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- PDB-8dcg: Structure of guanylylated RNA ligase RtcB from Pyrococcus horikoshii -

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Basic information

Entry
Database: PDB / ID: 8dcg
TitleStructure of guanylylated RNA ligase RtcB from Pyrococcus horikoshii
ComponentstRNA-splicing ligase RtcB
KeywordsLIGASE / RNA ligase / RtcB / RtcB-GMP / guanylylation / tRNA splicing / RNA repair
Function / homology
Function and homology information


RNA splicing, via endonucleolytic cleavage and ligation / 3'-phosphate/5'-hydroxy nucleic acid ligase / GMP binding / RNA ligase (ATP) activity / intron homing / intein-mediated protein splicing / tRNA processing / manganese ion binding / endonuclease activity / Hydrolases; Acting on ester bonds ...RNA splicing, via endonucleolytic cleavage and ligation / 3'-phosphate/5'-hydroxy nucleic acid ligase / GMP binding / RNA ligase (ATP) activity / intron homing / intein-mediated protein splicing / 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'-MONOPHOSPHATE / tRNA-splicing ligase RtcB
Similarity search - Component
Biological speciesPyrococcus horikoshii OT3 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 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)115,46235
Polymers111,5082
Non-polymers3,95433
Water1,31573
1
A: tRNA-splicing ligase RtcB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,77918
Polymers55,7541
Non-polymers2,02517
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: tRNA-splicing ligase RtcB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,68317
Polymers55,7541
Non-polymers1,92916
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)143.560, 143.560, 80.301
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43
Space group name HallP4cw
Symmetry operation#1: x,y,z
#2: -y,x,z+3/4
#3: y,-x,z+1/4
#4: -x,-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 , 4 types, 104 molecules

#3: Chemical ChemComp-5GP / GUANOSINE-5'-MONOPHOSPHATE / Guanosine monophosphate


Mass: 363.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O8P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical...
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 25 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 73 / 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: 3.71 Å3/Da / Density % sol: 66.85 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 2.2 M ammonium sulfate cryoprotectant: 2.2 M ammonium sulfate, 22% (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: 1.8917 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Feb 9, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.8917 Å / Relative weight: 1
ReflectionResolution: 2.35→47.85 Å / Num. obs: 67599 / % possible obs: 99 % / Redundancy: 12.6 % / Biso Wilson estimate: 45.4 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.033 / Net I/σ(I): 19.1
Reflection shellResolution: 2.35→2.4 Å / Redundancy: 11 % / Mean I/σ(I) obs: 2.2 / Num. unique obs: 4104 / CC1/2: 0.711 / Rpim(I) all: 0.341 / % possible all: 90.4

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Processing

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

4dwq


Resolution: 2.35→47.85 Å / SU ML: 0.2427 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 22.4176
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2168 3286 4.87 %
Rwork0.1905 64229 -
obs0.1918 67515 98.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 52.73 Å2
Refinement stepCycle: LAST / Resolution: 2.35→47.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7534 0 221 73 7828
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00757913
X-RAY DIFFRACTIONf_angle_d0.961510714
X-RAY DIFFRACTIONf_chiral_restr0.05811133
X-RAY DIFFRACTIONf_plane_restr0.0091379
X-RAY DIFFRACTIONf_dihedral_angle_d7.3811146
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.380.3381210.27572363X-RAY DIFFRACTION85.07
2.38-2.420.20661240.23322783X-RAY DIFFRACTION97.16
2.42-2.460.23571180.23182747X-RAY DIFFRACTION99.03
2.46-2.50.25081540.21592755X-RAY DIFFRACTION98.34
2.5-2.550.24971570.22712789X-RAY DIFFRACTION99.63
2.55-2.60.24251480.22852743X-RAY DIFFRACTION97.64
2.6-2.650.27871310.22822806X-RAY DIFFRACTION99.97
2.65-2.710.26291380.23362786X-RAY DIFFRACTION99.39
2.71-2.770.25231320.22672827X-RAY DIFFRACTION99.87
2.77-2.840.25421420.22432816X-RAY DIFFRACTION99.93
2.84-2.920.29661450.22532808X-RAY DIFFRACTION99.9
2.92-30.25131330.21762842X-RAY DIFFRACTION99.9
3-3.10.2431400.21552793X-RAY DIFFRACTION100
3.1-3.210.24051510.2252847X-RAY DIFFRACTION100
3.21-3.340.23581670.2072774X-RAY DIFFRACTION100
3.34-3.490.21681200.20042850X-RAY DIFFRACTION100
3.49-3.680.18571470.17592819X-RAY DIFFRACTION99.83
3.68-3.910.21121760.17712785X-RAY DIFFRACTION100
3.91-4.210.19641310.16042866X-RAY DIFFRACTION100
4.21-4.630.16541670.14822799X-RAY DIFFRACTION100
4.63-5.30.1921640.15922829X-RAY DIFFRACTION99.97
5.3-6.670.21911320.1872872X-RAY DIFFRACTION99.97
6.68-47.850.21091480.18332930X-RAY DIFFRACTION99.84
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)
13.06573430442-0.00731115883093-0.7000046921191.553925177970.09646749684792.22703042503-0.00265896832961-0.1732362891440.3998325158980.03700857544490.0506633359337-0.1287729762-0.277752571146-0.0214984768693-0.04704492657880.3716260274010.0300299646598-0.03725717579190.387417399581-0.04652264316020.42908817317254.3828629203-40.458722707914.1545048015
21.394063631810.293326829060.6251903887631.673719156420.5895669700251.97703709075-0.05464268121050.05760676973930.174843747413-0.24430723392-0.0733648812320.272903859776-0.156428754898-0.3921689374420.1440033722120.3064148254530.0538108681452-0.04081818957350.380661128518-0.0004562415979820.3448909387830.8044571603-56.1522961423-4.24734241597
31.65531014624-0.334241852115-0.1863291847991.926042056621.161380957841.6334119891-0.0456896371103-0.1384338040880.0652653363616-0.0288727134179-0.009645376874180.03409772596940.0602820061254-0.1997417190670.05090811178040.3403975732390.06034155413440.004944237676590.3272561230830.01465293473370.30752231048435.9940901447-58.05909752571.10445377501
42.263966786150.9774428997140.6983790789751.616965261840.3095087169292.813992350550.129605795554-0.2961924420650.4174786581940.131785883845-0.162300023940.116127394386-0.467274059056-0.311121344650.04334040245840.3994426711990.1507986458650.01983767673620.523904788689-0.122865514310.52175815235534.8533395562-35.632850566717.6558855282
51.31730611254-0.1745543912140.2707933742171.965434869141.081291959522.246721918240.00330951981123-0.169595518143-0.08336290190890.108313537321-0.0642602445530.05579242800620.14609399534-0.1496293648040.04658923490450.3026134577050.01512000414520.03873619829920.3541897634020.02267835127720.35774550589837.9343098347-58.85230705817.86083483455
62.23171224208-0.221033061040.5162089708790.9295397965950.660955068071.36074031574-0.03980197126980.2098341489830.400085897669-0.3066491110490.0149585167255-0.173755007187-0.3395626539610.08535581767190.00680824120640.4424876014940.0266064350540.02723892609780.3591353559020.03372698100840.46117163366648.9083167934-49.7851317947-5.91840077117
71.21576092312-0.0210160094837-0.1165510863641.07746420461-0.003753638327651.23953033454-0.01914564628430.01365297462220.1738949610910.00407565439930.0967180157225-0.0542507859156-0.03369600583160.214133231233-0.0322971351820.3496774478980.0508359497909-0.03394803228990.340505365522-0.00792638466390.3284770042324.1203615011-24.5359467828-28.3019978917
81.718681640541.247362975392.35787635951.390169683391.164968896633.86496921030.173882668905-0.356750610563-0.4081375520960.2333992374930.043987512399-0.1293581189911.01727903920.212946922011-0.2164049101460.6579445978880.08802354702560.0770542969580.4459323710580.05431425576540.54255138383414.6787190566-51.4051040323-22.0493107823
92.23444175639-0.204051739655-1.468625623120.8528247192590.2129486952442.5427057645-0.141827528215-0.0880289551949-0.141032808716-0.01558946448140.107885521780.09913762291280.3185630367480.1340844115510.0302040729220.3602578616870.0642497076344-0.03340034826040.320612302696-0.0005277508851270.33973223930315.0022163393-36.2499838078-27.7478452377
101.30165746262-0.394271998108-0.3451716098251.71487821416-0.625657557221.71291470385-0.0527110156046-0.2125913703180.2768267106190.1468922683260.00636286723485-0.201968714706-0.1570524309780.2537929988390.02369550440530.372256920020.037803692741-0.005734069617260.369515914051-0.04103059719460.45150290906620.1997251528-24.0040756979-15.1026593026
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 237 )AA158 - 237158 - 237
44chain 'A' and (resid 238 through 275 )AA238 - 275238 - 275
55chain 'A' and (resid 276 through 373 )AA276 - 373276 - 373
66chain 'A' and (resid 374 through 481 )AA374 - 481374 - 481
77chain 'B' and (resid 1 through 126 )BD1 - 1261 - 126
88chain 'B' and (resid 127 through 158 )BD127 - 158127 - 158
99chain 'B' and (resid 159 through 383 )BD159 - 383159 - 383
1010chain 'B' and (resid 384 through 481 )BD384 - 481384 - 481

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