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- PDB-9do4: Structure of T4 RNA Ligase 1 bound to ATP and Mg -

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Basic information

Entry
Database: PDB / ID: 9do4
TitleStructure of T4 RNA Ligase 1 bound to ATP and Mg
ComponentsRNA ligase 1
KeywordsLIGASE / T4 RNA ligase 1
Function / homology
Function and homology information


virus tail fiber assembly / RNA ligase (ATP) / RNA ligase (ATP) activity / RNA repair / ATP binding / metal ion binding
Similarity search - Function
T4 RNA ligase 1 / : / T4 RNA ligase 1, C-terminal domain / T4 RNA ligase 1, N-terminal / RNA ligase
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / RNA ligase 1
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsWimberly-Gard, G.M. / Shuman, S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35-GM126945 United States
CitationJournal: To Be Published
Title: Structure of T4 RNA Ligase 1 bound to ATP and Mg
Authors: Wimberly-Gard, G.M. / Shuman, S.
History
DepositionSep 18, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 2, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: RNA ligase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,6524
Polymers46,0961
Non-polymers5563
Water32418
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1130 Å2
ΔGint-17 kcal/mol
Surface area17210 Å2
Unit cell
Length a, b, c (Å)104.197, 40.114, 107.032
Angle α, β, γ (deg.)90.00, 116.37, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein RNA ligase 1 / Gene product 63 / gp63 / Rnl1 / T4 RNA Ligase 1


Mass: 46095.941 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T4 (virus) / Gene: 63 / Production host: Escherichia coli (E. coli) / References: UniProt: P00971, RNA ligase (ATP)
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.17 Å3/Da / Density % sol: 43.42 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: 300mM MGCl2, 100mM NaCl, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.920105 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: May 13, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.920105 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. obs: 12514 / % possible obs: 99.8 % / Redundancy: 4.5 % / Biso Wilson estimate: 52.403 Å2 / CC1/2: 0.989 / Rmerge(I) obs: 0.19 / Rpim(I) all: 0.099 / Net I/σ(I): 5.5
Reflection shellResolution: 2.6→2.72 Å / Rmerge(I) obs: 1.588 / Num. unique obs: 1511 / CC1/2: 0.381 / Rpim(I) all: 0.824

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Processing

Software
NameVersionClassification
PHENIX(1.21.1_5286: ???)refinement
XDSJun 30, 2023 BUILT=20230630data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→27.83 Å / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 31.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2958 597 4.77 %RANDOM
Rwork0.2211 ---
obs0.2247 12507 99.78 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.6→27.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2761 0 33 18 2812
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008
X-RAY DIFFRACTIONf_angle_d0.966
X-RAY DIFFRACTIONf_dihedral_angle_d18.1651005
X-RAY DIFFRACTIONf_chiral_restr0.051429
X-RAY DIFFRACTIONf_plane_restr0.008500
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.860.35991620.28122942X-RAY DIFFRACTION100
2.86-3.270.36181430.26272956X-RAY DIFFRACTION100
3.27-4.120.30221390.21612952X-RAY DIFFRACTION100

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