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- PDB-1s68: Structure and Mechanism of RNA Ligase -

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Basic information

Entry
Database: PDB / ID: 1s68
TitleStructure and Mechanism of RNA Ligase
ComponentsRNA Ligase 2
KeywordsLIGASE / RIBONUCLEIC ACID LIGASE / RNA REPAIR / T4
Function / homology
Function and homology information


RNA ligase (ATP) / RNA ligase (ATP) activity / RNA repair / ATP binding / metal ion binding
Similarity search - Function
RNA ligase 2, C-terminal / RNA ligase 2, viral / T4 RNA ligase 2 C-terminal / RNA ligase, Rnl2 / RNA ligase 1/2, C-terminal domain superfamily / RNA ligase domain, REL/Rln2 / RNA ligase / Dna Ligase; domain 1 - #70 / DNA ligase/mRNA capping enzyme / D-amino Acid Aminotransferase; Chain A, domain 1 ...RNA ligase 2, C-terminal / RNA ligase 2, viral / T4 RNA ligase 2 C-terminal / RNA ligase, Rnl2 / RNA ligase 1/2, C-terminal domain superfamily / RNA ligase domain, REL/Rln2 / RNA ligase / Dna Ligase; domain 1 - #70 / DNA ligase/mRNA capping enzyme / D-amino Acid Aminotransferase; Chain A, domain 1 / Dna Ligase; domain 1 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / RNA ligase 2
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.9 Å
AuthorsHo, C.K. / Wang, L.K. / Lima, C.D. / Shuman, S.
CitationJournal: Structure / Year: 2004
Title: Structure and mechanism of RNA ligase.
Authors: Ho, C.K. / Wang, L.K. / Lima, C.D. / Shuman, S.
History
DepositionJan 22, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 24, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA Ligase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6782
Polymers28,3301
Non-polymers3471
Water4,360242
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.717, 89.892, 47.737
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-348-

HOH

21A-539-

HOH

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Components

#1: Protein RNA Ligase 2


Mass: 28330.332 Da / Num. of mol.: 1 / Fragment: N-terminal domain (residues 1-249)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T4 (virus) / Genus: T4-like viruses / Species: Enterobacteria phage T4 sensu lato / Gene: Y10A, 24.1 / Plasmid: PET16B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 DE3 / References: UniProt: P32277
#2: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 242 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.34 Å3/Da / Density % sol: 47.08 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 100mM Tris, 8.5, 0.2M sodium acetate, 5mM DTT, 28% PEG-3350, VAPOR DIFFUSION, HANGING DROP, temperature 296K
Crystal grow
*PLUS
Temperature: 23 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
1100 mMTris-HCl1droppH8.5
20.2 Msodium acetate1drop
35 mMdithiothreitol1drop
428 %PEG33501drop
520 %glycerol1reservoir

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
ROTATING ANODERIGAKU RU20011.5418
SYNCHROTRONNSLS X4A20.979
Detector
TypeIDDetectorDateDetails
RIGAKU RAXIS IV1IMAGE PLATEMay 15, 2003osmic
ADSC QUANTUM 42CCDMay 15, 2003sag focus
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1OSMIC MULTILAYERSINGLE WAVELENGTHMx-ray1
2SAGITALLY FOCUSED Si(111)SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.54181
20.9791
ReflectionResolution: 1.9→50 Å / Num. obs: 19766 / % possible obs: 97.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 23.2 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 18.2
Reflection shellResolution: 1.9→2.02 Å / Rmerge(I) obs: 0.322 / Mean I/σ(I) obs: 2.6 / % possible all: 83.2
Reflection
*PLUS
Num. measured all: 79243 / Rmerge(I) obs: 0.06
Reflection shell
*PLUS
% possible obs: 83.2 %

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RESOLVEphasing
RefinementMethod to determine structure: SIRAS / Resolution: 1.9→34.05 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1235118.63 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.227 1000 5.1 %RANDOM
Rwork0.19 ---
obs0.19 19459 96.2 %-
all-20228 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 48.892 Å2 / ksol: 0.377748 e/Å3
Displacement parametersBiso mean: 29.1 Å2
Baniso -1Baniso -2Baniso -3
1--3.03 Å20 Å20 Å2
2--6.06 Å20 Å2
3----3.03 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.2 Å
Luzzati d res low-6 Å
Luzzati sigma a0.21 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 1.9→34.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1865 0 23 242 2130
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d23.4
X-RAY DIFFRACTIONc_improper_angle_d0.74
X-RAY DIFFRACTIONc_mcbond_it1.321.5
X-RAY DIFFRACTIONc_mcangle_it2.092
X-RAY DIFFRACTIONc_scbond_it2.542
X-RAY DIFFRACTIONc_scangle_it3.642.5
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.294 141 4.9 %
Rwork0.268 2710 -
obs--86.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
X-RAY DIFFRACTION5AMP_XPLOR.PARAMP_XPLOR.TOP
Refinement
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 34 Å / % reflection Rfree: 5 % / Rfactor Rwork: 0.19
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.74

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