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- PDB-2dff: Crystal structure of Tk-RNase HII(1-204)-C -

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Basic information

Entry
Database: PDB / ID: 2dff
TitleCrystal structure of Tk-RNase HII(1-204)-C
ComponentsRibonuclease HII
KeywordsHYDROLASE / Chameleon sequence / ribonuclease HII / Thermococcus kodakaraensis / fusion protein
Function / homology
Function and homology information


ribonuclease H2 complex / DNA replication, removal of RNA primer / ribonuclease H / mismatch repair / RNA-DNA hybrid ribonuclease activity / manganese ion binding / RNA binding / cytoplasm
Similarity search - Function
Ribonuclease HII, archaea / Ribonuclease hii. Domain 2 / Ribonuclease HII, helix-loop-helix cap domain superfamily / Ribonuclease H2, subunit A / Ribonuclease HII/HIII / Ribonuclease HII/HIII domain / Ribonuclease HII / Ribonuclease (RNase) H type-2 domain profile. / Ribonuclease H-like superfamily/Ribonuclease H / Nucleotidyltransferase; domain 5 ...Ribonuclease HII, archaea / Ribonuclease hii. Domain 2 / Ribonuclease HII, helix-loop-helix cap domain superfamily / Ribonuclease H2, subunit A / Ribonuclease HII/HIII / Ribonuclease HII/HIII domain / Ribonuclease HII / Ribonuclease (RNase) H type-2 domain profile. / Ribonuclease H-like superfamily/Ribonuclease H / Nucleotidyltransferase; domain 5 / Arc Repressor Mutant, subunit A / Ribonuclease H superfamily / Ribonuclease H-like superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesThermococcus kodakarensis (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsKatagiri, Y. / Takano, K. / Chon, H. / Matsumura, H. / Koga, Y. / Kanaya, S.
CitationJournal: Proteins / Year: 2007
Title: Conformational contagion in a protein: Structural properties of a chameleon sequence
Authors: Takano, K. / Katagiri, Y. / Mukaiyama, A. / Chon, H. / Matsumura, H. / Koga, Y. / Kanaya, S.
History
DepositionMar 1, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 6, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 999SEQUENCE The C-terminal 9 residues, TQDMINKST are chameleon sequencein.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ribonuclease HII


Theoretical massNumber of molelcules
Total (without water)23,9621
Polymers23,9621
Non-polymers00
Water79344
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.525, 67.109, 52.209
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a monomer generated from the monomer in the asymmetric unit.

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Components

#1: Protein Ribonuclease HII / RNase HII


Mass: 23962.420 Da / Num. of mol.: 1 / Mutation: chameleon sequence
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus kodakarensis (archaea) / Strain: KOD1 / Plasmid: pJAL700K-C02 / Production host: Escherichia coli (E. coli) / Strain (production host): HB101 / References: UniProt: O74035, ribonuclease H
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / 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: 2.14 Å3/Da / Density % sol: 42.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2M Magnesium Chloride hexahydrate, 20% PEG 3350, 10% glycerol, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 28, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 6307 / % possible obs: 93.9 % / Biso Wilson estimate: 22.3 Å2
Reflection shellResolution: 2.6→2.69 Å / % possible all: 71.3

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Processing

Software
NameVersionClassification
CNS1refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1IO2

1io2


Resolution: 2.7→38.96 Å / Rfactor Rfree error: 0.017 / Data cutoff high absF: 1152174.74 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.299 322 5.6 %RANDOM
Rwork0.248 ---
obs0.248 5787 96.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 117.793 Å2 / ksol: 0.407882 e/Å3
Displacement parametersBiso mean: 52.7 Å2
Baniso -1Baniso -2Baniso -3
1--21.99 Å20 Å20 Å2
2---13.21 Å20 Å2
3---35.2 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.54 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a0.62 Å0.41 Å
Refinement stepCycle: LAST / Resolution: 2.7→38.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1569 0 0 44 1613
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.82
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.077 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.423 30 3.8 %
Rwork0.323 766 -
obs--82.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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