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- PDB-1tfr: RNASE H FROM BACTERIOPHAGE T4 -

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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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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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

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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

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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

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