[English] 日本語
Yorodumi
- PDB-1tfr: RNASE H FROM BACTERIOPHAGE T4 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1tfr
TitleRNASE H FROM BACTERIOPHAGE T4
ComponentsT4 RNASE H
KeywordsHYDROLASE / 5U-3U EXONUCLEASE / RNA:RNA / DNA:DNA / METAL-DEPENDENT / MAGNESIUM-CONTAINING / HYDROLASE (NUCLEIC ACID)
Function / homology
Function and homology information


DNA replication, Okazaki fragment processing / 5'-3' RNA exonuclease activity / 5'-flap endonuclease activity / DNA replication, removal of RNA primer / ribonuclease H / RNA-DNA hybrid ribonuclease activity / DNA binding
Similarity search - Function
T4 RNase H, C-terminal / T4 RNase H, C terminal / Flap endonuclease / 5'-nuclease / 5'-3' exonuclease, alpha-helical arch, N-terminal / 5'-3' exonuclease, N-terminal resolvase-like domain / 5'-3' exonuclease / 5'-3' exonuclease / Helix-hairpin-helix motif, class 2 / Helix-hairpin-helix class 2 (Pol1 family) motifs ...T4 RNase H, C-terminal / T4 RNase H, C terminal / Flap endonuclease / 5'-nuclease / 5'-3' exonuclease, alpha-helical arch, N-terminal / 5'-3' exonuclease, N-terminal resolvase-like domain / 5'-3' exonuclease / 5'-3' exonuclease / Helix-hairpin-helix motif, class 2 / Helix-hairpin-helix class 2 (Pol1 family) motifs / 5'-3' exonuclease, C-terminal domain superfamily / PIN-like domain superfamily / 5' to 3' exonuclease, C-terminal subdomain / DNA polymerase; domain 1 / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / Resolution: 2.06 Å
AuthorsMueser, T.C. / Nossal, N.G. / Hyde, C.C.
Citation
Journal: Cell(Cambridge,Mass.) / Year: 1996
Title: Structure of bacteriophage T4 RNase H, a 5' to 3' RNA-DNA and DNA-DNA exonuclease with sequence similarity to the RAD2 family of eukaryotic proteins.
Authors: Mueser, T.C. / Nossal, N.G. / Hyde, C.C.
#1: Journal: Methods Enzymol. / Year: 1995
Title: Purification of Bacteriophage T4 DNA Replication Proteins
Authors: Nossal, N.G. / Hinton, D.M. / Hobbs, L.J. / Spacciapoli, P.
#2: Journal: J.Biol.Chem. / Year: 1991
Title: Bacteriophage T4 Encodes an Rnase H which Removes RNA Primers Made by the T4 Replication System in Vitro
Authors: Hollingsworth, H.C. / Nossal, N.G.
#3: Journal: Nucleic Acids Res. / Year: 1989
Title: Organization of the Bacteriophage T4 Genome between Map Positions 150.745 And 145.824
Authors: Hahn, S. / Ruger, W.
#4: Journal: Nucleic Acids Res. / Year: 1986
Title: The Region of Phage T4 Genes 34, 33 and 59: Primary Structures and Organization on the Genome
Authors: Hahn, S. / Kruse, U. / Ruger, W.
History
DepositionApr 27, 1996Processing site: BNL
Revision 1.0Nov 8, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _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.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_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_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_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: T4 RNASE H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6603
Polymers35,6111
Non-polymers492
Water3,225179
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.470, 87.580, 54.560
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein T4 RNASE H / T4 5U TO 3U EXONUCLEASE


Mass: 35610.914 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: TWO OCTAHEDRALLY-COORDINATED MG2+ IONS IN ACTIVE SITE
Source: (gene. exp.) Enterobacteria phage T4 (virus) / Genus: T4-like viruses / Species: Enterobacteria phage T4 sensu lato / Strain: T4D / Gene (production host): T4RNH / Production host: Escherichia coli (E. coli) / References: UniProt: P13319, ribonuclease H
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 179 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 48 %
Crystal grow
*PLUS
Temperature: 21 ℃ / pH: 6.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 OD280/mlprotein1drop
250 mM1dropNH4Cl
3300 mMmagnesium acetate1reservoir
4100 mMsodium cacodylate1reservoir
518 %PEG80001reservoir

-
Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Oct 18, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.06→6 Å / Num. obs: 22706 / % possible obs: 93.6 % / Observed criterion σ(I): 0 / Redundancy: 2.58 % / Rmerge(I) obs: 0.05
Reflection
*PLUS
Num. measured all: 58561

-
Processing

Software
NameClassification
PROLSQrefinement
PROCESSdata reduction
RefinementResolution: 2.06→6 Å / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.29 -10 %
Rwork0.205 --
obs-19591 90.29 %
Displacement parametersBiso mean: 31.98 Å2
Refine analyzeLuzzati coordinate error obs: 0.21 Å
Refinement stepCycle: LAST / Resolution: 2.06→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2506 0 2 179 2687
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.010.01
X-RAY DIFFRACTIONp_angle_d0.0320.02
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0330.025
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it2.9812
X-RAY DIFFRACTIONp_mcangle_it4.273
X-RAY DIFFRACTIONp_scbond_it5.1923
X-RAY DIFFRACTIONp_scangle_it6.9395
X-RAY DIFFRACTIONp_plane_restr0.010.01
X-RAY DIFFRACTIONp_chiral_restr0.0710.05
X-RAY DIFFRACTIONp_singtor_nbd0.1770.2
X-RAY DIFFRACTIONp_multtor_nbd0.190.2
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1970.2
X-RAY DIFFRACTIONp_planar_tor19.715
X-RAY DIFFRACTIONp_staggered_tor31.420
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor22
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.205
Solvent computation
*PLUS
Displacement parameters
*PLUS

+
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