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- PDB-5h7e: Crystal Structure of native drCPDase -

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Basic information

Entry
Database: PDB / ID: 5h7e
TitleCrystal Structure of native drCPDase
ComponentsRNA 2',3'-cyclic phosphodiesterase
KeywordsHYDROLASE / RNA repair / CPDase / 2 / 3 -cyclic phosphodiesterase
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
Similarity search - Function
Phosphoesterase, HXTX / 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
RNA 2',3'-cyclic phosphodiesterase
Similarity search - Component
Biological speciesDeinococcus radiodurans (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsHan, W. / Hua, Y. / Zhao, Y.
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2017
Title: Crystal structure of the RNA 2',3'-cyclic phosphodiesterase from Deinococcus radiodurans
Authors: Han, W. / Cheng, J. / Zhou, C. / Hua, Y. / Zhao, Y.
History
DepositionNov 18, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 27, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1188
Polymers20,4531
Non-polymers6657
Water2,126118
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area210 Å2
ΔGint-15 kcal/mol
Surface area9940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.220, 91.220, 169.830
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-432-

HOH

21A-496-

HOH

31A-513-

HOH

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Components

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


Mass: 20453.457 Da / Num. of mol.: 1 / Fragment: core domain, UNP residues 35-216
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus radiodurans (radioresistant)
Strain: ATCC13939 / Gene: DR_2339 / Plasmid: pET28 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: O32509, Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / 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: 3.41 Å3/Da / Density % sol: 63.94 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 3.5 / Details: Citric Acid, Ammonium Sulfate

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 9, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.6→30 Å / Num. obs: 34981 / % possible obs: 96.8 % / Observed criterion σ(I): -3 / Redundancy: 5.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.049 / Net I/σ(I): 19.24
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsCC1/2Diffraction-ID% possible all
1.6-1.640.852.150.663197.1
1.64-1.690.6732.80.783199.1
1.69-1.740.523.680.863198.8
1.74-1.790.3525.320.936198.8
1.79-1.850.26270.963198.6
1.85-1.910.1959.360.979198.3
1.91-1.980.13812.750.989198.2
1.98-2.070.116.330.994198.1
2.07-2.160.07919.780.996197.7
2.16-2.260.06423.890.997197.3
2.26-2.390.05327.150.998197.2
2.39-2.530.04829.460.998197
2.53-2.70.04532.210.998196.4
2.7-2.920.03936.790.998196.1
2.92-3.20.03640.830.999195.6
3.2-3.580.03343.980.999194.9
3.58-4.130.03245.930.998193.9
4.13-5.060.03146.440.998191.8
5.06-7.160.0345.70.998190.8
7.160.03141.630.997164.6

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
XSCALEdata scaling
PDB_EXTRACT3.2data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4QAK

4qak


Resolution: 1.6→29.408 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1963 1738 4.97 %
Rwork0.1747 --
obs0.1758 34977 96.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.6→29.408 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1405 0 37 118 1560
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0151473
X-RAY DIFFRACTIONf_angle_d1.782012
X-RAY DIFFRACTIONf_dihedral_angle_d17.684873
X-RAY DIFFRACTIONf_chiral_restr0.102221
X-RAY DIFFRACTIONf_plane_restr0.01258
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6002-1.64730.31931490.25422736X-RAY DIFFRACTION97
1.6473-1.70050.2511440.22172770X-RAY DIFFRACTION99
1.7005-1.76120.20541410.21242830X-RAY DIFFRACTION99
1.7612-1.83170.23621360.19042813X-RAY DIFFRACTION99
1.8317-1.91510.21671450.18542764X-RAY DIFFRACTION98
1.9151-2.0160.20811650.17362779X-RAY DIFFRACTION98
2.016-2.14230.19181420.1722803X-RAY DIFFRACTION98
2.1423-2.30770.18841560.15992749X-RAY DIFFRACTION97
2.3077-2.53980.20811310.17032816X-RAY DIFFRACTION97
2.5398-2.9070.19391410.17892760X-RAY DIFFRACTION96
2.907-3.66140.16671500.15982766X-RAY DIFFRACTION95
3.6614-29.41270.19761380.17392653X-RAY DIFFRACTION88
Refinement TLS params.Method: refined / Origin x: -25.0734 Å / Origin y: -28.7913 Å / Origin z: -13.1568 Å
111213212223313233
T0.1214 Å20.0254 Å2-0.0006 Å2-0.1813 Å2-0.0022 Å2--0.1234 Å2
L2.5441 °20.6236 °2-0.7587 °2-2.5524 °2-1.0363 °2--2.0058 °2
S-0.0288 Å °0.1783 Å °-0.0239 Å °-0.2474 Å °-0.0063 Å °-0.1881 Å °0.0858 Å °0.1307 Å °0.0244 Å °
Refinement TLS groupSelection details: all

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