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- PDB-4kb1: Crystal structure of RNase T in complex with a bluge DNA (two nuc... -

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Database: PDB / ID: 4kb1
TitleCrystal structure of RNase T in complex with a bluge DNA (two nucleotide insertion CT )
  • Bulge DNA
  • Ribonuclease T
KeywordsHydrolase/dna / DnaQ / DEDD / exonuclease / DNA repair / Hydrolase-dna complex
Function / homology
Function and homology information

tRNA 3'-end processing / RNA exonuclease activity, producing 5'-phosphomonoesters / DNA replication proofreading / 3'-5' exonuclease activity / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / nucleic acid binding / magnesium ion binding / identical protein binding / cytosol
Similarity search - Function
Ribonuclease T / Exonuclease / Exonuclease, RNase T/DNA polymerase III / EXOIII / Ribonuclease H-like superfamily/Ribonuclease H / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily / Ribonuclease H-like superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Ribonuclease T
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
AuthorsHsiao, Y.-Y. / Yuan, H.S.
CitationJournal: Plos Biol. / Year: 2014
Title: Structural insights into DNA repair by RNase T--an exonuclease processing 3' end of structured DNA in repair pathways.
Authors: Hsiao, Y.Y. / Fang, W.H. / Lee, C.C. / Chen, Y.P. / Yuan, H.S.
DepositionApr 23, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 5, 2014Provider: repository / Type: Initial release
Revision 1.1May 28, 2014Group: Database references

Structure visualization

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Deposited unit
A: Ribonuclease T
B: Ribonuclease T
C: Bulge DNA
D: Bulge DNA
hetero molecules

Theoretical massNumber of molelcules
Total (without water)62,4548
A: Ribonuclease T
C: Bulge DNA
hetero molecules

Theoretical massNumber of molelcules
Total (without water)31,2274
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1460 Å2
ΔGint-29 kcal/mol
Surface area12960 Å2
B: Ribonuclease T
D: Bulge DNA
hetero molecules

Theoretical massNumber of molelcules
Total (without water)31,2274
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1460 Å2
ΔGint-28 kcal/mol
Surface area12660 Å2
Unit cell
Length a, b, c (Å)60.556, 81.844, 73.744
Angle α, β, γ (deg.)90.00, 105.71, 90.00
Int Tables number4
Space group name H-MP1211


#1: Protein Ribonuclease T / / Exoribonuclease T / RNase T

Mass: 25719.035 Da / Num. of mol.: 2 / Fragment: RNase T / Mutation: NO
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: b1652, JW1644, rnt / Plasmid: pET-28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIPL
References: UniProt: P30014, Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters
#2: DNA chain Bulge DNA

Mass: 5459.515 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: Chemical

Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water

Mass: 18.015 Da / Num. of mol.: 569 / Source method: isolated from a natural source / Formula: H2O

Experimental details


ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

Sample preparation

CrystalDensity Matthews: 2.82 Å3/Da / Density % sol: 56.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.10% w/v n-Octyl- -D-glucoside, 0.1 M Sodium citrate tribasic dehydrate, 22% Polyethylene glycol 3350, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jun 3, 2011
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. all: 65372 / Num. obs: 65372 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rsym value: 0.062 / Net I/σ(I): 27.93
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 2.87 / Num. unique all: 6473 / Rsym value: 0.411 / % possible all: 98.8


HKL-2000data collection
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NGY
Resolution: 1.8→28.621 Å / SU ML: 0.18 / σ(F): 0 / Phase error: 20.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1989 3222 5.07 %RANDOM
Rwork0.1831 ---
all0.1839 63562 --
obs0.1839 63562 99.01 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→28.621 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3180 722 4 569 4475
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044060
X-RAY DIFFRACTIONf_angle_d0.8645656
X-RAY DIFFRACTIONf_dihedral_angle_d18.8851502
X-RAY DIFFRACTIONf_chiral_restr0.057631
X-RAY DIFFRACTIONf_plane_restr0.003617
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.82690.29621390.2562599X-RAY DIFFRACTION99
1.8269-1.85540.28111120.23942641X-RAY DIFFRACTION99
1.8554-1.88580.24191510.22552588X-RAY DIFFRACTION99
1.8858-1.91830.24721310.21942607X-RAY DIFFRACTION99
1.9183-1.95320.26541490.22182654X-RAY DIFFRACTION99
1.9532-1.99080.24371360.21562633X-RAY DIFFRACTION99
1.9908-2.03140.22531530.20572594X-RAY DIFFRACTION99
2.0314-2.07560.20081370.19762610X-RAY DIFFRACTION99
2.0756-2.12380.24881260.19612622X-RAY DIFFRACTION99
2.1238-2.17690.21461500.19262641X-RAY DIFFRACTION100
2.1769-2.23570.25971200.19522656X-RAY DIFFRACTION100
2.2357-2.30150.21991550.19162585X-RAY DIFFRACTION100
2.3015-2.37580.22051540.18992638X-RAY DIFFRACTION99
2.3758-2.46060.22321360.18972642X-RAY DIFFRACTION99
2.4606-2.55910.19831310.19392649X-RAY DIFFRACTION99
2.5591-2.67550.21931450.20112602X-RAY DIFFRACTION99
2.6755-2.81640.20891220.19712688X-RAY DIFFRACTION99
2.8164-2.99270.22441270.19292618X-RAY DIFFRACTION99
2.9927-3.22350.19721440.18352623X-RAY DIFFRACTION99
3.2235-3.54730.18121560.16452643X-RAY DIFFRACTION99
3.5473-4.05940.1511520.152628X-RAY DIFFRACTION99
4.0594-5.10970.14451560.1452632X-RAY DIFFRACTION99
5.1097-28.6250.1941400.18082547X-RAY DIFFRACTION94

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