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- PDB-5d1p: Archaeal ATP-dependent RNA ligase - form 2 -

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Basic information

Entry
Database: PDB / ID: 5d1p
TitleArchaeal ATP-dependent RNA ligase - form 2
ComponentsATP-dependent RNA ligase
KeywordsLIGASE / ATP-dependent RNA ligase / Archaea
Function / homology
Function and homology information


Nuclear Transport Factor 2; Chain: A, - #740 / RNA ligase, Pab1020 family / RNA ligase Pab1020, C-terminal domain / Ligase Pab1020 C-terminal region / 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 / Nuclear Transport Factor 2; Chain: A, ...Nuclear Transport Factor 2; Chain: A, - #740 / RNA ligase, Pab1020 family / RNA ligase Pab1020, C-terminal domain / Ligase Pab1020 C-terminal region / 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 / Nuclear Transport Factor 2; Chain: A, / Dna Ligase; domain 1 / Roll / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesMethanothermobacter thermautotrophicus (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.199 Å
AuthorsMurakami, K.S.
CitationJournal: Nucleic Acids Res. / Year: 2016
Title: Structural and mutational analysis of archaeal ATP-dependent RNA ligase identifies amino acids required for RNA binding and catalysis.
Authors: Gu, H. / Yoshinari, S. / Ghosh, R. / Ignatochkina, A.V. / Gollnick, P.D. / Murakami, K.S. / Ho, C.K.
History
DepositionAug 4, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 30, 2016Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ATP-dependent RNA ligase
B: ATP-dependent RNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,98710
Polymers86,3622
Non-polymers6258
Water7,278404
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7720 Å2
ΔGint-166 kcal/mol
Surface area31210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.500, 115.304, 91.567
Angle α, β, γ (deg.)90.00, 104.55, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein ATP-dependent RNA ligase


Mass: 43180.789 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanothermobacter thermautotrophicus (strain ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H) (archaea)
Strain: ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H
Gene: MTH_1221 / Production host: Escherichia coli (E. coli) / References: UniProt: O27289
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 404 / 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: 2.99 Å3/Da / Density % sol: 58.83 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Tris-HCl (pH 8.5), 0.2 M Lithium Sulfate and 40 % PEG400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5414 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Jan 8, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5414 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. obs: 45957 / % possible obs: 89.3 % / Redundancy: 3.3 % / Net I/σ(I): 9.69

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.199→29.365 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2413 2002 4.29 %
Rwork0.1916 --
obs0.1937 46656 90.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.199→29.365 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6034 0 32 404 6470
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0226180
X-RAY DIFFRACTIONf_angle_d1.3068358
X-RAY DIFFRACTIONf_dihedral_angle_d16.6972400
X-RAY DIFFRACTIONf_chiral_restr0.05892
X-RAY DIFFRACTIONf_plane_restr0.0061098
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1988-2.25380.3702900.28981888X-RAY DIFFRACTION55
2.2538-2.31470.31231010.25932238X-RAY DIFFRACTION64
2.3147-2.38280.27841180.24172795X-RAY DIFFRACTION79
2.3828-2.45970.26481410.22753206X-RAY DIFFRACTION91
2.4597-2.54750.28691490.23443290X-RAY DIFFRACTION94
2.5475-2.64950.2891490.23233307X-RAY DIFFRACTION94
2.6495-2.770.28071430.23213395X-RAY DIFFRACTION97
2.77-2.91590.27361600.23013437X-RAY DIFFRACTION98
2.9159-3.09840.3071600.23383475X-RAY DIFFRACTION99
3.0984-3.33730.26541540.1963493X-RAY DIFFRACTION99
3.3373-3.67260.23531550.1793517X-RAY DIFFRACTION99
3.6726-4.20270.22011630.16483511X-RAY DIFFRACTION99
4.2027-5.28990.16521590.153522X-RAY DIFFRACTION100
5.2899-29.36710.22061600.16693580X-RAY DIFFRACTION100

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