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- PDB-3nh1: Crystal structure of RNase T in complex with a preferred ssDNA (T... -

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Basic information

Entry
Database: PDB / ID: 3nh1
TitleCrystal structure of RNase T in complex with a preferred ssDNA (TAGG) with two Mg in the active site
Components
  • 5'-D(*TP*TP*AP*TP*AP*GP*G)-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 / 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: 2.107 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 ...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: 5'-D(*TP*TP*AP*TP*AP*GP*G)-3'
F: 5'-D(*TP*TP*AP*TP*AP*GP*G)-3'
G: 5'-D(*TP*TP*AP*TP*AP*GP*G)-3'
H: 5'-D(*TP*TP*AP*TP*AP*GP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,68016
Polymers111,4868
Non-polymers1948
Water6,179343
1
A: Ribonuclease T
B: Ribonuclease T
E: 5'-D(*TP*TP*AP*TP*AP*GP*G)-3'
F: 5'-D(*TP*TP*AP*TP*AP*GP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,8408
Polymers55,7434
Non-polymers974
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5780 Å2
ΔGint-38 kcal/mol
Surface area17790 Å2
MethodPISA
2
C: Ribonuclease T
D: Ribonuclease T
G: 5'-D(*TP*TP*AP*TP*AP*GP*G)-3'
H: 5'-D(*TP*TP*AP*TP*AP*GP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,8408
Polymers55,7434
Non-polymers974
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5480 Å2
ΔGint-32 kcal/mol
Surface area16830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.482, 46.482, 315.877
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 / RNase T / Exoribonuclease 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: 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*TP*AP*GP*G)-3'


Mass: 2152.446 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: ssDNA
#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


Mass: 18.015 Da / Num. of mol.: 343 / 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: 1.767152 Å3/Da / Density % sol: 30.396488 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1M MES monohydrate pH 6.0, 20% w/v PEG MME 2000, 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: Apr 30, 2010
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: 2.1→30 Å / Num. all: 43799 / Num. obs: 43799 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Rsym value: 0.056 / Net I/σ(I): 24.2
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 4.7 / Num. unique all: 4281 / Rsym value: 0.269 / % possible all: 99.4

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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: 2.107→23.377 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.851 / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.99 / Phase error: 22.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2286 3383 7.74 %RANDOM
Rwork0.1706 40348 --
all0.1937 43731 --
obs0.175 43731 99.21 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.878 Å2 / ksol: 0.358 e/Å3
Displacement parametersBiso max: 86.58 Å2 / Biso mean: 31.0035 Å2 / Biso min: 11.88 Å2
Baniso -1Baniso -2Baniso -3
1--0.0943 Å20 Å20 Å2
2---0.0943 Å20 Å2
3---0.1887 Å2
Refinement stepCycle: LAST / Resolution: 2.107→23.377 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6359 321 8 343 7031
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076871
X-RAY DIFFRACTIONf_angle_d1.0129387
X-RAY DIFFRACTIONf_dihedral_angle_d17.7062424
X-RAY DIFFRACTIONf_chiral_restr0.071035
X-RAY DIFFRACTIONf_plane_restr0.0041179
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1065-2.13660.26521050.17881460X-RAY DIFFRACTION90
2.1366-2.16840.25281460.18611721X-RAY DIFFRACTION99
2.1684-2.20230.26831540.18381699X-RAY DIFFRACTION99
2.2023-2.23840.26791540.19251693X-RAY DIFFRACTION99
2.2384-2.2770.27531370.20361638X-RAY DIFFRACTION99
2.277-2.31830.30581480.19271725X-RAY DIFFRACTION99
2.3183-2.36290.23161520.18491647X-RAY DIFFRACTION100
2.3629-2.41110.29851420.17091693X-RAY DIFFRACTION100
2.4111-2.46340.26041480.18951702X-RAY DIFFRACTION100
2.4634-2.52070.25071550.18171637X-RAY DIFFRACTION100
2.5207-2.58360.25421460.18521767X-RAY DIFFRACTION100
2.5836-2.65340.30591200.18391630X-RAY DIFFRACTION100
2.6534-2.73130.27721510.18451767X-RAY DIFFRACTION100
2.7313-2.81940.24251340.18571610X-RAY DIFFRACTION100
2.8194-2.920.21171540.17861726X-RAY DIFFRACTION100
2.92-3.03660.25581570.18821635X-RAY DIFFRACTION100
3.0366-3.17450.25871320.18561728X-RAY DIFFRACTION100
3.1745-3.34140.26061500.181738X-RAY DIFFRACTION100
3.3414-3.55010.19791260.16341703X-RAY DIFFRACTION100
3.5501-3.82310.21111170.15191721X-RAY DIFFRACTION100
3.8231-4.20580.19491240.14351707X-RAY DIFFRACTION100
4.2058-4.80980.16531360.13421663X-RAY DIFFRACTION100
4.8098-6.04250.20271470.15421657X-RAY DIFFRACTION98
6.0425-23.37890.15961480.16141681X-RAY DIFFRACTION99

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