[English] 日本語
Yorodumi
- PDB-4kb1: Crystal structure of RNase T in complex with a bluge DNA (two nuc... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4kb1
TitleCrystal structure of RNase T in complex with a bluge DNA (two nucleotide insertion CT )
Components
  • Bulge DNA
  • 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: 1.8 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ribonuclease T
B: Ribonuclease T
C: Bulge DNA
D: Bulge DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,4548
Polymers62,3574
Non-polymers974
Water10,251569
1
A: Ribonuclease T
C: Bulge DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2274
Polymers31,1792
Non-polymers492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1460 Å2
ΔGint-29 kcal/mol
Surface area12960 Å2
MethodPISA
2
B: Ribonuclease T
D: Bulge DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2274
Polymers31,1792
Non-polymers492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1460 Å2
ΔGint-28 kcal/mol
Surface area12660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.556, 81.844, 73.744
Angle α, β, γ (deg.)90.00, 105.71, 90.00
Int Tables number4
Space group name H-MP1211

-
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
References: UniProt: P30014, Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters
#2: DNA chain Bulge DNA


Mass: 5459.515 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.: 569 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.82 Å3/Da / Density % sol: 56.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.10% w/v n-Octyl- -D-glucoside, 0.1 M Sodium citrate tribasic dehydrate, 22% Polyethylene glycol 3350, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
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: 1.8→30 Å / Num. all: 65372 / Num. obs: 65372 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rsym value: 0.062 / Net I/σ(I): 27.93
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 2.87 / Num. unique all: 6473 / Rsym value: 0.411 / % possible all: 98.8

-
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: 1.8→28.621 Å / SU ML: 0.18 / σ(F): 0 / Phase error: 20.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1989 3222 5.07 %RANDOM
Rwork0.1831 ---
all0.1839 63562 --
obs0.1839 63562 99.01 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→28.621 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3180 722 4 569 4475
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044060
X-RAY DIFFRACTIONf_angle_d0.8645656
X-RAY DIFFRACTIONf_dihedral_angle_d18.8851502
X-RAY DIFFRACTIONf_chiral_restr0.057631
X-RAY DIFFRACTIONf_plane_restr0.003617
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.82690.29621390.2562599X-RAY DIFFRACTION99
1.8269-1.85540.28111120.23942641X-RAY DIFFRACTION99
1.8554-1.88580.24191510.22552588X-RAY DIFFRACTION99
1.8858-1.91830.24721310.21942607X-RAY DIFFRACTION99
1.9183-1.95320.26541490.22182654X-RAY DIFFRACTION99
1.9532-1.99080.24371360.21562633X-RAY DIFFRACTION99
1.9908-2.03140.22531530.20572594X-RAY DIFFRACTION99
2.0314-2.07560.20081370.19762610X-RAY DIFFRACTION99
2.0756-2.12380.24881260.19612622X-RAY DIFFRACTION99
2.1238-2.17690.21461500.19262641X-RAY DIFFRACTION100
2.1769-2.23570.25971200.19522656X-RAY DIFFRACTION100
2.2357-2.30150.21991550.19162585X-RAY DIFFRACTION100
2.3015-2.37580.22051540.18992638X-RAY DIFFRACTION99
2.3758-2.46060.22321360.18972642X-RAY DIFFRACTION99
2.4606-2.55910.19831310.19392649X-RAY DIFFRACTION99
2.5591-2.67550.21931450.20112602X-RAY DIFFRACTION99
2.6755-2.81640.20891220.19712688X-RAY DIFFRACTION99
2.8164-2.99270.22441270.19292618X-RAY DIFFRACTION99
2.9927-3.22350.19721440.18352623X-RAY DIFFRACTION99
3.2235-3.54730.18121560.16452643X-RAY DIFFRACTION99
3.5473-4.05940.1511520.152628X-RAY DIFFRACTION99
4.0594-5.10970.14451560.1452632X-RAY DIFFRACTION99
5.1097-28.6250.1941400.18082547X-RAY DIFFRACTION94

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more