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- PDB-1iuh: Crystal structure of TT0787 of thermus thermophilus HB8 -

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Basic information

Entry
Database: PDB / ID: 1iuh
TitleCrystal structure of TT0787 of thermus thermophilus HB8
Components2'-5' RNA Ligase
KeywordsLIGASE / thermus thermophilus / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics
Function / homology
Function and homology information


RNA 2',3'-cyclic 3'-phosphodiesterase / RNA 2',3'-cyclic 3'-phosphodiesterase activity / 2',3'-cyclic-nucleotide 3'-phosphodiesterase activity
Similarity search - Function
Phosphoesterase, HXTX / LigT like Phosphoesterase / RNA 2',3'-cyclic phosphodiesterase / Cyclic Phosphodiesterase; Chain: A, / Cyclic phosphodiesterase / Cyclic phosphodiesterase / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
RNA 2',3'-cyclic phosphodiesterase / RNA 2',3'-cyclic phosphodiesterase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2.5 Å
AuthorsKato, M. / Sakai, H. / Shirouzu, M. / Kuramitsu, S. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: J.MOL.BIOL. / Year: 2003
Title: Crystal Structure of the 2'-5' RNA Ligase from Thermus thermophilus HB8
Authors: Kato, M. / Shirouzu, M. / Terada, T. / Yamaguchi, H. / Murayama, K. / Sakai, H. / Kuramitsu, S. / Yokoyama, S.
History
DepositionMar 5, 2002Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 17, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 2'-5' RNA Ligase


Theoretical massNumber of molelcules
Total (without water)22,4461
Polymers22,4461
Non-polymers00
Water1,33374
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.982, 75.816, 159.640
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein 2'-5' RNA Ligase


Mass: 22445.906 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Plasmid: pET11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q84CU4, UniProt: Q5SHB1*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / 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: 2.56 Å3/Da / Density % sol: 51.91 %
Crystal growTemperature: 303 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: PEG4000, ammonium sulfate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 303K
Crystal grow
*PLUS
Temperature: 30 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
14.5 mg/mlprotein1drop
215 %(w/v)PEG40001reservoir
30.1 Mammonium acetate1reservoir
40.1 Msodium acetate1reservoirpH4.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Sep 1, 2001 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 8130 / % possible obs: 97.7 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 25.5 Å2 / Rsym value: 0.039
Reflection
*PLUS
Lowest resolution: 30 Å / Redundancy: 3.6 % / Num. measured all: 29650 / Rmerge(I) obs: 0.039
Reflection shell
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 2.59 Å / % possible obs: 96.1 % / Rmerge(I) obs: 0.131 / Mean I/σ(I) obs: 7.8

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Processing

Software
NameVersionClassification
DENZOdata reduction
SOLVEphasing
CNS1.1refinement
RefinementMethod to determine structure: MIR / Resolution: 2.5→20.35 Å / Rfactor Rfree error: 0.009 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.271 866 10.7 %RANDOM
Rwork0.198 ---
obs0.198 8130 97.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 41.1788 Å2 / ksol: 0.366271 e/Å3
Displacement parametersBiso mean: 30.1 Å2
Baniso -1Baniso -2Baniso -3
1--9.37 Å20 Å20 Å2
2--9.39 Å20 Å2
3----0.02 Å2
Refine analyzeLuzzati coordinate error free: 0.4 Å / Luzzati sigma a free: 0.39 Å
Refinement stepCycle: LAST / Resolution: 2.5→20.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1481 0 0 74 1555
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.021
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg2.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.58
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.371.5
X-RAY DIFFRACTIONc_mcangle_it2.252
X-RAY DIFFRACTIONc_scbond_it2.362
X-RAY DIFFRACTIONc_scangle_it3.492.5
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.328 128 10.2 %
Rwork0.217 1131 -
obs--94.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Refinement
*PLUS
Highest resolution: 2.5 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.58

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