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- PDB-3h8s: Structure of D19N T4 RNase H in the presence of divalent magnesium -

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Basic information

Entry
Database: PDB / ID: 3h8s
TitleStructure of D19N T4 RNase H in the presence of divalent magnesium
ComponentsRibonuclease H
KeywordsHYDROLASE / BPT4 RNase H / 5'-3' exonuclease / Endonuclease / Nuclease
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.51 Å
AuthorsTomanicek, S.J. / Mueser, T.C.
CitationJournal: To be Published
Title: Additional Order Appears in the Absence of Metals in a FEN-1 protein: Structural Analysis of Magnesium Binding to Bacteriophage T4 RNaseH
Authors: Tomanicek, S.J. / Devos, J.M. / Mueser, T.C.
History
DepositionApr 29, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 12, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Oct 13, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_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.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
Revision 1.4Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ribonuclease H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6342
Polymers35,6101
Non-polymers241
Water1,06359
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.312, 75.298, 88.090
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Ribonuclease H / RNase H


Mass: 35609.926 Da / Num. of mol.: 1 / Mutation: D19N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T4 (virus) / Strain: T4D / Gene: 33.2, das, rnh / Plasmid: pNN2202-D19N / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) PlysS / References: UniProt: P13319, ribonuclease H
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / 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: 2.48 Å3/Da / Density % sol: 50.45 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 100 mM Na PIPES, 200 mM MgCl2, 14% PEG 8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→45 Å / Num. obs: 10519 / % possible obs: 83.1 % / Redundancy: 3 % / Biso Wilson estimate: 28.79 Å2 / Rmerge(I) obs: 0.035 / Χ2: 1.071 / Net I/σ(I): 26.4
Reflection shellResolution: 2.5→2.59 Å / Rmerge(I) obs: 0.098 / Mean I/σ(I) obs: 8.9 / Num. unique all: 679 / Χ2: 1.62 / % possible all: 55.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
PHENIXrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1TFR native T4 RNase H

1tfr


Resolution: 2.51→30.753 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.28 / σ(F): 2.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.234 494 4.7 %5% random data subset
Rwork0.19 ---
obs0.192 10515 44.96 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 30.437 Å2 / ksol: 0.356 e/Å3
Displacement parametersBiso max: 102.69 Å2 / Biso mean: 36.53 Å2 / Biso min: 10.81 Å2
Baniso -1Baniso -2Baniso -3
1-8.716 Å20 Å2-0 Å2
2--2.873 Å20 Å2
3----11.589 Å2
Refinement stepCycle: LAST / Resolution: 2.51→30.753 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2333 0 1 59 2393
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022393
X-RAY DIFFRACTIONf_angle_d0.453233
X-RAY DIFFRACTIONf_chiral_restr0.034350
X-RAY DIFFRACTIONf_plane_restr0.002396
X-RAY DIFFRACTIONf_dihedral_angle_d12.849869
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.51-2.7620.244860.2151877196334
2.762-3.1620.2681270.2242330245742
3.162-3.9820.2411430.1972846298951
3.982-30.7560.1971380.162968310653

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