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- PDB-5h7f: Crystal Structure of Mn-derivative drCPDase -

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Basic information

Entry
Database: PDB / ID: 5h7f
TitleCrystal Structure of Mn-derivative 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: 1.601 Å
AuthorsHan, W. / Hua, Y. / Zhao, Y.
CitationJournal: To be published
Title: Crystal Structure of Mn-derivative drCPDase
Authors: Han, W. / Hua, Y. / Zhao, Y.
History
DepositionNov 18, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 22, 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)20,8385
Polymers20,4531
Non-polymers3844
Water1,964109
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area210 Å2
ΔGint-15 kcal/mol
Surface area10080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.200, 91.200, 170.000
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-440-

HOH

21A-484-

HOH

31A-500-

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-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 109 / 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: 63.96 %
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: 33310 / % possible obs: 92.3 % / Observed criterion σ(I): -3 / Redundancy: 3.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.049 / Net I/σ(I): 13.52
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsCC1/2Diffraction-ID% possible all
1.6-1.641.0871.190.407191.6
1.64-1.690.8991.460.51193.1
1.69-1.740.7171.930.656192.9
1.74-1.790.4792.750.798193.8
1.79-1.850.3463.80.878193.9
1.85-1.910.26750.937192.6
1.91-1.990.1767.270.963192.5
1.99-2.070.1269.60.982193.6
2.07-2.160.09712.190.988192.9
2.16-2.260.07515.030.993193.1
2.26-2.390.06317.140.995195.3
2.39-2.530.05219.590.997195
2.53-2.710.04922.040.997193.8
2.71-2.920.03926.220.997193.1
2.92-3.20.03331.620.998192.6
3.2-3.580.02934.870.998191.1
3.58-4.130.02837.790.998189.3
4.13-5.060.02540.280.999186.4
5.06-7.160.02639.290.999185.3
7.160.02338.810.998161.1

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.10_2155refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4QAK

4qak


Resolution: 1.601→28.93 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.55
RfactorNum. reflection% reflection
Rfree0.2109 1639 4.92 %
Rwork0.1851 --
obs0.1863 33297 92.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 92.98 Å2 / Biso mean: 35.5096 Å2 / Biso min: 15.11 Å2
Refinement stepCycle: final / Resolution: 1.601→28.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1402 0 20 109 1531
Biso mean--63.8 41.64 -
Num. residues----182
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0131469
X-RAY DIFFRACTIONf_angle_d1.272012
X-RAY DIFFRACTIONf_chiral_restr0.093221
X-RAY DIFFRACTIONf_plane_restr0.008262
X-RAY DIFFRACTIONf_dihedral_angle_d18.796873
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6014-1.64850.32781430.28542599274292
1.6485-1.70170.29381340.27792595272993
1.7017-1.76250.2531300.25672660279093
1.7625-1.83310.23931290.21352679280894
1.8331-1.91650.2581340.222591272593
1.9165-2.01750.23731510.20362638278993
2.0175-2.14390.20881380.17992652279093
2.1439-2.30930.21451500.17422642279294
2.3093-2.54160.18041260.17432748287495
2.5416-2.90910.2221420.18222681282394
2.9091-3.6640.1791400.16452660280092
3.664-28.93430.20521220.17632513263584
Refinement TLS params.Method: refined / Origin x: -7.9972 Å / Origin y: -33.6438 Å / Origin z: 15.1035 Å
111213212223313233
T0.2143 Å20.0147 Å20.0015 Å2-0.1436 Å20.0026 Å2--0.1424 Å2
L2.4959 °2-0.2277 °20.6357 °2-1.8475 °2-0.1616 °2--1.3462 °2
S0.0073 Å °0.2224 Å °0.1013 Å °-0.1723 Å °-0.0073 Å °0.0833 Å °-0.0995 Å °-0.0006 Å °0.0038 Å °
Refinement TLS groupSelection details: all

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