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- PDB-1i3a: RNASE HII FROM ARCHAEOGLOBUS FULGIDUS WITH COBALT HEXAMMINE CHLORIDE -

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Basic information

Entry
Database: PDB / ID: 1i3a
TitleRNASE HII FROM ARCHAEOGLOBUS FULGIDUS WITH COBALT HEXAMMINE CHLORIDE
ComponentsRIBONUCLEASE HII
KeywordsHYDROLASE / mixed beta sheet / helix-loop-helix
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
COBALT HEXAMMINE(III) / Ribonuclease HII
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsChapados, B.R. / Chai, Q. / Hosfield, D.J. / Qiu, J. / Shen, B. / Tainer, J.A.
CitationJournal: J.Mol.Biol. / Year: 2001
Title: Structural biochemistry of a type 2 RNase H: RNA primer recognition and removal during DNA replication.
Authors: Chapados, B.R. / Chai, Q. / Hosfield, D.J. / Qiu, J. / Shen, B. / Tainer, J.A.
History
DepositionFeb 13, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 11, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 3, 2024Group: 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
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RIBONUCLEASE HII
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5542
Polymers25,3931
Non-polymers1611
Water2,144119
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.555, 74.555, 139.684
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-351-

HOH

DetailsThe biologically relevent molecule is a monomer in the asymmetric unit

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Components

#1: Protein RIBONUCLEASE HII / RNASE H11


Mass: 25393.240 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Gene: RNHB / Plasmid: PET28B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O29634, ribonuclease H
#2: Chemical ChemComp-NCO / COBALT HEXAMMINE(III)


Mass: 161.116 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CoH18N6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 119 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.21 Å3/Da / Density % sol: 44.24 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 10% MPEG 5000, 10% butanol, 20 mM sodium citrate, 100 mM Tris pH 8.5, (soak: 10mM Co(III)(NH2)6), VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal grow
*PLUS
Details: drop consists of equal amounts of protein and precipitant solutions
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
140 mg/mlprotein1drop
210 %mPEG50001reservoirprecipitant
310 %butanol1reservoirprecipitant
420 mMsodium citrate1reservoirprecipitant
5100 mMTris-HCl1reservoirprecipitant

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Data collection

DiffractionMean temperature: 94 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.863 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 17, 2000
RadiationMonochromator: NULL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.863 Å / Relative weight: 1
ReflectionResolution: 2.15→35 Å / Num. all: 13210 / Num. obs: 13210 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.3 % / Biso Wilson estimate: 14.6 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 14.3
Reflection shellResolution: 2.15→2.23 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.414 / % possible all: 93.3
Reflection
*PLUS
Num. measured all: 82747
Reflection shell
*PLUS
% possible obs: 93.3 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS0.9refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: ARNASE HII refined model (rcsb012848)

Resolution: 2.15→19.75 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: NULL
RfactorNum. reflection% reflectionSelection details
Rfree0.272 630 5 %RANDOM
Rwork0.223 ---
all0.223 13141 --
obs0.223 12057 --
Refinement stepCycle: LAST / Resolution: 2.15→19.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1581 0 7 119 1707
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg1.17
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scangle_it

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