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- PDB-5ldo: Crystal structure of E.coli LigT complexed with 3'-AMP -

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Basic information

Entry
Database: PDB / ID: 5ldo
TitleCrystal structure of E.coli LigT complexed with 3'-AMP
ComponentsRNA 2',3'-cyclic phosphodiesterase
KeywordsHYDROLASE / Enzyme / 2H phosphoesterase/ligase
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 / ligase activity / ATP binding
Similarity search - Function
2'-5' RNA ligase superfamily / 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
Chem-3AM / RNA 2',3'-cyclic phosphodiesterase
Similarity search - Component
Biological speciesEscherichia coli BL21 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.752 Å
AuthorsMyllykoski, M. / Kursula, P.
CitationJournal: PLoS ONE / Year: 2017
Title: Structural aspects of nucleotide ligand binding by a bacterial 2H phosphoesterase.
Authors: Myllykoski, M. / Kursula, P.
History
DepositionJun 27, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 18, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 8, 2017Group: Database references
Revision 1.2Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: RNA 2',3'-cyclic phosphodiesterase
B: RNA 2',3'-cyclic phosphodiesterase
C: RNA 2',3'-cyclic phosphodiesterase
D: RNA 2',3'-cyclic phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,5275
Polymers80,1804
Non-polymers3471
Water543
1
A: RNA 2',3'-cyclic phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,3922
Polymers20,0451
Non-polymers3471
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: RNA 2',3'-cyclic phosphodiesterase


Theoretical massNumber of molelcules
Total (without water)20,0451
Polymers20,0451
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: RNA 2',3'-cyclic phosphodiesterase


Theoretical massNumber of molelcules
Total (without water)20,0451
Polymers20,0451
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: RNA 2',3'-cyclic phosphodiesterase


Theoretical massNumber of molelcules
Total (without water)20,0451
Polymers20,0451
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.410, 88.350, 73.970
Angle α, β, γ (deg.)90.00, 114.95, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
RNA 2',3'-cyclic phosphodiesterase / RNA 2' / 3'-CPDase


Mass: 20045.029 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli BL21(DE3) (bacteria) / Gene: thpR, ECBD_3472 / Plasmid: pTH 27 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A140NFI1, Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases
#2: Chemical ChemComp-3AM / [(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-4-hydroxy-2-(hydroxymethyl)oxolan-3-yl] dihydrogen phosphate / 3'-AMP


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 2.34 Å3/Da / Density % sol: 47.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M Tris-HCl pH 7.5, 0.2 M MgCl2, 18% (w/v) PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.04 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 12, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.04 Å / Relative weight: 1
ReflectionResolution: 2.75→30 Å / Num. obs: 19216 / % possible obs: 99.3 % / Redundancy: 3.8 % / Biso Wilson estimate: 46.1 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.092 / Net I/σ(I): 14.11
Reflection shellResolution: 2.75→2.82 Å / Redundancy: 3.76 % / Rmerge(I) obs: 0.804 / Mean I/σ(I) obs: 1.76 / CC1/2: 0.629 / % possible all: 97.8

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDBid: 5ldi

5ldi


Resolution: 2.752→28.746 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 26.93
RfactorNum. reflection% reflectionSelection details
Rfree0.2587 1922 10.01 %Random selection
Rwork0.2117 ---
obs0.2164 19194 99.61 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 48.21 Å2
Refinement stepCycle: LAST / Resolution: 2.752→28.746 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5449 0 23 3 5475
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035632
X-RAY DIFFRACTIONf_angle_d0.837663
X-RAY DIFFRACTIONf_dihedral_angle_d11.8562076
X-RAY DIFFRACTIONf_chiral_restr0.032823
X-RAY DIFFRACTIONf_plane_restr0.003990
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7522-2.8210.38531260.31251183X-RAY DIFFRACTION98
2.821-2.89720.32441410.28671223X-RAY DIFFRACTION100
2.8972-2.98230.35641410.26571250X-RAY DIFFRACTION100
2.9823-3.07850.2961310.25621213X-RAY DIFFRACTION100
3.0785-3.18840.33031380.25831238X-RAY DIFFRACTION100
3.1884-3.31590.27861360.23791244X-RAY DIFFRACTION100
3.3159-3.46650.33061340.23411218X-RAY DIFFRACTION100
3.4665-3.6490.26411370.23471244X-RAY DIFFRACTION100
3.649-3.87710.26021360.20991230X-RAY DIFFRACTION99
3.8771-4.17560.2521350.19531241X-RAY DIFFRACTION99
4.1756-4.59430.20121400.17941239X-RAY DIFFRACTION100
4.5943-5.25560.21681410.16461243X-RAY DIFFRACTION100
5.2556-6.60820.22141430.19981238X-RAY DIFFRACTION100
6.6082-28.74730.21071430.1731268X-RAY DIFFRACTION99

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