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- PDB-5ldm: Crystal structure of E.coli LigT complexed with 2'-AMP -

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Basic information

Entry
Database: PDB / ID: 5ldm
TitleCrystal structure of E.coli LigT complexed with 2'-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
ADENOSINE-2'-MONOPHOSPHATE / RNA 2',3'-cyclic phosphodiesterase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.46 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

Downloads & links

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Assembly

Deposited unit
A: RNA 2',3'-cyclic phosphodiesterase
B: RNA 2',3'-cyclic phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,8205
Polymers40,0902
Non-polymers7303
Water1,13563
1
A: RNA 2',3'-cyclic phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4283
Polymers20,0451
Non-polymers3832
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 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
Unit cell
Length a, b, c (Å)108.070, 108.070, 72.640
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212

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Components

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


Mass: 20045.029 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain B / 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-2AM / ADENOSINE-2'-MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / 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: 2.71 Å3/Da / Density % sol: 54.6 %
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, 12% (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 13, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.04 Å / Relative weight: 1
ReflectionResolution: 2.46→30 Å / Num. obs: 15451 / % possible obs: 95.4 % / Redundancy: 6.6 % / Biso Wilson estimate: 47.4 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.079 / Net I/σ(I): 18.01
Reflection shellResolution: 2.46→2.52 Å / Redundancy: 2.58 % / Rmerge(I) obs: 0.621 / Mean I/σ(I) obs: 1.51 / CC1/2: 0.712 / % possible all: 52.4

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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: 2.46→29.035 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.61
RfactorNum. reflection% reflectionSelection details
Rfree0.2528 1544 10.01 %Random selection
Rwork0.197 ---
obs0.2028 15432 95.53 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 64.03 Å2
Refinement stepCycle: LAST / Resolution: 2.46→29.035 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2770 0 47 63 2880
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052943
X-RAY DIFFRACTIONf_angle_d0.9374015
X-RAY DIFFRACTIONf_dihedral_angle_d18.4051097
X-RAY DIFFRACTIONf_chiral_restr0.053427
X-RAY DIFFRACTIONf_plane_restr0.003517
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4602-2.53950.3944780.3424728X-RAY DIFFRACTION57
2.5395-2.63020.3851380.2971210X-RAY DIFFRACTION93
2.6302-2.73550.30051430.25631295X-RAY DIFFRACTION100
2.7355-2.85990.34161440.25281289X-RAY DIFFRACTION100
2.8599-3.01050.3091460.24251314X-RAY DIFFRACTION100
3.0105-3.19890.31511450.23371304X-RAY DIFFRACTION100
3.1989-3.44550.2641460.21551309X-RAY DIFFRACTION100
3.4455-3.79160.28471460.20191307X-RAY DIFFRACTION100
3.7916-4.33860.21121500.16731338X-RAY DIFFRACTION100
4.3386-5.46030.1971480.1471353X-RAY DIFFRACTION100
5.4603-29.03720.20891600.16881441X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
18.1637-0.29664.34952.55540.61517.66280.62820.25291.16040.2181-0.2598-0.8641-0.29540.8725-0.25140.4212-0.04690.00330.38780.01660.639323.8002-39.538221.2884
25.8992-1.10971.00643.1745-5.11189.7205-0.3041.09380.5658-1.3141-0.0036-0.33570.2866-0.27670.21080.45360.0133-0.01910.58510.03190.39836.4018-32.924410.2894
38.9813-3.0195.6055.8562-2.61457.87860.17191.11570.3767-0.409-0.2762-0.79450.06030.8630.0910.4431-0.06310.03350.4187-0.01060.492221.994-36.390621.5925
45.3229-1.04830.96532.5241-0.85262.14820.013-0.13370.58020.4577-0.0632-0.5205-0.09060.28110.02820.4755-0.0368-0.09030.4008-0.1030.42814.8952-36.219327.6629
52.04653.6438-2.05418.6376-2.21814.19610.3935-0.7842-0.1971.1134-0.3104-0.8129-0.41470.6838-0.25810.7815-0.0503-0.13820.4843-0.11270.626619.8735-37.951835.7304
66.0063-3.4078-0.19124.1324-2.54534.7599-0.3036-0.2311.92120.8311-0.3837-0.5133-1.01430.40680.99760.6478-0.1104-0.08190.505-0.03770.845816.977-27.370124.2355
75.4111-0.82370.71284.62610.74990.1114-0.04850.23830.4599-0.0842-0.0478-0.3241-0.1271-0.07030.04410.349-0.0147-0.00150.4196-0.01110.23811.6882-37.475618.4298
83.14071.8777-4.4379.5638-2.98246.5569-0.33290.4755-0.1605-0.40580.3491-0.48690.5995-0.48930.43640.373-0.0459-0.09310.5034-0.05830.55521.6774-45.267921.0763
97.3815-0.67351.55831.26072.67196.8451-0.6629-0.4466-1.20430.7610.78510.52991.39490.2143-0.06820.5674-0.04520.14280.4332-0.02720.671946.8987-27.832113.9091
106.5782-1.1274-2.74996.88522.6175.5295-0.2171-0.4157-0.67350.26380.23860.09310.41380.2367-0.03910.334-0.0203-0.08440.37250.03610.391741.9146-20.673116.8025
115.38210.06370.48872.5646-0.93711.73050.02370.6431-0.4346-0.48470.0290.25790.26720.00990.00640.4484-0.0007-0.0610.4898-0.13690.410538.3977-16.26336.3133
125.7326-0.1749-3.08388.2915.70528.13150.50711.4035-0.9924-0.328-0.7790.42081.3424-0.99780.27260.979-0.0873-0.19390.7997-0.30381.144138.61-27.27793.1007
132.58580.4472-0.85014.8161.44590.27040.0488-0.1289-0.09220.0135-0.11710.75880.0838-0.26490.08060.32430.01530.02020.3931-0.00140.420337.9469-14.958716.5448
144.1983.4304-2.74184.6094-5.5479.63960.295-0.4573-0.45720.9237-0.2340.1923-0.485-0.3683-0.13370.5662-0.04880.11950.52970.0290.610148.9203-24.609816.9464
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 14 )
2X-RAY DIFFRACTION2chain 'A' and (resid 15 through 38 )
3X-RAY DIFFRACTION3chain 'A' and (resid 39 through 53 )
4X-RAY DIFFRACTION4chain 'A' and (resid 54 through 96 )
5X-RAY DIFFRACTION5chain 'A' and (resid 97 through 113 )
6X-RAY DIFFRACTION6chain 'A' and (resid 114 through 134 )
7X-RAY DIFFRACTION7chain 'A' and (resid 135 through 162 )
8X-RAY DIFFRACTION8chain 'A' and (resid 163 through 176 )
9X-RAY DIFFRACTION9chain 'B' and (resid 2 through 14 )
10X-RAY DIFFRACTION10chain 'B' and (resid 15 through 66 )
11X-RAY DIFFRACTION11chain 'B' and (resid 67 through 110 )
12X-RAY DIFFRACTION12chain 'B' and (resid 111 through 125 )
13X-RAY DIFFRACTION13chain 'B' and (resid 126 through 158 )
14X-RAY DIFFRACTION14chain 'B' and (resid 159 through 176 )

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