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- PDB-4kb0: Crystal structure of RNase T in complex with a bluge DNA (Two nuc... -

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Basic information

Entry
Database: PDB / ID: 4kb0
TitleCrystal structure of RNase T in complex with a bluge DNA (Two nucleotide insertion CC )
Components
  • DNA (5'-D(*GP*GP*CP*CP*CP*TP*CP*TP*TP*TP*AP*GP*GP*GP*CP*CP*CP*C)-3')
  • Ribonuclease T
KeywordsHydrolase/dna / DnaQ / DEDD / exonuclease / DNA repair / 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 / DNA (> 10) / Ribonuclease T
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.004 Å
AuthorsHsiao, Y.-Y. / Yuan, H.S.
CitationJournal: Plos Biol. / Year: 2014
Title: Structural insights into DNA repair by RNase T--an exonuclease processing 3' end of structured DNA in repair pathways.
Authors: Hsiao, Y.Y. / Fang, W.H. / Lee, C.C. / Chen, Y.P. / Yuan, H.S.
History
DepositionApr 23, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 5, 2014Provider: repository / Type: Initial release
Revision 1.1May 28, 2014Group: Database references
Revision 1.2Sep 20, 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: DNA (5'-D(*GP*GP*CP*CP*CP*TP*CP*TP*TP*TP*AP*GP*GP*GP*CP*CP*CP*C)-3')
D: DNA (5'-D(*GP*GP*CP*CP*CP*TP*CP*TP*TP*TP*AP*GP*GP*GP*CP*CP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,4248
Polymers62,3274
Non-polymers974
Water7,620423
1
A: Ribonuclease T
C: DNA (5'-D(*GP*GP*CP*CP*CP*TP*CP*TP*TP*TP*AP*GP*GP*GP*CP*CP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2124
Polymers31,1642
Non-polymers492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1450 Å2
ΔGint-28 kcal/mol
Surface area12730 Å2
MethodPISA
2
B: Ribonuclease T
D: DNA (5'-D(*GP*GP*CP*CP*CP*TP*CP*TP*TP*TP*AP*GP*GP*GP*CP*CP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2124
Polymers31,1642
Non-polymers492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1470 Å2
ΔGint-28 kcal/mol
Surface area12630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.257, 81.944, 73.444
Angle α, β, γ (deg.)90.00, 105.46, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Ribonuclease T / Exoribonuclease T / RNase T


Mass: 25719.035 Da / Num. of mol.: 2 / Fragment: RNase T / Mutation: NO
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: b1652, JW1644, rnt / Plasmid: pET-28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIPL strain
References: UniProt: P30014, Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters
#2: DNA chain DNA (5'-D(*GP*GP*CP*CP*CP*TP*CP*TP*TP*TP*AP*GP*GP*GP*CP*CP*CP*C)-3')


Mass: 5444.503 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 423 / 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: 2.8 Å3/Da / Density % sol: 56.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 6% v/v Tacsimate pH 6.0, 0.1 M MES monohydrate pH 6.0, 25% w/v Polyethylene glycol 4000 , VAPOR DIFFUSION, HANGING DROP, temperature 293K

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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: Jun 3, 2011
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→30 Å / Num. all: 44590 / Num. obs: 44590 / % possible obs: 96.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Rsym value: 0.086 / Net I/σ(I): 19
Reflection shellResolution: 2→2.07 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 2.36 / Num. unique all: 4176 / Rsym value: 0.468 / % possible all: 91

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NGY

3ngy


Resolution: 2.004→29.799 Å / SU ML: 0.22 / σ(F): 0 / Phase error: 21.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2106 3468 7.78 %RANDOM
Rwork0.1885 ---
all0.1902 44562 --
obs0.1902 44562 96.25 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.004→29.799 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3164 720 4 423 4311
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024042
X-RAY DIFFRACTIONf_angle_d0.6875630
X-RAY DIFFRACTIONf_dihedral_angle_d18.4781496
X-RAY DIFFRACTIONf_chiral_restr0.046628
X-RAY DIFFRACTIONf_plane_restr0.002614
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0037-2.03110.32031080.28041498X-RAY DIFFRACTION87
2.0311-2.06020.33231250.27111528X-RAY DIFFRACTION91
2.0602-2.09090.2831470.27691542X-RAY DIFFRACTION91
2.0909-2.12360.30351390.25161536X-RAY DIFFRACTION92
2.1236-2.15840.30061320.24521639X-RAY DIFFRACTION93
2.1584-2.19560.28241260.23671571X-RAY DIFFRACTION95
2.1956-2.23550.25331420.22151628X-RAY DIFFRACTION95
2.2355-2.27850.23281310.22261613X-RAY DIFFRACTION95
2.2785-2.3250.26751410.20931642X-RAY DIFFRACTION97
2.325-2.37550.26671240.19981637X-RAY DIFFRACTION96
2.3755-2.43070.24661430.20621661X-RAY DIFFRACTION97
2.4307-2.49150.24671290.19781661X-RAY DIFFRACTION97
2.4915-2.55880.2141300.18641700X-RAY DIFFRACTION98
2.5588-2.63410.22291390.19731655X-RAY DIFFRACTION97
2.6341-2.7190.25751450.20311647X-RAY DIFFRACTION98
2.719-2.81610.19571440.19031694X-RAY DIFFRACTION98
2.8161-2.92880.21391480.18531645X-RAY DIFFRACTION98
2.9288-3.0620.21861470.18671694X-RAY DIFFRACTION98
3.062-3.22320.19281470.18511677X-RAY DIFFRACTION99
3.2232-3.42490.20661470.17861692X-RAY DIFFRACTION99
3.4249-3.68890.16911490.15841680X-RAY DIFFRACTION99
3.6889-4.05930.16991250.16031718X-RAY DIFFRACTION99
4.0593-4.64480.15071580.14741694X-RAY DIFFRACTION99
4.6448-5.84470.19511660.16871694X-RAY DIFFRACTION99
5.8447-29.80270.18161360.18571748X-RAY DIFFRACTION99

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