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- PDB-3v9w: Crystal structure of RNase T in complex with a preferred ssDNA (T... -

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Basic information

Entry
Database: PDB / ID: 3v9w
TitleCrystal structure of RNase T in complex with a preferred ssDNA (TTA) with two Mg in the active site
Components
  • DNA (5'-D(*GP*CP*TP*TP*A)-3')
  • Ribonuclease T
KeywordsHYDROLASE/DNA / DEDD nucleases family / exo-nucleases / 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: 1.702 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: Ribonuclease T
D: Ribonuclease T
E: DNA (5'-D(*GP*CP*TP*TP*A)-3')
F: DNA (5'-D(*GP*CP*TP*TP*A)-3')
G: DNA (5'-D(*GP*CP*TP*TP*A)-3')
H: DNA (5'-D(*GP*CP*TP*TP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,06720
Polymers108,5688
Non-polymers49912
Water14,484804
1
A: Ribonuclease T
B: Ribonuclease T
E: DNA (5'-D(*GP*CP*TP*TP*A)-3')
F: DNA (5'-D(*GP*CP*TP*TP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,49910
Polymers54,2844
Non-polymers2156
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6150 Å2
ΔGint-105 kcal/mol
Surface area16510 Å2
MethodPISA
2
C: Ribonuclease T
D: Ribonuclease T
G: DNA (5'-D(*GP*CP*TP*TP*A)-3')
H: DNA (5'-D(*GP*CP*TP*TP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,56810
Polymers54,2844
Non-polymers2846
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5990 Å2
ΔGint-107 kcal/mol
Surface area17540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.340, 46.340, 315.354
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

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


Mass: 25646.973 Da / Num. of mol.: 4 / Mutation: E92G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / 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(*GP*CP*TP*TP*A)-3')


Mass: 1495.023 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: Synthetic construct
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Co
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 804 / 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: 1.8 Å3/Da / Density % sol: 31.69 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 6%(v/v) Tacsimate, 0.1M MES monohydrate, 25%(w/v) Polyethylene glycol 4000, pH 6.0, 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: Apr 30, 2010
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: 1.7→30 Å / Num. all: 80910 / Num. obs: 80910 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.6 % / Rsym value: 0.0054 / Net I/σ(I): 23.91
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 3.03 / Num. unique all: 8190 / Rsym value: 0.352 / % possible all: 99.7

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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: 1.702→26.394 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8523 / SU ML: 0.45 / σ(F): 1.97 / Phase error: 22.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2262 6243 7.72 %RANDOM
Rwork0.1918 ---
all0.1944 80817 --
obs0.1944 80817 97.29 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.891 Å2 / ksol: 0.369 e/Å3
Displacement parametersBiso max: 70.03 Å2 / Biso mean: 25.2441 Å2 / Biso min: 6.9 Å2
Baniso -1Baniso -2Baniso -3
1-1.0907 Å20 Å2-0 Å2
2--1.0907 Å2-0 Å2
3----2.1814 Å2
Refinement stepCycle: LAST / Resolution: 1.702→26.394 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6282 244 12 804 7342
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046706
X-RAY DIFFRACTIONf_angle_d0.8729135
X-RAY DIFFRACTIONf_chiral_restr0.0631009
X-RAY DIFFRACTIONf_plane_restr0.0031160
X-RAY DIFFRACTIONf_dihedral_angle_d13.6792379
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7016-1.7210.32832130.27192534274798
1.721-1.74120.29912110.258725452756100
1.7412-1.76240.30462070.240324562663100
1.7624-1.78470.26042170.227826962913100
1.7847-1.80820.29831830.242224362619100
1.8082-1.8330.31621940.23852626282099
1.833-1.85920.28722240.22962575279999
1.8592-1.88690.27962080.21592458266699
1.8869-1.91640.28292270.23262555278298
1.9164-1.94780.24482260.22142513273999
1.9478-1.98140.23212210.20382466268799
1.9814-2.01740.25392080.20926342842100
2.0174-2.05620.23851990.21132487268699
2.0562-2.09810.242180.21452508272697
2.0981-2.14370.23871950.1962485268099
2.1437-2.19360.25042110.1972578278999
2.1936-2.24840.23132220.20642392261498
2.2484-2.30920.23752170.22606282398
2.3092-2.37710.2161960.18842470266699
2.3771-2.45370.23222270.18752585281299
2.4537-2.54140.24612360.19122429266598
2.5414-2.6430.21232270.18662478270598
2.643-2.76320.25982220.19872538276098
2.7632-2.90870.24932040.19182473267797
2.9087-3.09070.22061970.19822422261993
3.0907-3.32890.20831800.18182324250491
3.3289-3.66310.19621860.17152093227984
3.6631-4.19140.17691690.15512293246288
4.1914-5.27380.17481910.15082494268598
5.2738-26.39760.2032070.19362425263295

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