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- PDB-1eke: CRYSTAL STRUCTURE OF CLASS II RIBONUCLEASE H (RNASE HII) WITH MES... -

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Basic information

Entry
Database: PDB / ID: 1eke
TitleCRYSTAL STRUCTURE OF CLASS II RIBONUCLEASE H (RNASE HII) WITH MES LIGAND
ComponentsRIBONUCLEASE HII
KeywordsHYDROLASE / Nuclease / Endonuclease / Structural Genomics / BSGC structure funded by NIH / Protein Structure Initiative / PSI / Berkeley Structural Genomics Center
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 H2, subunit A / Ribonuclease HII, helix-loop-helix cap domain superfamily / Ribonuclease HII/HIII / Ribonuclease HII/HIII domain / Ribonuclease HII / Ribonuclease H-like superfamily/Ribonuclease H / Nucleotidyltransferase; domain 5 / Arc Repressor Mutant, subunit A ...Ribonuclease HII, archaea / Ribonuclease hii. Domain 2 / Ribonuclease H2, subunit A / Ribonuclease HII, helix-loop-helix cap domain superfamily / Ribonuclease HII/HIII / Ribonuclease HII/HIII domain / Ribonuclease HII / 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 speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD PHASING / Resolution: 2 Å
AuthorsLai, L.H. / Yokota, H. / Hung, L.W. / Kim, R. / Kim, S.H. / Berkeley Structural Genomics Center (BSGC)
CitationJournal: Structure / Year: 2000
Title: Crystal structure of archaeal RNase HII: a homologue of human major RNase H
Authors: Lai, L. / Yokota, H. / Hung, L.W. / Kim, R. / Kim, S.H.
History
DepositionMar 7, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 13, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RIBONUCLEASE HII
B: RIBONUCLEASE HII
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,7784
Polymers53,3872
Non-polymers3902
Water5,639313
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.484, 55.424, 72.145
Angle α, β, γ (deg.)90.00, 111.85, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein RIBONUCLEASE HII


Mass: 26693.609 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Production host: Escherichia coli (E. coli) / References: UniProt: Q57599, ribonuclease H
#2: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 313 / Fragment: 2-(N-MORPHOLINO)ETHANESULFONATE / 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: 2.36 Å3/Da / Density % sol: 48 %
Crystal growTemperature: 293 K / Method: seeding / pH: 6.2
Details: PEG 3350, potassium thiocyanate, magnesium chloride, pH 6.2, seeding, temperature 293K
Crystal grow
*PLUS
Temperature: 22 ℃ / Method: vapor diffusion, hanging drop / Details: used seeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
115 mg/mlprotein1drop
225 mMMES1drop
31 mM1dropMgCl2
42 mMdithiothreitol1drop
50.1 M1dropKSCN
69 %PEG33501drop
70.2 M1reservoirKSCN
818 %PEG33501reservoir

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1
DetectorDetector: CCD
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. all: 30523 / Num. obs: 29715 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Biso Wilson estimate: 14.1 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 18.3
Reflection shellResolution: 2→2.03 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.225 / Num. unique all: 1410 / % possible all: 94.6
Reflection
*PLUS
Num. measured all: 173694
Reflection shell
*PLUS
% possible obs: 94.6 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNS0.5refinement
RefinementMethod to determine structure: MAD PHASING / Resolution: 2→20 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 346794.7 / Data cutoff high rms absF: 10000 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: cns / Details: Used Maximum likelihood target
RfactorNum. reflection% reflectionSelection details
Rfree0.262 1467 4.9 %RANDOM
Rwork0.21 ---
all0.21256 30523 --
obs0.21 29715 97.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 45.92 Å2 / ksol: 0.325 e/Å3
Displacement parametersBiso mean: 33.7 Å2
Baniso -1Baniso -2Baniso -3
1-7.96 Å20 Å2-2.83 Å2
2---4.74 Å20 Å2
3----3.22 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.23 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3585 0 24 341 3950
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d21.1
X-RAY DIFFRACTIONc_improper_angle_d0.72
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.306 218 5 %
Rwork0.25 4186 -
obs--86.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
Software
*PLUS
Name: CNS / Version: 0.5 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 4.9 % / Rfactor obs: 0.21 / Rfactor Rwork: 0.21
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 33.7 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.72
LS refinement shell
*PLUS
Rfactor Rfree: 0.306 / % reflection Rfree: 5 % / Rfactor Rwork: 0.25

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