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- PDB-5d1o: Archaeal ATP-dependent RNA ligase - form 1 -

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Basic information

Entry
Database: PDB / ID: 5d1o
TitleArchaeal ATP-dependent RNA ligase - form 1
Components(ATP-dependent RNA ...) x 2
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
ADENOSINE-5'-TRIPHOSPHATE / Conserved protein
Similarity search - Component
Biological speciesMethanothermobacter thermautotrophicus (archaea)
MethodX-RAY DIFFRACTION / Resolution: 2.648 Å
AuthorsMurakami, K.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM087350 United States
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
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)87,0619
Polymers86,0492
Non-polymers1,0127
Water1,31573
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7330 Å2
ΔGint-129 kcal/mol
Surface area31010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.250, 114.870, 91.290
Angle α, β, γ (deg.)90.00, 104.42, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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ATP-dependent RNA ... , 2 types, 2 molecules AB

#1: Protein ATP-dependent RNA ligase


Mass: 42868.586 Da / Num. of mol.: 1
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: Protein ATP-dependent RNA ligase


Mass: 43180.789 Da / Num. of mol.: 1
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

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Non-polymers , 4 types, 80 molecules

#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / 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: 2.98 Å3/Da / Density % sol: 58.71 %
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 21, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5414 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. all: 67995 / Num. obs: 32926 / % possible obs: 94.4 % / Redundancy: 2.06 % / Net I/σ(I): 4.83

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
CrystalCleardata reduction
CrystalCleardata scaling
PHASERphasing
RefinementResolution: 2.648→27.713 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2653 1176 5.03 %
Rwork0.2059 --
obs0.209 23402 79.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.648→27.713 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6012 0 57 73 6142
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.056196
X-RAY DIFFRACTIONf_angle_d1.4048377
X-RAY DIFFRACTIONf_dihedral_angle_d23.8852388
X-RAY DIFFRACTIONf_chiral_restr0.056897
X-RAY DIFFRACTIONf_plane_restr0.0061102
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6478-2.76820.35851360.28672605X-RAY DIFFRACTION75
2.7682-2.9140.30761480.26942663X-RAY DIFFRACTION78
2.914-3.09630.37291390.27212657X-RAY DIFFRACTION77
3.0963-3.33510.27941300.22072631X-RAY DIFFRACTION76
3.3351-3.670.27921390.20192651X-RAY DIFFRACTION77
3.67-4.19950.24561500.2042778X-RAY DIFFRACTION80
4.1995-5.28490.23341690.17813116X-RAY DIFFRACTION90
5.2849-27.71450.24141650.18183125X-RAY DIFFRACTION88

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