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- PDB-9yjl: Joint X-ray/neutron structure of wild-type Bacillus halodurans RN... -

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Basic information

Entry
Database: PDB / ID: 9yjl
TitleJoint X-ray/neutron structure of wild-type 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 / MOLECULAR REPLACEMENT / Resolution: 2.48 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

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Assembly

Deposited unit
A: Ribonuclease H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,1002
Polymers16,0041
Non-polymers961
Water1,06359
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.201, 67.201, 60.814
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: 16004.066 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: 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.: 59 / 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: 2.48 Å3/Da / Density % sol: 50.34 %
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)
SPALLATION SOURCEORNL Spallation Neutron Source MANDI12-4.16
ROTATING ANODERIGAKU MICROMAX-007 HF21.54
Detector
TypeIDDetectorDate
ORNL ANGER CAMERA1POSITION SENSITIVE DETECTORJul 5, 2023
DECTRIS EIGER R 4M2PIXELJul 6, 2023
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1LAUELneutron1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
121
24.161
31.541
Reflection

Entry-ID: 9YJL

Resolution (Å)Num. obs% possible obs (%)Redundancy (%)CC1/2Rmerge(I) obsRpim(I) allDiffraction-IDNet I/σ(I)
2.48-14.7551995.54.60.950.2010.09617.6
1.9-60.81284099.67.40.9970.0580.023225
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allDiffraction-ID% possible all
2.48-2.573.60.2332.84650.2950.131180.6
1.9-1.975.50.6631.612500.6230.297296.7

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Processing

Software
NameVersionClassification
nCNS1.0.8refinement
Mantiddata reduction
LAUENORMdata scaling
PHASERphasing
Refinement

Biso max: 76.01 Å2 / Biso mean: 35.69 Å2 / Biso min: 15.82 Å2 / R Free selection details: random / 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: 47.7202 Å2 / ksol: 0.646568 e/Å3

Resolution (Å)Refine-IDRfactor RfreeRfactor Rfree errorRfactor RworkNum. reflection RfreeNum. reflection RworkNum. reflection obs% reflection Rfree (%)% reflection obs (%)Diffraction-ID
2.48-14.7NEUTRON DIFFRACTION0.3110.0220.279305521455195.593.81
1.9-40X-RAY DIFFRACTION0.2260.0090.21960910951116905.390.82
Refine analyze
Refine-ID#notag 0
X-RAY DIFFRACTION
FreeObs
Luzzati coordinate error0.50.46
Luzzati d res low-5
Luzzati sigma a0.740.66
Luzzati d res high-2.5
NEUTRON DIFFRACTION
FreeObs
Luzzati coordinate error0.250.24
Luzzati d res low-5
Luzzati sigma a0.210.21
Luzzati d res high-1.9
Refine funct minimized
Refine-IDType
X-RAY DIFFRACTIONJoint X-ray/neutron ML
NEUTRON DIFFRACTIONJoint X-ray/neutron ML
Refinement stepCycle: LAST / Resolution: 2.48→14.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1092 0 5 59 1156
Refine LS restraints
Refine-IDTypeDev ideal
NEUTRON DIFFRACTIONx_bond_d0.008
NEUTRON DIFFRACTIONx_angle_deg1.1
NEUTRON DIFFRACTIONx_torsion_deg19.5
NEUTRON DIFFRACTIONx_torsion_impr_deg0.77
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_angle_deg1.1
X-RAY DIFFRACTIONx_torsion_deg19.5
X-RAY DIFFRACTIONx_torsion_impr_deg0.77
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRefine-IDRfactor Rfree error% reflection obs (%)
2.5-2.610.373284.70.388571NEUTRON DIFFRACTION0.0784
2.61-2.740.405365.20.399661NEUTRON DIFFRACTION0.06797.5
2.74-2.920.385446.40.355642NEUTRON DIFFRACTION0.05895.7
2.92-3.140.419365.20.352650NEUTRON DIFFRACTION0.0797.6
3.14-3.450.35537.60.308640NEUTRON DIFFRACTION0.04898
3.45-3.940.292324.50.301678NEUTRON DIFFRACTION0.05297.9
3.94-4.930.314334.60.318687NEUTRON DIFFRACTION0.05599.4
4.93-14.70.451435.90.434685NEUTRON DIFFRACTION0.06994.4
1.9-1.990.271494.80.28980X-RAY DIFFRACTION0.03965.4
1.99-2.090.28624.80.2441236X-RAY DIFFRACTION0.03681.5
2.09-2.220.267735.10.2491345X-RAY DIFFRACTION0.03189.7
2.22-2.390.249714.80.2381395X-RAY DIFFRACTION0.0391.9
2.39-2.630.263855.60.2551436X-RAY DIFFRACTION0.02995.5
2.63-3.020.258905.80.2291469X-RAY DIFFRACTION0.02796.6
3.02-3.80.188885.60.1991491X-RAY DIFFRACTION0.0297.5
3.8-29.410.213915.40.1921599X-RAY DIFFRACTION0.02299.1

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