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- PDB-2e4l: Thermodynamic and Structural Analysis of Thermolabile RNase HI fr... -

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Basic information

Entry
Database: PDB / ID: 2e4l
TitleThermodynamic and Structural Analysis of Thermolabile RNase HI from Shewanella oneidensis MR-1
ComponentsRibonuclease HI
KeywordsHYDROLASE / endoribonuclease / RNase HI / Shewanella oneidensis MR-1
Function / homology
Function and homology information


DNA replication, removal of RNA primer / ribonuclease H / RNA-DNA hybrid ribonuclease activity / nucleic acid binding / magnesium ion binding / cytoplasm
Similarity search - Function
Ribonuclease HI / : / Ribonuclease H-like superfamily/Ribonuclease H / RNase H / RNase H type-1 domain profile. / Ribonuclease H domain / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily / Ribonuclease H-like superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesShewanella oneidensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsTadokoro, T. / You, D.J. / Chon, H. / Matsumura, H. / Koga, Y. / Takano, K. / Kanaya, S.
CitationJournal: Biochemistry / Year: 2007
Title: Structural, thermodynamic, and mutational analyses of a psychrotrophic RNase HI.
Authors: Tadokoro, T. / You, D.J. / Abe, Y. / Chon, H. / Matsumura, H. / Koga, Y. / Takano, K. / Kanaya, S.
History
DepositionDec 13, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 1, 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 ...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 / pdbx_struct_special_symmetry
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ribonuclease HI


Theoretical massNumber of molelcules
Total (without water)17,8071
Polymers17,8071
Non-polymers00
Water2,936163
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.128, 77.128, 76.661
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number89
Space group name H-MP422
Components on special symmetry positions
IDModelComponents
11A-163-

HOH

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Components

#1: Protein Ribonuclease HI / RNase HI


Mass: 17807.359 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella oneidensis (bacteria) / Strain: MR-1 / Gene: rnhA / Plasmid: pET25b / Production host: Escherichia coli (E. coli) / References: UniProt: Q8EE30, ribonuclease H
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 163 / 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: 3.1 Å3/Da / Density % sol: 60.6 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorDate: Mar 9, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. obs: 43245 / % possible obs: 99.7 % / Biso Wilson estimate: 18.2 Å2 / Rmerge(I) obs: 0.096 / Net I/σ(I): 23.5
Reflection shellResolution: 1.8→1.86 Å / Rmerge(I) obs: 0.518 / Mean I/σ(I) obs: 2.61 / % possible all: 98.2

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Processing

Software
NameVersionClassification
REFMAC5refinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2RN2

2rn2


Resolution: 2→27.22 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.928 / SU B: 4.12 / SU ML: 0.119 / Cross valid method: THROUGHOUT / ESU R: 0.144 / ESU R Free: 0.133 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21851 801 4.9 %RANDOM
Rwork0.18871 ---
obs0.19017 15432 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 23.202 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2→27.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1223 0 0 163 1386
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0350.0211252
X-RAY DIFFRACTIONr_bond_other_d0.0010.021111
X-RAY DIFFRACTIONr_angle_refined_deg2.3141.9281692
X-RAY DIFFRACTIONr_angle_other_deg1.01532597
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1363154
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.16415229
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.290.2179
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.021389
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02244
X-RAY DIFFRACTIONr_nbd_refined0.2560.3282
X-RAY DIFFRACTIONr_nbd_other0.2490.31064
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2370.5123
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.4530.317
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1410.320
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.5440.519
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.7281.5767
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.94921226
X-RAY DIFFRACTIONr_scbond_it4.4013485
X-RAY DIFFRACTIONr_scangle_it6.7284.5466
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.259 56
Rwork0.196 1133
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top

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