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- PDB-4ibn: Crystal structure of LC9-RNase H1, a type 1 RNase H with the type... -

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Basic information

Entry
Database: PDB / ID: 4ibn
TitleCrystal structure of LC9-RNase H1, a type 1 RNase H with the type 2 active-site motif
ComponentsRibonuclease H
KeywordsHYDROLASE / RNase H / Ribonuclease H / Hydrolase'
Function / homology
Function and homology information


ribonuclease H / RNA-DNA hybrid ribonuclease activity / nucleic acid binding
Similarity search - Function
Ribonuclease HI / Ribonuclease H-like superfamily/Ribonuclease H / RNase H / 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
Biological speciesuncultured organism (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.62 Å
AuthorsNguyen, T.-N. / You, D.-J. / Kanaya, E. / Koga, Y. / Kanaya, S.
CitationJournal: Febs Lett. / Year: 2013
Title: Crystal structure of metagenome-derived LC9-RNase H1 with atypical DEDN active site motif
Authors: Nguyen, T.-N. / You, D.-J. / Kanaya, E. / Koga, Y. / Kanaya, S.
History
DepositionDec 9, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 20, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ribonuclease H


Theoretical massNumber of molelcules
Total (without water)23,8331
Polymers23,8331
Non-polymers00
Water2,576143
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.633, 39.913, 50.254
Angle α, β, γ (deg.)90.000, 102.640, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Ribonuclease H / / LC9-RNase H1


Mass: 23832.584 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) uncultured organism (environmental samples)
Plasmid: pET25b / Production host: Escherichia coli (E. coli) / Strain (production host): MIC2067(DE3) / References: UniProt: E0X765, ribonuclease H
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 143 / 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: 1.71 Å3/Da / Density % sol: 28.05 % / Mosaicity: 0.962 °
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 100mM Tris-HCl, 200mM MgCl2.6H2O, 30% PEG 4000, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: BRUKER SMART 6500 / Detector: CCD / Date: Jun 9, 2012
RadiationMonochromator: horizontal focusing mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.62→50 Å / Num. obs: 20537 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 13.7 % / Rmerge(I) obs: 0.077 / Rsym value: 0.077 / Χ2: 0.993 / Net I/σ(I): 43.648
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.62-1.6513.70.34910000.367196.2
1.65-1.68150.31710200.3741100
1.68-1.7115.10.28610090.3991100
1.71-1.75150.25710530.4151100
1.75-1.7815.10.2259950.4341100
1.78-1.82150.18110330.491100
1.82-1.8715.20.1710200.5571100
1.87-1.9215.10.1510400.6141100
1.92-1.9815.10.13410100.6771100
1.98-2.0415.10.12110390.7731100
2.04-2.1115.10.10410340.8551100
2.11-2.215.10.110450.961100
2.2-2.315.20.09410391.0161100
2.3-2.4215.10.08510191.0731100
2.42-2.5715.10.08210251.1961100
2.57-2.7715.10.08810471.5171100
2.77-3.0514.80.09210412.2731100
3.05-3.4914.40.08310292.565199.1
3.49-4.414.20.05910011.886195.1
4.4-5013.70.0510381.527194.9

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.88 Å40.63 Å
Translation1.88 Å40.63 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2EHG

2ehg


Resolution: 1.62→49.04 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.949 / WRfactor Rfree: 0.2203 / WRfactor Rwork: 0.1814 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8556 / SU B: 1.881 / SU ML: 0.067 / SU R Cruickshank DPI: 0.1101 / SU Rfree: 0.1069 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.11 / ESU R Free: 0.107 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2152 1039 5.1 %RANDOM
Rwork0.1771 ---
all0.179 20537 --
obs0.179 20485 99.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 69.29 Å2 / Biso mean: 25.5324 Å2 / Biso min: 13.11 Å2
Baniso -1Baniso -2Baniso -3
1-0.93 Å2-0 Å20.89 Å2
2--0.39 Å2-0 Å2
3----0.93 Å2
Refinement stepCycle: LAST / Resolution: 1.62→49.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1613 0 0 143 1756
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0211655
X-RAY DIFFRACTIONr_angle_refined_deg1.0221.9142255
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3725210
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.5632280
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.59315236
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4511520
X-RAY DIFFRACTIONr_chiral_restr0.0880.2235
X-RAY DIFFRACTIONr_gen_planes_refined0.0170.0211323
X-RAY DIFFRACTIONr_mcbond_it1.8521.51043
X-RAY DIFFRACTIONr_mcangle_it2.99121657
X-RAY DIFFRACTIONr_scbond_it4.3433612
X-RAY DIFFRACTIONr_scangle_it6.8624.5598
LS refinement shellResolution: 1.621→1.663 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.212 76 -
Rwork0.175 1417 -
all-1493 -
obs--99.14 %

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