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- PDB-3h8j: Native T4 RNase H in the absence of divalent metal ions -

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Basic information

Entry
Database: PDB / ID: 3h8j
TitleNative T4 RNase H in the absence of divalent metal ions
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 / Resolution: 1.8 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 1.2Sep 6, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

Deposited unit
A: Ribonuclease H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7303
Polymers35,6111
Non-polymers1192
Water5,080282
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)36.257, 86.458, 57.796
Angle α, β, γ (deg.)90.00, 92.04, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Ribonuclease H / RNase H


Mass: 35610.914 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T4 (virus) / Strain: T4D / Gene: 33.2, das, rnh / Plasmid: pNN2202 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3) PlysS / References: UniProt: P13319, ribonuclease H
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 282 / 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: 2.54 Å3/Da / Density % sol: 51.62 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 300 mM ammonium acetate, 100 mM sodium cacodylate, 15% 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: NSLS / Beamline: X9B
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.8→20 Å / Num. obs: 33128 / Redundancy: 4 % / Biso Wilson estimate: 15.47 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 28.3
Reflection shellResolution: 1.8→1.86 Å / Rmerge(I) obs: 0.185 / Mean I/σ(I) obs: 7.4 / Num. unique all: 3285

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Processing

Software
NameVersionClassification
AMoREphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1TFR native T4 RNase H

1tfr


Resolution: 1.8→19.253 Å / SU ML: 0.23 / σ(F): 0.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2134 1017 3.15 %5% random data subset
Rwork0.1924 ---
obs0.1931 32304 97.96 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.403 Å2 / ksol: 0.388 e/Å3
Displacement parametersBiso mean: 18.89 Å2
Refinement stepCycle: LAST / Resolution: 1.8→19.253 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2440 0 6 282 2728
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_angle_deg0.807
X-RAY DIFFRACTIONf_bond_d0.004
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
1.8-1.89480.19541370.19084176417692
1.8948-2.01340.23911320.19414460446098
2.0134-2.16870.25261270.20154518451898
2.1687-2.38660.18921410.19444450445098
2.3866-2.73110.26481580.204145354535100
2.7311-3.43770.22831600.202945424542100
3.4377-19.25420.17311620.170946064606100

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