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- PDB-3ngz: Crystal structure of RNase T in complex with a non-preferred ssDN... -

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Basic information

Entry
Database: PDB / ID: 3ngz
TitleCrystal structure of RNase T in complex with a non-preferred ssDNA (GC) with one Mg in the active site
Components
  • 5'-D(P*GP*C)-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: 2.1 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_seq_id / _pdbx_struct_conn_angle.ptnr1_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: 5'-D(P*GP*C)-3'
D: 5'-D(P*GP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,6078
Polymers52,4414
Non-polymers1664
Water10,521584
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)96.747, 105.585, 47.180
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 / RNase T / Exoribonuclease 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: 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(P*GP*C)-3'


Mass: 573.430 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: ssDNA
#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.: 2 / Source method: obtained synthetically / Formula: Co
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 584 / 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: 2.3 Å3/Da / Density % sol: 46.46 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 18% v/v 2-Propanol, 0.1M Sodium citrate tribasic dihydrate pH 5.5, 20% PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jan 22, 2010
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. obs: 28759 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Biso Wilson estimate: 16.06 Å2 / Rsym value: 0.12 / Net I/σ(I): 18.6
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 4.5 % / Mean I/σ(I) obs: 5 / Num. unique all: 1438 / Rsym value: 0.437 / % possible all: 99.6

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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: 2.1→28.459 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7316 / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 31.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.26 2227 7.78 %RANDOM
Rwork0.1948 26401 --
obs0.1998 28628 98.76 %-
all-28628 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.325 Å2 / ksol: 0.319 e/Å3
Displacement parametersBiso max: 91.62 Å2 / Biso mean: 20.1841 Å2 / Biso min: 5.24 Å2
Baniso -1Baniso -2Baniso -3
1-9.6733 Å2-0 Å2-0 Å2
2---5.896 Å2-0 Å2
3----3.7773 Å2
Refinement stepCycle: LAST / Resolution: 2.1→28.459 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3165 82 4 584 3835
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063331
X-RAY DIFFRACTIONf_angle_d0.9854533
X-RAY DIFFRACTIONf_dihedral_angle_d15.7731169
X-RAY DIFFRACTIONf_chiral_restr0.069501
X-RAY DIFFRACTIONf_plane_restr0.003583
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.14570.32951420.2181659X-RAY DIFFRACTION99
2.1457-2.19560.29291480.2111581X-RAY DIFFRACTION100
2.1956-2.25050.28191310.21611657X-RAY DIFFRACTION99
2.2505-2.31130.30191140.20041632X-RAY DIFFRACTION99
2.3113-2.37930.26511580.19261600X-RAY DIFFRACTION99
2.3793-2.4560.29021480.19541639X-RAY DIFFRACTION100
2.456-2.54380.28511500.19441599X-RAY DIFFRACTION98
2.5438-2.64550.2831160.20241667X-RAY DIFFRACTION99
2.6455-2.76580.26431450.20641663X-RAY DIFFRACTION100
2.7658-2.91150.30521250.19581625X-RAY DIFFRACTION99
2.9115-3.09370.26441420.20551651X-RAY DIFFRACTION99
3.0937-3.33230.24281390.19021668X-RAY DIFFRACTION99
3.3323-3.6670.21471540.18491631X-RAY DIFFRACTION98
3.667-4.19620.22341310.16741680X-RAY DIFFRACTION99
4.1962-5.28120.21881450.17011693X-RAY DIFFRACTION98
5.2812-28.46210.24061390.2051756X-RAY DIFFRACTION97

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