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- PDB-3v9x: Crystal structure of RNase T in complex with a preferred ssDNA (A... -

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Basic information

Entry
Database: PDB / ID: 3v9x
TitleCrystal structure of RNase T in complex with a preferred ssDNA (AAA) with two Mg in the active site
Components
  • DNA (5'-D(*TP*TP*AP*TP*AP*AP*A)-3')
  • Ribonuclease T
KeywordsHYDROLASE/DNA / DEDD nucleases family / 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: 1.9 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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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

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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*TP*AP*AP*A)-3')
F: DNA (5'-D(*TP*TP*AP*TP*AP*AP*A)-3')
G: DNA (5'-D(*TP*TP*AP*TP*AP*AP*A)-3')
H: DNA (5'-D(*TP*TP*AP*TP*AP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,55216
Polymers111,3588
Non-polymers1948
Water9,440524
1
A: Ribonuclease T
B: Ribonuclease T
E: DNA (5'-D(*TP*TP*AP*TP*AP*AP*A)-3')
F: DNA (5'-D(*TP*TP*AP*TP*AP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,7768
Polymers55,6794
Non-polymers974
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6360 Å2
ΔGint-73 kcal/mol
Surface area17530 Å2
MethodPISA
2
C: Ribonuclease T
D: Ribonuclease T
G: DNA (5'-D(*TP*TP*AP*TP*AP*AP*A)-3')
H: DNA (5'-D(*TP*TP*AP*TP*AP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,7768
Polymers55,6794
Non-polymers974
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5960 Å2
ΔGint-72 kcal/mol
Surface area16600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.280, 46.280, 314.379
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: 25719.035 Da / Num. of mol.: 4
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(*TP*TP*AP*TP*AP*AP*A)-3')


Mass: 2120.448 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.: 8 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 524 / 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: 1.7455 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 6.0, 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(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. all: 58869 / Num. obs: 58869 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / Rsym value: 0.06 / Net I/σ(I): 25.29
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 3.98 / Num. unique all: 5942 / Rsym value: 0.353 / % possible all: 99.9

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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: 1.9→23.27 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8405 / SU ML: 0.49 / σ(F): 1.97 / Phase error: 23.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2228 4567 7.77 %RANDOM
Rwork0.1847 ---
obs0.1877 58768 98.9 %-
all-58768 --
Solvent computationShrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 52.647 Å2 / ksol: 0.39 e/Å3
Displacement parametersBiso max: 72.88 Å2 / Biso mean: 27.8563 Å2 / Biso min: 10.12 Å2
Baniso -1Baniso -2Baniso -3
1-2.5911 Å20 Å2-0 Å2
2--2.5911 Å2-0 Å2
3----5.1821 Å2
Refinement stepCycle: LAST / Resolution: 1.9→23.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6387 272 8 524 7191
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066845
X-RAY DIFFRACTIONf_angle_d0.939338
X-RAY DIFFRACTIONf_chiral_restr0.0651032
X-RAY DIFFRACTIONf_plane_restr0.0041182
X-RAY DIFFRACTIONf_dihedral_angle_d14.5632428
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 (%)
1.8997-1.92130.36141420.256419232065100
1.9213-1.94390.28731570.229818061963100
1.9439-1.96760.28541500.222117581908100
1.9676-1.99250.2561600.218918732033100
1.9925-2.01870.28881460.216818421988100
2.0187-2.04630.26231700.208217801950100
2.0463-2.07550.24561540.194618241978100
2.0755-2.10650.25751660.204418902056100
2.1065-2.13940.25911600.187517311891100
2.1394-2.17450.28551480.206718241972100
2.1745-2.21190.25931690.205218462015100
2.2119-2.25210.27671560.189817641920100
2.2521-2.29540.26811460.196718962042100
2.2954-2.34220.28261420.197518021944100
2.3422-2.39310.24541740.187917821956100
2.3931-2.44870.22291430.195519082051100
2.4487-2.50990.24991460.187617611907100
2.5099-2.57760.28661510.195518922043100
2.5776-2.65340.24491450.202217921937100
2.6534-2.73890.25091710.195118111982100
2.7389-2.83660.22891740.18451768194299
2.8366-2.950.211420.18591818196099
2.95-3.0840.24371620.18661863202599
3.084-3.24610.20331400.18031733187398
3.2461-3.44890.19551610.17221710187196
3.4489-3.71420.19281440.161761190595
3.7142-4.08620.16991380.15381694183293
4.0862-4.67330.17551340.14911772190695
4.6733-5.87220.1711340.17771811194599
5.8722-23.27150.18491420.19451766190897

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