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- PDB-9yk5: 100K X-ray structure of mixed metal D132N Bacillus halodurans RNa... -

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Basic information

Entry
Database: PDB / ID: 9yk5
Title100K X-ray structure of mixed metal D132N Bacillus halodurans RNase H1 complex with RNA/DNA duplex
Components
  • DNA (5'-D(*AP*TP*GP*TP*CP*G)-3')
  • RNA (5'-R(*UP*CP*GP*AP*CP*A)-3')
  • Ribonuclease H
KeywordsHYDROLASE/RNA/DNA / rna hydrolase / nucleic acid binding / RNA/DNA hybrid / mixed metal complex / HYDROLASE / HYDROLASE-RNA-DNA complex
Function / homology
Function and homology information


DNA replication, removal of RNA primer / 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 / Ribonuclease H1 N-terminal domain / : / Ribosomal protein L9/RNase H1, N-terminal / RNase H type-1 domain profile. / Ribonuclease H domain / Ribonuclease H superfamily / Ribonuclease H-like superfamily
Similarity search - Domain/homology
: / PHOSPHITE ION / DNA / RNA / Ribonuclease H
Similarity search - Component
Biological speciesHalalkalibacterium halodurans (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsKovalevsky, A. / Gerlits, O.
Funding support1items
OrganizationGrant numberCountry
Not funded
Citation
Journal: Curr Res Struct Biol / Year: 2026
Title: Structural insights into RNase H catalytic mechanism from room-temperature X-ray and neutron crystallography of apo- and RNA/DNA hybrid-bound enzyme.
Authors: Gerlits, O. / Collins, A. / Kovalevsky, A.
#1: Journal: To Be Published
Title: Generalized X-ray and neutron crystallographic analysis: more accurate and complete structures for biological macromolecules
Authors: Adams, P.D. / Mustyakimov, M. / Afonine, P.V. / Langan, P.
#2: Journal: To Be Published
Title: Structural insights into RNase H catalytic mechanism from room-temperature X-ray and neutron crystallography of apo- and RNA/DNA hybrid-bound enzyme
Authors: Gerlits, O. / Collins, A. / Kovalevsky, A.
History
DepositionOct 6, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2026Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2026Group: Database references / Category: citation
Item: _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ribonuclease H
B: RNA (5'-R(*UP*CP*GP*AP*CP*A)-3')
C: DNA (5'-D(*AP*TP*GP*TP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,8616
Polymers19,7023
Non-polymers1583
Water55831
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2430 Å2
ΔGint-30 kcal/mol
Surface area8510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.619, 37.217, 62.310
Angle α, β, γ (deg.)90.00, 96.61, 90.00
Int Tables number5
Space group name H-MC121

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Components

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

#1: Protein Ribonuclease H / RNase H


Mass: 16003.082 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Halalkalibacterium halodurans (bacteria)
Gene: rnhA, BH0863 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9KEI9, ribonuclease H
#2: RNA chain RNA (5'-R(*UP*CP*GP*AP*CP*A)-3')


Mass: 1875.189 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Halalkalibacterium halodurans (bacteria)
#3: DNA chain DNA (5'-D(*AP*TP*GP*TP*CP*G)-3')


Mass: 1824.228 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Halalkalibacterium halodurans (bacteria)

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Non-polymers , 4 types, 34 molecules

#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-PO3 / PHOSPHITE ION


Mass: 78.972 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.38 Å3/Da / Density % sol: 48.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M HEPES pH 7.5, 0.2 M NaCl, and 12-16% PEG 10,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Jun 11, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2→61.9 Å / Num. obs: 12959 / % possible obs: 99.9 % / Redundancy: 4.3 % / CC1/2: 0.867 / Rmerge(I) obs: 0.137 / Rpim(I) all: 0.082 / Net I/σ(I): 11.5
Reflection shellResolution: 2→2.07 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.686 / Mean I/σ(I) obs: 1 / Num. unique obs: 1294 / CC1/2: 0.624 / Rpim(I) all: 0.373 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
PDB_EXTRACTdata extraction
CrysalisProdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→26.2 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2781 649 5.03 %random
Rwork0.2538 ---
obs0.255 12893 99.49 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→26.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1089 249 2 31 1371
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061396
X-RAY DIFFRACTIONf_angle_d0.821946
X-RAY DIFFRACTIONf_dihedral_angle_d16.14271
X-RAY DIFFRACTIONf_chiral_restr0.038219
X-RAY DIFFRACTIONf_plane_restr0.005203
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.150.37451470.32472422X-RAY DIFFRACTION99
2.16-2.370.2811250.27152428X-RAY DIFFRACTION100
2.37-2.710.30751250.26642443X-RAY DIFFRACTION100
2.71-3.420.23961410.2392449X-RAY DIFFRACTION100
3.42-26.20.22051110.21022502X-RAY DIFFRACTION98

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