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- PDB-2r7y: Selenium Derivatized RNA/DNA Hybrid in complex with RNase H CATAL... -

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Basic information

Entry
Database: PDB / ID: 2r7y
TitleSelenium Derivatized RNA/DNA Hybrid in complex with RNase H CATALYTIC DOMAIN MUTANT D132N
Components
  • DNA (5'-D(*DAP*DTP*(SDG)P*DTP*DCP*(SDG))-3')
  • RNA (5'-R(*UP*CP*GP*AP*CP*A)-3')
  • Ribonuclease H
KeywordsHydrolase/RNA/DNA / Selenium-DNA/RNA / RNASE H / RIBONUCLEASE H RNA-DNA Complex / Cytoplasm / Endonuclease / Hydrolase / Magnesium / Manganese / Metal-binding / Hydrolase-RNA-DNA COMPLEX
Function / homology
Function and homology information


ribonuclease H / RNA-DNA hybrid ribonuclease activity / nucleic acid binding / metal ion binding / cytoplasm
Similarity search - Function
Ribonuclease H, Bacteroides-type / Ribonuclease H1, N-terminal / Ribonuclease H1, N-terminal domain superfamily / Caulimovirus viroplasmin / Ribonuclease H-like superfamily/Ribonuclease H / Ribosomal protein L9/RNase H1, N-terminal / Ribonuclease H domain / RNase H type-1 domain profile. / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily ...Ribonuclease H, Bacteroides-type / Ribonuclease H1, N-terminal / Ribonuclease H1, N-terminal domain superfamily / Caulimovirus viroplasmin / Ribonuclease H-like superfamily/Ribonuclease H / Ribosomal protein L9/RNase H1, N-terminal / Ribonuclease H domain / RNase H type-1 domain profile. / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily / Ribonuclease H-like superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / DNA / RNA / Ribonuclease H
Similarity search - Component
Biological speciesBacillus halodurans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsJiang, J.-S. / Gerlits, O. / Huang, Z.
CitationJournal: To be Published
Title: Selenium Derivatized RNA/DNA Hybrid in complex with RNase H CATALYTIC DOMAIN MUTANT D132N
Authors: Jiang, J.-S. / Gerlits, O. / Huang, Z.
History
DepositionSep 10, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 6, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: RNA (5'-R(*UP*CP*GP*AP*CP*A)-3')
C: DNA (5'-D(*DAP*DTP*(SDG)P*DTP*DCP*(SDG))-3')
A: Ribonuclease H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2126
Polymers19,0693
Non-polymers1443
Water3,207178
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)80.660, 37.819, 61.937
Angle α, β, γ (deg.)90.00, 96.60, 90.00
Int Tables number5
Space group name H-MC121

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Components

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RNA chain / DNA chain / Protein , 3 types, 3 molecules BCA

#1: RNA chain RNA (5'-R(*UP*CP*GP*AP*CP*A)-3')


Mass: 1875.189 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain DNA (5'-D(*DAP*DTP*(SDG)P*DTP*DCP*(SDG))-3')


Mass: 1950.150 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein Ribonuclease H / / RNase H


Mass: 15243.206 Da / Num. of mol.: 1 / Mutation: D132N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus halodurans (bacteria) / Gene: rnhA / Plasmid: PET15B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 PLYSS / References: UniProt: Q9KEI9, ribonuclease H

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Non-polymers , 3 types, 181 molecules

#4: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 178 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50.85 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M MES, 12% PEG 20000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1MES11
2PEG 2000011
3MES12
4PEG 2000012

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.9797,0.9800,0.9795
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Aug 12, 2006
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97971
20.981
30.97951
ReflectionResolution: 1.8→40 Å / Num. all: 17460 / Num. obs: 17227 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Biso Wilson estimate: 19 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 15.3
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.278 / Mean I/σ(I) obs: 10.5 / Num. unique all: 1707 / % possible all: 98.6

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Processing

Software
NameVersionClassification
CNS1.2refinement
CBASSdata collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 1.8→23.45 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 873417.7 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.231 1187 7.3 %RANDOM
Rwork0.185 ---
all0.189 17460 --
obs0.185 16187 92.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 58.1419 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 25.1 Å2
Baniso -1Baniso -2Baniso -3
1-3.24 Å20 Å2-0.96 Å2
2--0.48 Å20 Å2
3----3.72 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.05 Å0.06 Å
Refinement stepCycle: LAST / Resolution: 1.8→23.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1077 245 6 178 1506
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d20.2
X-RAY DIFFRACTIONc_improper_angle_d1.19
X-RAY DIFFRACTIONc_mcbond_it1.341.5
X-RAY DIFFRACTIONc_mcangle_it1.962
X-RAY DIFFRACTIONc_scbond_it2.142
X-RAY DIFFRACTIONc_scangle_it3.12.5
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.225 153 7 %
Rwork0.2 2043 -
obs--76.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramdna-rna.top
X-RAY DIFFRACTION3ion.paramwater.top
X-RAY DIFFRACTION4dna-rna_ums.parion.top
X-RAY DIFFRACTION5ums.top

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