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- PDB-3va3: Crystal structure of RNase T in complex with a duplex DNA product... -

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Basic information

Entry
Database: PDB / ID: 3va3
TitleCrystal structure of RNase T in complex with a duplex DNA product (stem loop DNA with 2 nucleotide 3' overhang)
Components
  • DNA (5'-D(*GP*GP*CP*CP*CP*TP*CP*TP*TP*TP*AP*GP*GP*GP*CP*CP*TP*T)-3')
  • Ribonuclease T
KeywordsHYDROLASE/DNA / DEDD nucleases family / exo-nuclease / HYDROLASE-DNA complex
Function / homology
Function and homology information


rRNA 3'-end processing / regulatory ncRNA 3'-end processing / tRNA 3'-end processing / DNA replication proofreading / single-stranded DNA 3'-5' DNA exonuclease activity / 3'-5' exonuclease activity / cellular response to UV / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / 3'-5'-RNA exonuclease activity / nucleic acid binding ...rRNA 3'-end processing / regulatory ncRNA 3'-end processing / tRNA 3'-end processing / DNA replication proofreading / single-stranded DNA 3'-5' DNA exonuclease activity / 3'-5' exonuclease activity / cellular response to UV / 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 / DNA (> 10) / Ribonuclease T
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.714 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
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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(*GP*GP*CP*CP*CP*TP*CP*TP*TP*TP*AP*GP*GP*GP*CP*CP*TP*T)-3')
D: DNA (5'-D(*GP*GP*CP*CP*CP*TP*CP*TP*TP*TP*AP*GP*GP*GP*CP*CP*TP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,3616
Polymers62,2434
Non-polymers1182
Water66737
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6200 Å2
ΔGint-67 kcal/mol
Surface area18210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.266, 112.684, 57.793
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 / Exoribonuclease T / RNase T


Mass: 25646.973 Da / Num. of mol.: 2 / 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*GP*CP*CP*CP*TP*CP*TP*TP*TP*AP*GP*GP*GP*CP*CP*TP*T)-3')


Mass: 5474.526 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Synthetic construct
#3: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Co
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / 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: 2.62 Å3/Da / Density % sol: 53.1 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 0.1M Sodium acetate trihydrate, 10%(w/v) Polyethylene glycol 1000, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 0.9999 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 29, 2010
RadiationMonochromator: SAGITALLY FOCUSED Si(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. all: 17286 / Num. obs: 17286 / % possible obs: 94.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Rsym value: 0.102 / Net I/σ(I): 13.36
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 2.24 / Num. unique all: 1667 / Rsym value: 0.412 / % possible all: 93.5

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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

3ngy


Resolution: 2.714→28.932 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7073 / SU ML: 0.76 / σ(F): 0 / Phase error: 34.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2904 1358 7.88 %RANDOM
Rwork0.2631 ---
all0.2653 17239 --
obs0.2653 17239 93.96 %-
Solvent computationShrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 24.177 Å2 / ksol: 0.252 e/Å3
Displacement parametersBiso max: 118.47 Å2 / Biso mean: 60.8134 Å2 / Biso min: 42.66 Å2
Baniso -1Baniso -2Baniso -3
1--14.4969 Å2-0 Å20 Å2
2---32.3874 Å20 Å2
3---46.8843 Å2
Refinement stepCycle: LAST / Resolution: 2.714→28.932 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3149 318 2 37 3506
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033576
X-RAY DIFFRACTIONf_angle_d0.6854911
X-RAY DIFFRACTIONf_chiral_restr0.044546
X-RAY DIFFRACTIONf_plane_restr0.003591
X-RAY DIFFRACTIONf_dihedral_angle_d15.9031287
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7137-2.81060.43341370.38961492162991
2.8106-2.9230.43681510.36681541169294
2.923-3.05590.36981440.3381591173595
3.0559-3.21680.3121420.30521603174596
3.2168-3.41810.29121280.27881621174997
3.4181-3.68150.32821190.27611463158287
3.6815-4.05110.24671140.24671466158087
4.0511-4.63520.23871480.20091670181898
4.6352-5.83210.24921260.23431691181798
5.8321-28.9340.25971490.24091743189296

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