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- PDB-2hvs: Structure of T4 RNA Ligase 2 with Nicked 5'-Adenylated nucleic ac... -

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Basic information

Entry
Database: PDB / ID: 2hvs
TitleStructure of T4 RNA Ligase 2 with Nicked 5'-Adenylated nucleic acid duplex containing a 2'-deoxyribonucleotide at the nick
Components
  • 5'-D(*AP*TP*TP*CP*CP*GP*AP*TP*AP*GP*TP*GP*GP*GP*GP*TP*CP*GP*CP*AP*AP*TP*TP*G)-3'
  • 5'-D(*CP*AP*AP*TP*TP*GP*CP*GP*AP*C)-R(P*(OMC)P*C)-3'
  • 5'-D(P*CP*AP*CP*TP*AP*TP*CP*GP*GP*AP*AP*T)-3'
  • T4 RNA Ligase 2
KeywordsLIGASE/DNA/RNA / RNA / LIGASE / LYSINE ADENYLATE / T4 / PROTEIN DNA-RNA COMPLEX / LIGASE-DNA-RNA COMPLEX
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 / RNA ligase 2, C-terminal / RNA ligase 1/2, C-terminal domain superfamily / RNA ligase 2, viral / T4 RNA ligase 2 C-terminal / RNA ligase, Rnl2 / RNA ligase domain, REL/Rln2 / RNA ligase / Dna Ligase; domain 1 - #70 / DNA ligase/mRNA capping enzyme ...RNA ligase / RNA ligase 2, C-terminal / RNA ligase 1/2, C-terminal domain superfamily / RNA ligase 2, viral / T4 RNA ligase 2 C-terminal / RNA ligase, Rnl2 / 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 / Arc Repressor Mutant, subunit A / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / DNA / DNA (> 10) / DNA/RNA hybrid / DNA/RNA hybrid (> 10) / RNA ligase 2
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsNandakumar, J. / Lima, C.D.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2006
Title: RNA Ligase Structures Reveal the Basis for RNA Specificity and Conformational Changes that Drive Ligation Forward.
Authors: Nandakumar, J. / Shuman, S. / Lima, C.D.
History
DepositionJul 30, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 17, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 28, 2013Group: Non-polymer description
Revision 1.4Oct 18, 2017Group: Refinement description / Category: software
Revision 1.5Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE According to authors, glycine at position 112 is correct. This mutation likely represents ...SEQUENCE According to authors, glycine at position 112 is correct. This mutation likely represents a natural mutation in the 'population' of T4 phage

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: 5'-D(*AP*TP*TP*CP*CP*GP*AP*TP*AP*GP*TP*GP*GP*GP*GP*TP*CP*GP*CP*AP*AP*TP*TP*G)-3'
D: 5'-D(*CP*AP*AP*TP*TP*GP*CP*GP*AP*C)-R(P*(OMC)P*C)-3'
E: 5'-D(P*CP*AP*CP*TP*AP*TP*CP*GP*GP*AP*AP*T)-3'
F: 5'-D(*AP*TP*TP*CP*CP*GP*AP*TP*AP*GP*TP*GP*GP*GP*GP*TP*CP*GP*CP*AP*AP*TP*TP*G)-3'
G: 5'-D(*CP*AP*AP*TP*TP*GP*CP*GP*AP*C)-R(P*(OMC)P*C)-3'
H: 5'-D(P*CP*AP*CP*TP*AP*TP*CP*GP*GP*AP*AP*T)-3'
A: T4 RNA Ligase 2
B: T4 RNA Ligase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,20013
Polymers104,8788
Non-polymers1,3225
Water1,76598
1
C: 5'-D(*AP*TP*TP*CP*CP*GP*AP*TP*AP*GP*TP*GP*GP*GP*GP*TP*CP*GP*CP*AP*AP*TP*TP*G)-3'
D: 5'-D(*CP*AP*AP*TP*TP*GP*CP*GP*AP*C)-R(P*(OMC)P*C)-3'
E: 5'-D(P*CP*AP*CP*TP*AP*TP*CP*GP*GP*AP*AP*T)-3'
A: T4 RNA Ligase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,2047
Polymers52,4394
Non-polymers7663
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
F: 5'-D(*AP*TP*TP*CP*CP*GP*AP*TP*AP*GP*TP*GP*GP*GP*GP*TP*CP*GP*CP*AP*AP*TP*TP*G)-3'
G: 5'-D(*CP*AP*AP*TP*TP*GP*CP*GP*AP*C)-R(P*(OMC)P*C)-3'
H: 5'-D(P*CP*AP*CP*TP*AP*TP*CP*GP*GP*AP*AP*T)-3'
B: T4 RNA Ligase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,9956
Polymers52,4394
Non-polymers5562
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.416, 106.740, 124.203
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsAsymmetric unit contains two complexes of T4 RNA Ligase 2 complexed with nicked duplex related by a non-crystallographic pseudo-translation along the x-axis.

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Components

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DNA chain , 2 types, 4 molecules CFEH

#1: DNA chain 5'-D(*AP*TP*TP*CP*CP*GP*AP*TP*AP*GP*TP*GP*GP*GP*GP*TP*CP*GP*CP*AP*AP*TP*TP*G)-3'


Mass: 7440.800 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: DNA chain 5'-D(P*CP*AP*CP*TP*AP*TP*CP*GP*GP*AP*AP*T)-3'


Mass: 3646.405 Da / Num. of mol.: 2 / Source method: obtained synthetically

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DNA/RNA hybrid / Protein , 2 types, 4 molecules DGAB

#2: DNA/RNA hybrid 5'-D(*CP*AP*AP*TP*TP*GP*CP*GP*AP*C)-R(P*(OMC)P*C)-3'


Mass: 3637.395 Da / Num. of mol.: 2 / Source method: obtained synthetically
#4: Protein T4 RNA Ligase 2


Mass: 37714.168 Da / Num. of mol.: 2
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: PET-HIS-SMT3-RNL2 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P32277

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Non-polymers , 3 types, 103 molecules

#5: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER / Bis-tris methane


Mass: 209.240 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#6: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 98 / 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: 2.59 Å3/Da / Density % sol: 52.54 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 100 mM Bis-Tris, 22% PEG-4000, 9% PEG-6000, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Components of the solutions
IDNameCrystal-IDSol-ID
1Bis-TrisBis-tris methane11
2PEG-400011
3PEG-600011
4HOH11
5Bis-TrisBis-tris methane12
6PEG-400012
7PEG-600012
8HOH12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9797 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 16, 2005
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9797 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. all: 39043 / Num. obs: 38379 / % possible obs: 98.3 % / Observed criterion σ(I): 0 / Redundancy: 8 % / Rmerge(I) obs: 0.077 / Χ2: 1.057 / Net I/σ(I): 15.6
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.403 / Mean I/σ(I) obs: 2.1 / Num. unique all: 3416 / Χ2: 0.792 / % possible all: 88.9

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNS1.1refinement
PDB_EXTRACT2data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2HVR

2hvr


Resolution: 2.5→19.82 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 3139794.25 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.283 1898 5 %RANDOM
Rwork0.239 ---
all-39038 --
obs-38335 98.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 18.049 Å2 / ksol: 0.24 e/Å3
Displacement parametersBiso mean: 72.8 Å2
Baniso -1Baniso -2Baniso -3
1--13.9 Å20 Å20 Å2
2--10.12 Å20 Å2
3---3.78 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a0.6 Å0.65 Å
Refinement stepCycle: LAST / Resolution: 2.5→19.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5042 1960 88 98 7188
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d21.4
X-RAY DIFFRACTIONc_improper_angle_d0.89
X-RAY DIFFRACTIONc_mcbond_it2.071.5
X-RAY DIFFRACTIONc_mcangle_it3.462
X-RAY DIFFRACTIONc_scbond_it3.012
X-RAY DIFFRACTIONc_scangle_it4.572.5
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.373 265 4.5 %
Rwork0.37 5649 -
obs-5914 92.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4btb.parambtb.top
X-RAY DIFFRACTION5dna-rna-apc_rep.paramdna-rna-apc.top

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