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- PDB-2ehg: Crystal structure of hyperthermophilic archaeal RNase HI -

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Basic information

Entry
Database: PDB / ID: 2ehg
TitleCrystal structure of hyperthermophilic archaeal RNase HI
Componentsribonuclease HI
KeywordsHYDROLASE / RNase HI / hyperthermophilic archaeon / Sulfolobus tokodaii / double-stranded RNA-dependent RNase
Function / homology
Function and homology information


ribonuclease H / RNA-DNA hybrid ribonuclease activity / DNA binding / RNA binding / metal ion binding / cytoplasm
Similarity search - Function
: / Reverse transcriptase-like / Ribonuclease H-like superfamily/Ribonuclease 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
Ribonuclease HI / :
Similarity search - Component
Biological speciesSulfolobus tokodaii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.6 Å
AuthorsYou, D.J. / Chon, H. / Koga, Y. / Takano, K. / Kanaya, S.
CitationJournal: To be Published
Title: Crystal Structure of Type 1 RNase H from a Hyperthermophilic Archaeon with Double-stranded RNA-dependent RNase Activity
Authors: You, D.J. / Chon, H. / Koga, Y. / Takano, K. / Kanaya, S.
History
DepositionMar 6, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 11, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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)16,8361
Polymers16,8361
Non-polymers00
Water2,504139
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.206, 39.206, 91.147
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein ribonuclease HI / Hypothetical protein ST0753


Mass: 16835.830 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus tokodaii (archaea) / Strain: 7 / Plasmid: pET25b / Production host: Escherichia coli (E. coli) / Strain (production host): MIC2067(DE3)
References: UniProt: Q973Z8, UniProt: F9VN79*PLUS, ribonuclease H
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.08 Å3/Da / Density % sol: 40.86 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 10.5
Details: 0.1M CAPS-NaOH, 30% PEG400, pH 10.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSPring-8 BL41XU11
SYNCHROTRONSPring-8 BL41XU20.9796, 0.9793, 0.973
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDOct 3, 2005
ADSC QUANTUM 3152CCDNov 28, 2005
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.97961
30.97931
40.9731
ReflectionResolution: 1.52→26.52 Å / Num. obs: 21009 / % possible obs: 99.1 % / Biso Wilson estimate: 17.7 Å2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 28.1
Reflection shellResolution: 1.52→1.57 Å / Rmerge(I) obs: 0.199 / Mean I/σ(I) obs: 3.8 / % possible all: 93.9

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Processing

Software
NameVersionClassification
CNS1refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.6→26.52 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 933828.92 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.218 874 4.8 %RANDOM
Rwork0.194 ---
obs0.194 18091 99.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 51.7455 Å2 / ksol: 0.397575 e/Å3
Displacement parametersBiso mean: 16.8 Å2
Baniso -1Baniso -2Baniso -3
1-1.31 Å20 Å20 Å2
2--1.31 Å20 Å2
3----2.63 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.2 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a0.08 Å0.04 Å
Refinement stepCycle: LAST / Resolution: 1.6→26.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1180 0 0 139 1319
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1
X-RAY DIFFRACTIONc_dihedral_angle_d22.1
X-RAY DIFFRACTIONc_improper_angle_d0.74
X-RAY DIFFRACTIONc_mcbond_it0.651.5
X-RAY DIFFRACTIONc_mcangle_it1.072
X-RAY DIFFRACTIONc_scbond_it1.312
X-RAY DIFFRACTIONc_scangle_it2.042.5
LS refinement shellResolution: 1.6→1.7 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.222 142 4.8 %
Rwork0.201 2846 -
obs--99.7 %
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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