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- PDB-3nh0: Crystal structure of RNase T in complex with a non-preferred ssDN... -

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Basic information

Entry
Database: PDB / ID: 3nh0
TitleCrystal structure of RNase T in complex with a non-preferred ssDNA (AAC)
Components
  • 5'-D(*TP*TP*AP*CP*AP*AP*C)-3'
  • Ribonuclease T
KeywordsHYDROLASE/DNA / exoribonuclease / RNA processing / RNA maturation / protein-DNA interactions / protein-DNA complex / exo-nuclease / HYDROLASE-DNA complex
Function / homology
Function and homology information


rRNA 3'-end processing / tRNA 3'-end processing / regulatory ncRNA 3'-end processing / DNA replication proofreading / single-stranded DNA 3'-5' DNA exonuclease activity / 3'-5' exonuclease activity / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / 3'-5'-RNA exonuclease activity / nucleic acid binding / DNA damage response ...rRNA 3'-end processing / tRNA 3'-end processing / regulatory ncRNA 3'-end processing / DNA replication proofreading / single-stranded DNA 3'-5' DNA exonuclease activity / 3'-5' exonuclease activity / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / 3'-5'-RNA exonuclease activity / nucleic acid binding / DNA damage response / magnesium ion binding / protein homodimerization activity / 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: 2.3 Å
AuthorsHsiao, Y.-Y. / Yuan, H.S.
CitationJournal: Nat.Chem.Biol. / Year: 2011
Title: Structural basis for RNA trimming by RNase T in stable RNA 3'-end maturation
Authors: Hsiao, Y.-Y. / Yang, C.-C. / Lin, C.L. / Lin, J.L.J. / Duh, Y. / Yuan, H.S.
History
DepositionJun 14, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 16, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 21, 2011Group: Database references
Revision 1.3Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)55,6014
Polymers55,6014
Non-polymers00
Water4,864270
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5360 Å2
ΔGint-29 kcal/mol
Surface area17730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.075, 106.360, 46.991
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Ribonuclease T / / RNase T / Exoribonuclease 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: JM109 / ATCC 53323 / Gene: rnt / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): RIPL
References: UniProt: P30014, Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters
#2: DNA chain 5'-D(*TP*TP*AP*CP*AP*AP*C)-3'


Mass: 2081.412 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: ssDNA
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 270 / 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: 2.16 Å3/Da / Density % sol: 43.03 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 3
Details: 0.1M Citric acid pH 3.5, 14% PEG 1000, 10mM Spermidine, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 0.999 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: 0.999 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. all: 22313 / Num. obs: 22313 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Biso Wilson estimate: 22.26 Å2 / Rsym value: 0.09 / Net I/σ(I): 23.82
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 6 % / Mean I/σ(I) obs: 6.2 / Num. unique all: 2180 / Rsym value: 0.285 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
PHENIX(phenix.refine: 1.6_289)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3NGY

3ngy


Resolution: 2.3→27.148 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7616 / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2493 1726 7.84 %RANDOM
Rwork0.1957 20280 --
all0.221 22006 --
obs0.1999 22006 99.53 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 20 Å2 / ksol: 0.314 e/Å3
Displacement parametersBiso max: 98.6 Å2 / Biso mean: 24.0486 Å2 / Biso min: 9.18 Å2
Baniso -1Baniso -2Baniso -3
1-7.9915 Å2-0 Å2-0 Å2
2---6.5643 Å2-0 Å2
3----1.4272 Å2
Refinement stepCycle: LAST / Resolution: 2.3→27.148 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3184 122 0 270 3576
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043396
X-RAY DIFFRACTIONf_angle_d0.834629
X-RAY DIFFRACTIONf_dihedral_angle_d16.5011199
X-RAY DIFFRACTIONf_chiral_restr0.057512
X-RAY DIFFRACTIONf_plane_restr0.003589
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.36770.23931340.19111687X-RAY DIFFRACTION100
2.3677-2.4440.25821360.18561655X-RAY DIFFRACTION100
2.444-2.53130.26341370.19831677X-RAY DIFFRACTION100
2.5313-2.63260.26361410.21181655X-RAY DIFFRACTION100
2.6326-2.75230.32361530.21191681X-RAY DIFFRACTION100
2.7523-2.89720.27611510.20271661X-RAY DIFFRACTION100
2.8972-3.07850.26591400.23031648X-RAY DIFFRACTION99
3.0785-3.31590.25091570.21071683X-RAY DIFFRACTION100
3.3159-3.64880.25741340.19641704X-RAY DIFFRACTION100
3.6488-4.17520.27561370.19091685X-RAY DIFFRACTION98
4.1752-5.2540.20551540.15871727X-RAY DIFFRACTION100
5.254-27.15030.17541520.17541817X-RAY DIFFRACTION99

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