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- PDB-3v9s: Crystal structure of RNase T in complex with a product ssDNA (AAC... -

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Basic information

Entry
Database: PDB / ID: 3v9s
TitleCrystal structure of RNase T in complex with a product ssDNA (AAC) with one Mg in the active site
Components
  • DNA (5'-D(*TP*TP*AP*CP*AP*AP*C)-3')
  • Ribonuclease T
KeywordsHYDROLASE/DNA / DNase/RNase / 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 / Ribonuclease T
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsHsiao, Y.-Y. / Yuan, H.S.
CitationJournal: Nucleic Acids Res. / Year: 2012
Title: How an exonuclease decides where to stop in trimming of nucleic acids: crystal structures of RNase T-product complexes
Authors: Hsiao, Y.-Y. / Duh, Y. / Chen, Y.P. / Wang, Y.T. / Yuan, H.S.
History
DepositionDec 28, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 11, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2013Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)55,7087
Polymers55,6014
Non-polymers1083
Water8,251458
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5690 Å2
ΔGint-49 kcal/mol
Surface area17860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.063, 105.840, 46.918
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-94-

GLU

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Components

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


Mass: 25719.035 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / 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*AP*CP*AP*AP*C)-3')


Mass: 2081.412 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: chemical synthesis
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 458 / 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: 2.14 Å3/Da / Density % sol: 42.65 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 3.5
Details: 0.1M Citric acid, 14% PEG1000, 10mM Spermidine, 5mM Magnesium chloride, pH 3.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 0.9999 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 30, 2009
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 28735 / Num. obs: 28735 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Rsym value: 0.11 / Net I/σ(I): 15.9
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.487 / Mean I/σ(I) obs: 3.5 / Num. unique all: 2833 / % possible all: 99.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NGY
Resolution: 2.1→25.659 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7616 / SU ML: 0.54 / σ(F): 1.34 / Phase error: 28.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2456 2206 7.76 %RANDOM
Rwork0.2074 ---
obs0.2104 28443 99.16 %-
all-28443 --
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 32.846 Å2 / ksol: 0.326 e/Å3
Displacement parametersBiso max: 82.53 Å2 / Biso mean: 23.7811 Å2 / Biso min: 6.68 Å2
Baniso -1Baniso -2Baniso -3
1-6.4877 Å2-0 Å2-0 Å2
2---5.8504 Å2-0 Å2
3----0.6374 Å2
Refinement stepCycle: LAST / Resolution: 2.1→25.659 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3202 122 3 458 3785
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033416
X-RAY DIFFRACTIONf_angle_d0.7124652
X-RAY DIFFRACTIONf_chiral_restr0.054516
X-RAY DIFFRACTIONf_plane_restr0.002591
X-RAY DIFFRACTIONf_dihedral_angle_d14.2821211
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.14560.31891410.242516241765100
2.1456-2.19550.271350.232316081743100
2.1955-2.25040.32041260.28081582170896
2.2504-2.31120.28751480.23311590173898
2.3112-2.37920.29271380.213416081746100
2.3792-2.45590.2771320.208416381770100
2.4559-2.54360.26511420.220616221764100
2.5436-2.64540.29121100.224216641774100
2.6454-2.76560.29431350.216216431778100
2.7656-2.91120.25741480.217516251773100
2.9112-3.09330.22121410.209816431784100
3.0933-3.33170.23811330.19791643177699
3.3317-3.66610.24111400.19181653179399
3.6661-4.19460.20021380.17851648178699
4.1946-5.27720.17041340.17211702183699
5.2772-25.66130.24891650.21491744190998

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