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- PDB-3h7i: Structure of the metal-free D132N T4 RNase H -

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Basic information

Entry
Database: PDB / ID: 3h7i
TitleStructure of the metal-free D132N T4 RNase H
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: 1.502 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 27, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 12, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 13, 2021Group: Database references / Derived calculations / Category: database_2 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Sep 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)35,8023
Polymers35,6101
Non-polymers1922
Water6,143341
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)36.011, 85.858, 57.260
Angle α, β, γ (deg.)90.00, 92.00, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Ribonuclease H / / RNase H


Mass: 35609.926 Da / Num. of mol.: 1 / Mutation: D132N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T4 (virus) / Strain: T4D / Gene: 33.2, das, rnh / Plasmid: pNN2202-D132N / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) PlysS / References: UniProt: P13319, ribonuclease H
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 341 / 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: 50.49 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 200 mM ammonium acetate, 100 mM sodium cacodylate, 12% PEG 8000, 5% 2-methyl-2,4-pentanediol (MPD), pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorDetector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→45 Å / Num. obs: 52759 / Redundancy: 5.8 % / Biso Wilson estimate: 14.47 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 27.9
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.089 / Mean I/σ(I) obs: 10 / Num. unique all: 4156

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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: 1.502→35.989 Å / SU ML: 0.2 / σ(F): 2.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.213 1611 3.05 %5% random data subset
Rwork0.1799 ---
obs0.1809 52756 95.21 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.3 Å2 / ksol: 0.382 e/Å3
Displacement parametersBiso mean: 20.43 Å2
Refinement stepCycle: LAST / Resolution: 1.502→35.989 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2481 0 10 341 2832
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_angle_deg1.32
X-RAY DIFFRACTIONf_bond_d0.012
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.502-1.54570.2398990.20163260X-RAY DIFFRACTION74
1.5457-1.59560.21791220.17093913X-RAY DIFFRACTION88
1.5956-1.65260.18311400.15934157X-RAY DIFFRACTION94
1.6526-1.71880.20291170.16194335X-RAY DIFFRACTION96
1.7188-1.7970.21081340.17864334X-RAY DIFFRACTION97
1.797-1.89180.22771410.18624360X-RAY DIFFRACTION98
1.8918-2.01030.2131350.17944429X-RAY DIFFRACTION99
2.0103-2.16550.22031350.17884431X-RAY DIFFRACTION99
2.1655-2.38340.19381470.1744503X-RAY DIFFRACTION100
2.3834-2.72810.20691360.18184440X-RAY DIFFRACTION100
2.7281-3.43670.21520.18454502X-RAY DIFFRACTION100
3.4367-35.99950.22251530.17154481X-RAY DIFFRACTION99

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