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- PDB-3va0: Crystal structure of RNase T in complex with a di-nucleotide prod... -

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Basic information

Entry
Database: PDB / ID: 3va0
TitleCrystal structure of RNase T in complex with a di-nucleotide product (GG) with one Mg in the active site
Components
  • DNA (5'-D(*GP*G)-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 / Ribonuclease T
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.201 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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*G)-3')
D: DNA (5'-D(*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,7737
Polymers52,6654
Non-polymers1083
Water7,999444
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)95.688, 105.807, 47.074
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: 25719.035 Da / Num. of mol.: 2
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*G)-3')


Mass: 613.454 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Synthetic construct
#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


Mass: 18.015 Da / Num. of mol.: 444 / 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: 2.26 Å3/Da / Density % sol: 45.63 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 0.2M Magnesiumformate dihydrate, 0.1M Sodium acetate trihydrate, 18%(w/v) Polyethylene glycol monomethyl ester 5000, pH 4.0, 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 8, 2011
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: 2.2→30 Å / Num. all: 24276 / Num. obs: 24276 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rsym value: 0.074 / Net I/σ(I): 10.04
Reflection shellResolution: 2.2→2.27 Å / Redundancy: 3 % / Mean I/σ(I) obs: 2.47 / Num. unique all: 2143 / Rsym value: 0.232 / % possible all: 95.2

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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: 2.201→28.389 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8275 / SU ML: 0.63 / σ(F): 0 / Phase error: 23.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2431 1879 7.76 %RANDOM
Rwork0.2061 ---
all0.2089 24224 --
obs0.2089 24224 96.94 %-
Solvent computationShrinkage radii: 1.13 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 25.598 Å2 / ksol: 0.322 e/Å3
Displacement parametersBiso max: 55.06 Å2 / Biso mean: 21.0732 Å2 / Biso min: 9.81 Å2
Baniso -1Baniso -2Baniso -3
1-4.2189 Å2-0 Å2-0 Å2
2---1.4585 Å2-0 Å2
3----2.7604 Å2
Refinement stepCycle: LAST / Resolution: 2.201→28.389 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3195 82 3 444 3724
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023373
X-RAY DIFFRACTIONf_angle_d0.5884600
X-RAY DIFFRACTIONf_chiral_restr0.043504
X-RAY DIFFRACTIONf_plane_restr0.001589
X-RAY DIFFRACTIONf_dihedral_angle_d13.2081188
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2006-2.260.27131400.23561664180495
2.26-2.32650.32251300.2431671180196
2.3265-2.40160.26951500.23221668181896
2.4016-2.48740.25951370.22551699183696
2.4874-2.58690.26291470.22541673182096
2.5869-2.70450.2831500.22431670182097
2.7045-2.8470.27651240.21641714183896
2.847-3.02520.26841590.20851698185797
3.0252-3.25840.2441570.21151712186998
3.2584-3.58580.23341540.19321756191098
3.5858-4.10330.20561510.17971747189898
4.1033-5.16470.19251380.17521789192798
5.1647-28.39150.21821420.20521884202698

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