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- PDB-4dwq: RNA ligase RtcB-GMP/Mn(2+) complex -

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Basic information

Entry
Database: PDB / ID: 4dwq
TitleRNA ligase RtcB-GMP/Mn(2+) complex
ComponentstRNA-splicing ligase RtcB
KeywordsLIGASE / RtcB / guanylylation / RNA ligase / RtcB-GMP / Mn2+
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
tRNA-splicing ligase RtcB / tRNA-splicing ligase RtcB / 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. ...tRNA-splicing ligase RtcB / tRNA-splicing ligase RtcB / 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 / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-MONOPHOSPHATE / MALONATE ION / : / PHOSPHATE ION / PYROPHOSPHATE 2- / tRNA-splicing ligase RtcB
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsOkada, C. / Xia, S. / Englert, M. / Yao, M. / Soll, D. / Wang, J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Structural and mechanistic insights into guanylylation of RNA-splicing ligase RtcB joining RNA between 3'-terminal phosphate and 5'-OH.
Authors: Englert, M. / Xia, S. / Okada, C. / Nakamura, A. / Tanavde, V. / Yao, M. / Eom, S.H. / Konigsberg, W.H. / Soll, D. / Wang, J.
History
DepositionFeb 26, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 5, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 26, 2012Group: Database references
Revision 1.2Dec 19, 2012Group: Database references
Revision 1.3Jan 15, 2014Group: Structure summary
Revision 1.4Aug 2, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)109,14217
Polymers107,1652
Non-polymers1,97715
Water8,701483
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A: tRNA-splicing ligase RtcB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,75810
Polymers53,5821
Non-polymers1,1759
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: tRNA-splicing ligase RtcB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,3857
Polymers53,5821
Non-polymers8026
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)80.296, 137.756, 148.408
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein tRNA-splicing ligase RtcB / Pho hyp2 intein


Mass: 53582.418 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Gene: rtcB, PH1602 / Production host: Escherichia coli (E. coli)
References: UniProt: O59245, Ligases; Forming phosphoric-ester bonds

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Non-polymers , 7 types, 498 molecules

#2: Chemical ChemComp-5GP / GUANOSINE-5'-MONOPHOSPHATE


Mass: 363.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O8P
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H2O4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO4
#7: Chemical ChemComp-POP / PYROPHOSPHATE 2-


Mass: 175.959 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2O7P2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 483 / Source method: isolated from a natural source / Formula: H2O

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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: 3.83 Å3/Da / Density % sol: 67.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 2 M Na-Malonate pH 7.0, 20% glycerol, 10 mM MnCl2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.9 Å
DetectorType: APEX II CCD / Detector: CCD / Date: Oct 18, 2011
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. all: 73660 / Num. obs: 69979 / % possible obs: 95 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 2
Reflection shellResolution: 2.25→2.33 Å / % possible all: 94.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.25→101.29 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.942 / SU B: 3.833 / SU ML: 0.094 / Cross valid method: THROUGHOUT / ESU R: 0.164 / ESU R Free: 0.155 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.19349 3631 4.9 %RANDOM
Rwork0.14965 ---
all0.15182 73660 --
obs0.15182 69979 93.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.577 Å2
Baniso -1Baniso -2Baniso -3
1--0.19 Å2-0 Å20 Å2
2--0.34 Å2-0 Å2
3----0.16 Å2
Refinement stepCycle: LAST / Resolution: 2.25→101.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7534 0 115 483 8132
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0197865
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6251.97510623
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0525974
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.07422.665364
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.146151367
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5991586
X-RAY DIFFRACTIONr_chiral_restr0.10.21123
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215994
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.252→2.31 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 237 -
Rwork0.231 4810 -
obs--92.25 %

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