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- PDB-4kaz: Crystal structure of RNase T in complex with a Y structured DNA -

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Basic information

Entry
Database: PDB / ID: 4kaz
TitleCrystal structure of RNase T in complex with a Y structured DNA
Components
  • DNA (5'-D(*TP*TP*GP*GP*CP*CP*CP*TP*CP*TP*TP*TP*AP*GP*GP*GP*CP*CP*CP*C)-3')
  • 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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
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.
History
DepositionApr 23, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 5, 2014Provider: repository / Type: Initial release
Revision 1.1May 28, 2014Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ribonuclease T
B: DNA (5'-D(*TP*TP*GP*GP*CP*CP*CP*TP*CP*TP*TP*TP*AP*GP*GP*GP*CP*CP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8214
Polymers31,7722
Non-polymers492
Water3,027168
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1880 Å2
ΔGint-33 kcal/mol
Surface area12070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.675, 90.580, 46.621
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-408-

HOH

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Components

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


Mass: 25719.035 Da / Num. of mol.: 1
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 DNA (5'-D(*TP*TP*GP*GP*CP*CP*CP*TP*CP*TP*TP*TP*AP*GP*GP*GP*CP*CP*CP*C)-3')


Mass: 6052.890 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 168 / 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: 2.02 Å3/Da / Density % sol: 38.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 20% v/v 2-Propanol, 0.1 M MES monohydrate, 20% w/v Polyethylene glycol monomethyl ester 2000 , pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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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: 1.9→30 Å / Num. all: 20966 / Num. obs: 20966 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.5 % / Rsym value: 0.091 / Net I/σ(I): 32.23
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 7.7 % / Mean I/σ(I) obs: 3.92 / Num. unique all: 2070 / Rsym value: 0.457 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NGY

3ngy


Resolution: 1.9→28.767 Å / SU ML: 0.18 / σ(F): 0 / Phase error: 19.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2185 1072 5.13 %RANDOM
Rwork0.1889 ---
all0.1904 20916 --
obs0.1904 20916 99.97 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→28.767 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1585 301 2 168 2056
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071958
X-RAY DIFFRACTIONf_angle_d1.1482715
X-RAY DIFFRACTIONf_dihedral_angle_d19.102716
X-RAY DIFFRACTIONf_chiral_restr0.077302
X-RAY DIFFRACTIONf_plane_restr0.005305
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9001-1.98660.25231370.22972435X-RAY DIFFRACTION100
1.9866-2.09130.24091190.2152460X-RAY DIFFRACTION100
2.0913-2.22230.26651420.21032434X-RAY DIFFRACTION100
2.2223-2.39380.24411510.19752418X-RAY DIFFRACTION100
2.3938-2.63450.25991320.20282465X-RAY DIFFRACTION100
2.6345-3.01540.23381190.19692486X-RAY DIFFRACTION100
3.0154-3.79770.22181250.17412525X-RAY DIFFRACTION100
3.7977-28.77020.16951470.17072621X-RAY DIFFRACTION100

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