
22chain 'A' and (resid 89 through 157 )AA89 - 15789 - 157
33chain 'A' and (resid 158 through 383 )AA158 - 383158 - 383
44chain 'A' and (resid 384 through 481 )AA384 - 481384 - 481
55chain 'B' and (resid 1 through 88 )BE1 - 881 - 88
66chain 'B' and (resid 89 through 158 )BE89 - 15889 - 158
77chain 'B' and (resid 159 through 384 )BE159 - 384159 - 384
88chain 'B' and (resid 385 through 481 )BE385 - 481385 - 481

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