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- PDB-3v9u: Crystal structure of RNase T in complex with a preferred ssDNA (A... -

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Basic information

Entry
Database: PDB / ID: 3v9u
TitleCrystal structure of RNase T in complex with a preferred ssDNA (AAT) with two Mg in the active site
Components
  • DNA (5'-D(*TP*TP*AP*CP*AP*AP*T)-3')
  • Ribonuclease T
KeywordsHYDROLASE/DNA / DEDD nucleases family / exo-nucleases / 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: 2.298 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_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_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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


Theoretical massNumber of molelcules
Total (without water)111,41419
Polymers110,9748
Non-polymers44011
Water3,693205
1
A: Ribonuclease T
B: Ribonuclease T
E: DNA (5'-D(*TP*TP*AP*CP*AP*AP*T)-3')
F: DNA (5'-D(*TP*TP*AP*CP*AP*AP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,70210
Polymers55,4874
Non-polymers2156
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5920 Å2
ΔGint-99 kcal/mol
Surface area16490 Å2
MethodPISA
2
C: Ribonuclease T
D: Ribonuclease T
G: DNA (5'-D(*TP*TP*AP*CP*AP*AP*T)-3')
H: DNA (5'-D(*TP*TP*AP*CP*AP*AP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,7129
Polymers55,4874
Non-polymers2255
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6040 Å2
ΔGint-95 kcal/mol
Surface area17290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.254, 46.254, 313.646
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: 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*T)-3')


Mass: 2096.423 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.: 5 / Source method: obtained synthetically / Formula: Co
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 205 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.75 Å3/Da / Density % sol: 29.53 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 20%(v/v) 2-Propanol, 0.1M MES monohydrate, 20%(w/v) Polyethylene glycol monomethyl ester 2000, pH 6, 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: 2.298→30 Å / Num. all: 33341 / Num. obs: 33341 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Rsym value: 0.071 / Net I/σ(I): 21.07
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 3.87 / Num. unique all: 3284 / Rsym value: 0.32 / % possible all: 99.8

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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: 2.298→23.229 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8097 / SU ML: 0.64 / σ(F): 1.99 / Phase error: 26.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2448 2571 7.73 %RANDOM
Rwork0.1849 ---
all0.1895 33262 --
obs0.1895 33262 99.71 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.203 Å2 / ksol: 0.391 e/Å3
Displacement parametersBiso max: 89.32 Å2 / Biso mean: 34.3879 Å2 / Biso min: 12.17 Å2
Baniso -1Baniso -2Baniso -3
1-2.2519 Å2-0 Å2-0 Å2
2--2.2519 Å2-0 Å2
3----4.5039 Å2
Refinement stepCycle: LAST / Resolution: 2.298→23.229 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6374 227 11 205 6817
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046785
X-RAY DIFFRACTIONf_angle_d0.8259240
X-RAY DIFFRACTIONf_chiral_restr0.0591022
X-RAY DIFFRACTIONf_plane_restr0.0031177
X-RAY DIFFRACTIONf_dihedral_angle_d14.5192400
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2983-2.34250.28561400.21711651179199
2.3425-2.39020.25591350.198916941829100
2.3902-2.44210.32551490.202917861935100
2.4421-2.49890.27711250.197216691794100
2.4989-2.56130.2831500.207417411891100
2.5613-2.63050.3181360.213916691805100
2.6305-2.70780.33071300.219617811911100
2.7078-2.7950.27361250.197316661791100
2.795-2.89470.26931610.197217621923100
2.8947-3.01040.27231320.202516561788100
3.0104-3.14710.29511500.198517251875100
3.1471-3.31260.2791560.196517361892100
3.3126-3.51950.2271630.182516811844100
3.5195-3.79010.22431300.17591698182899
3.7901-4.16960.19031490.159817001849100
4.1696-4.76840.20041530.147616681821100
4.7684-5.99050.21261420.18171695183799
5.9905-23.23050.21941450.17931713185899

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