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- PDB-2d4g: Structure of YjcG protein, a putative 2'-5' RNA ligase from Bacil... -

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Basic information

Entry
Database: PDB / ID: 2d4g
TitleStructure of YjcG protein, a putative 2'-5' RNA ligase from Bacillus subtilis
Componentshypothetical protein BSU11850
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / beta barrel / alpha helix
Function / homologyPutative phosphoesterase YjcG / Cyclic Phosphodiesterase; Chain: A, / Cyclic phosphodiesterase / Cyclic phosphodiesterase / hydrolase activity, acting on ester bonds / Hydrolases; Acting on ester bonds / Alpha-Beta Complex / Alpha Beta / Putative phosphoesterase YjcG
Function and homology information
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsLi, D. / Liang, Y.H. / Su, X.D.
CitationJournal: Proteins / Year: 2008
Title: Crystal structure of B. subtilis YjcG characterizing the YjcG-like group of 2H phosphoesterase superfamily.
Authors: Li, D. / Liu, C. / Liang, Y.H. / Li, L.F. / Su, X.D.
History
DepositionOct 19, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 17, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 27, 2013Group: Database references
Revision 1.4Oct 11, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: hypothetical protein BSU11850
B: hypothetical protein BSU11850


Theoretical massNumber of molelcules
Total (without water)39,6542
Polymers39,6542
Non-polymers00
Water4,396244
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1970 Å2
ΔGint-6 kcal/mol
Surface area16820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.660, 73.930, 61.770
Angle α, β, γ (deg.)90.00, 113.56, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-248-

HOH

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Components

#1: Protein hypothetical protein BSU11850 / hypothetical protein YjcG


Mass: 19826.973 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Plasmid: PET21-DEST / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21-DE3 / References: UniProt: O31629
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 244 / 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: 2.63 Å3/Da / Density % sol: 53.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.3
Details: 0.1M Bis-tris, 24% PEG-MME2000, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
31
Diffraction sourceSource: SYNCHROTRON / Site: BSRF / Beamline: 3W1A / Wavelength: 0.981, 0.97, 1.2
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 30, 2004
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9811
20.971
31.21
Reflection
IDNumberRmerge(I) obsΧ2D res high (Å)D res low (Å)% possible obs
1179810.0791.1352.35098.6
2140120.0651.1262.55098.9
3186960.080.8342.350100
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squared
4.95509510.072.072
3.934.9597.710.0621.634
3.443.9398.210.0631.431
3.123.4498.710.0721.248
2.93.129910.0851.115
2.732.999.310.1030.942
2.592.7399.510.1170.811
2.482.5999.610.1360.766
2.382.4899.810.1550.693
2.32.3899.810.1570.642
5.385096.220.0511.231
4.275.3898.120.0531.284
3.734.2798.720.0541.215
3.393.7399.120.061.238
3.153.3999.420.0641.122
2.963.1599.620.0741.055
2.822.9699.920.0830.936
2.692.8299.920.1020.905
2.592.6999.120.1170.975
2.52.5998.520.1811.308
4.955010030.0611.315
3.934.9599.930.0581.155
3.443.9399.930.0641.081
3.123.4499.930.0720.895
2.93.1210030.0880.798
2.732.910030.1110.688
2.592.7310030.1290.654
2.482.5999.930.1520.616
2.382.4810030.1730.57
2.32.3899.930.1950.555
ReflectionResolution: 2.3→50 Å / Num. all: 35918 / Num. obs: 33260 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.079 / Χ2: 1.135
Reflection shellResolution: 2.3→2.38 Å / % possible obs: 99.8 % / Rmerge(I) obs: 0.157 / Num. measured obs: 1818 / Χ2: 0.642 / % possible all: 99.8

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Phasing

PhasingMethod: MAD
Phasing set
ID
1
2
3
Phasing MAD set
Clust-IDExpt-IDSet-IDWavelength (Å)F double prime refinedF prime refined
13 wavelength10.9816.37-10.23
13 wavelength20.972.99-6.31
13 wavelength300.79-4.07
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1Se31.2380.4230.4990.1860.762
2Se8.1340.5720.1350.2660.592
3Se19.3990.4440.3090.1530.662
4Se42.6310.1190.4670.1140.853
Phasing dmFOM : 0.63 / FOM acentric: 0.64 / FOM centric: 0.6 / Reflection: 11230 / Reflection acentric: 10679 / Reflection centric: 551
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
7.7-19.7130.870.880.7747841860
4.8-7.70.780.790.7215221408114
3.9-4.80.790.80.71897179998
3.4-3.90.720.720.61919183485
2.9-3.40.550.560.4633783245133
2.7-2.90.380.380.292036197561

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVE2.03phasing
RESOLVE2.03phasing
CNSrefinement
PDB_EXTRACT1.7data extraction
MAR345data collection
RefinementMethod to determine structure: MAD / Resolution: 2.3→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.264 3196 8.9 %RANDOM
Rwork0.224 ---
all0.247 18236 --
obs0.235 17981 92.6 %-
Solvent computationBsol: 38.139 Å2
Displacement parametersBiso mean: 23.382 Å2
Baniso -1Baniso -2Baniso -3
1-0.912 Å20 Å2-5.797 Å2
2--0.392 Å20 Å2
3----1.303 Å2
Refinement stepCycle: LAST / Resolution: 2.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2726 0 0 244 2970
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water.param
X-RAY DIFFRACTION3mse.param

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