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- PDB-9yjm: Joint X-ray/neutron structure of D132N Bacillus halodurans RNase ... -

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Basic information

Entry
Database: PDB / ID: 9yjm
TitleJoint X-ray/neutron structure of D132N Bacillus halodurans RNase H1 in the apo-form
ComponentsRibonuclease H
KeywordsHYDROLASE / rna hydrolase / nucleic acid binding
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
DEUTERATED WATER / Ribonuclease H
Similarity search - Component
Biological speciesHalalkalibacterium halodurans (bacteria)
MethodX-RAY DIFFRACTION / NEUTRON DIFFRACTION / NUCLEAR REACTOR / MOLECULAR REPLACEMENT / Resolution: 2.4 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 3, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,0992
Polymers16,0031
Non-polymers961
Water86548
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.417, 67.417, 60.798
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Ribonuclease H / RNase H


Mass: 16003.082 Da / Num. of mol.: 1 / Mutation: D132N
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: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-DOD / water


Mass: 18.015 Da / Num. of mol.: 48 / Source method: isolated from a natural source / Formula: D2O / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

Experiment
MethodNumber of used crystals
X-RAY DIFFRACTION1
NEUTRON DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.49 Å3/Da / Density % sol: 50.65 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 0.1 M NaOAc pH 5.0, 0.2 M (NH4)2SO4, and 20% PEG 3350

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Data collection

Diffraction
IDMean temperature (K)Crystal-IDSerial crystal experiment
12931N
22931N
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
NUCLEAR REACTORORNL High Flux Isotope Reactor CG4D12.8-4.5
ROTATING ANODERIGAKU MICROMAX-007 HF21.54
Detector
TypeIDDetectorDate
MAATEL IMAGINE1IMAGE PLATEFeb 28, 2024
DECTRIS EIGER R 4M2PIXELMar 1, 2024
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1LAUELneutron1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
12.81
24.51
31.541
Reflection

Entry-ID: 9YJM

Resolution (Å)Num. obs% possible obs (%)Redundancy (%)CC1/2Rmerge(I) obsRpim(I) allDiffraction-IDNet I/σ(I)
2.4-41.74505981.35.60.9680.1430.05615.7
2.2-60.88440954.30.9840.140.07628.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allDiffraction-ID% possible all
2.4-2.5340.3262.45770.7360.156164.3
2.2-2.284.40.6631.28440.5540.355293.8

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Processing

Software
NameVersionClassification
LAUEGENdata reduction
SCALAdata scaling
PHASERphasing
nCNS1.0.8refinement
Refinement

Biso max: 82.44 Å2 / Biso mean: 35.84 Å2 / Biso min: 17.38 Å2 / % reflection Rfree: 5 % / Cross valid method: FREE R-VALUE / σ(F): 2.5 / Method to determine structure: MOLECULAR REPLACEMENT / Stereochemistry target values: Joint X-ray/neutron ML / Solvent model: CNS bulk solvent model used / Bsol: 10 Å2 / ksol: 0.533594 e/Å3

Resolution (Å)Refine-IDRfactor RfreeRfactor Rfree errorRfactor RworkNum. reflection RfreeNum. reflection RworkNum. reflection obs% reflection obs (%)Diffraction-IDR Free selection details
2.4-40NEUTRON DIFFRACTION0.2560.0260.2412194118433768.41
2.2-40X-RAY DIFFRACTION0.2340.0120.2043386427676580.42random
Refine analyze
Refine-ID#notag 0
NEUTRON DIFFRACTION
FreeObs
Luzzati coordinate error0.460.42
Luzzati d res low-5
Luzzati sigma a-0.5
X-RAY DIFFRACTION
FreeObs
Luzzati coordinate error0.290.24
Luzzati d res low-5
Luzzati sigma a-0.25
Refine funct minimized
Refine-IDType
X-RAY DIFFRACTIONJoint X-ray/neutron ML
NEUTRON DIFFRACTIONJoint X-ray/neutron ML
Refinement stepCycle: LAST / Resolution: 2.4→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1092 0 5 48 1145
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_angle_deg1
X-RAY DIFFRACTIONx_torsion_deg23.8
X-RAY DIFFRACTIONx_torsion_impr_deg0.75
NEUTRON DIFFRACTIONx_bond_d0.008
NEUTRON DIFFRACTIONx_angle_deg1
NEUTRON DIFFRACTIONx_torsion_deg23.8
NEUTRON DIFFRACTIONx_torsion_impr_deg0.75
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRefine-IDRfactor Rfree error% reflection obs (%)
2.42-2.530.359154.40.357323NEUTRON DIFFRACTION0.09343
2.53-2.670.333267.20.383337NEUTRON DIFFRACTION0.06546.9
2.67-2.840.434194.50.35406NEUTRON DIFFRACTION0.155.1
2.84-3.050.399255.30.33450NEUTRON DIFFRACTION0.0860.9
3.05-3.360.351264.40.315561NEUTRON DIFFRACTION0.06973.7
3.36-3.850.312324.90.291619NEUTRON DIFFRACTION0.05583.8
3.85-4.840.344395.40.289679NEUTRON DIFFRACTION0.05589.5
4.84-29.480.475374.70.485743NEUTRON DIFFRACTION0.07891.7
2.2-2.30.277233.70.268594X-RAY DIFFRACTION0.05860.3
2.3-2.420.29385.50.235659X-RAY DIFFRACTION0.04767.5
2.42-2.570.323435.70.231710X-RAY DIFFRACTION0.04972.5
2.57-2.770.234150.208786X-RAY DIFFRACTION0.03678.8
2.77-3.050.2495.50.197838X-RAY DIFFRACTION0.02985.8
3.05-3.490.233940.207928X-RAY DIFFRACTION0.03791.1
3.49-4.390.194585.90.167918X-RAY DIFFRACTION0.02692.7
4.39-26.320.209474.50.195994X-RAY DIFFRACTION0.0392.8

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