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- PDB-7w89: The structure of Deinococcus radiodurans Yqgf -

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Basic information

Entry
Database: PDB / ID: 7w89
TitleThe structure of Deinococcus radiodurans Yqgf
ComponentsPutative pre-16S rRNA nuclease
KeywordsHYDROLASE / RNase / RNA binding
Function / homology
Function and homology information


rRNA 5'-end processing / exonuclease activity / endonuclease activity / Hydrolases; Acting on ester bonds / cytoplasm
Similarity search - Function
Putative pre-16S rRNA nuclease / Holliday junction resolvase / YqgF/RNase H-like domain / YqgF/RNase H-like domain / Likely ribonuclease with RNase H fold. / YqgF/RNase H-like domain superfamily / Nucleotidyltransferase; domain 5 / Ribonuclease H-like superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesDeinococcus radiodurans (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.50006105724 Å
AuthorsCheng, K.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32100017 China
CitationJournal: Mbio / Year: 2022
Title: Biochemical and Structural Study of RuvC and YqgF from Deinococcus radiodurans.
Authors: Sun, Y. / Yang, J. / Xu, G. / Cheng, K.
History
DepositionDec 7, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 17, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 7, 2022Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Nov 9, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative pre-16S rRNA nuclease


Theoretical massNumber of molelcules
Total (without water)14,8411
Polymers14,8411
Non-polymers00
Water2,810156
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6450 Å2
Unit cell
Length a, b, c (Å)73.070, 49.380, 33.520
Angle α, β, γ (deg.)90.000, 101.665, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-290-

HOH

21A-331-

HOH

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Components

#1: Protein Putative pre-16S rRNA nuclease


Mass: 14841.159 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus radiodurans (radioresistant)
Strain: ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422
Gene: DR_2509 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9RRI2, Hydrolases; Acting on ester bonds
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 156 / 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: 2 Å3/Da / Density % sol: 38.35 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1 M MgCl2, 0.1M HEPES (pH 7.0), 15% PEG 4000

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 20, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.5→27.07 Å / Num. obs: 19580 / % possible obs: 93.7 % / Redundancy: 4.5 % / Biso Wilson estimate: 16.5 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 26.04
Reflection shellResolution: 1.5→1.54 Å / Rmerge(I) obs: 0.132 / Num. unique obs: 1430

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Processing

Software
NameVersionClassification
Cootmodel building
PHENIX1.11.1_2575refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OVQ

1ovq


Resolution: 1.50006105724→27.0688711921 Å / SU ML: 0.11487136053 / Cross valid method: FREE R-VALUE / σ(F): 1.4025631195 / Phase error: 18.1688009337
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.19556726321 874 4.87859335752 %
Rwork0.194754700845 17041 -
obs0.194792841433 17915 95.2064622416 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 15.6326682596 Å2
Refinement stepCycle: LAST / Resolution: 1.50006105724→27.0688711921 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms943 0 0 156 1099
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0101449670599955
X-RAY DIFFRACTIONf_angle_d1.042680110181289
X-RAY DIFFRACTIONf_chiral_restr0.0441592537837150
X-RAY DIFFRACTIONf_plane_restr0.00505225157136168
X-RAY DIFFRACTIONf_dihedral_angle_d20.6489825135363
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5001-1.5940.2244912545721450.1882566700772886X-RAY DIFFRACTION96.8061322261
1.594-1.71710.2089305406481450.1938109115522869X-RAY DIFFRACTION97.1944534021
1.7171-1.88990.1854137135981500.183758780132901X-RAY DIFFRACTION97.7571291253
1.8899-2.16320.193458151081650.1838742395632906X-RAY DIFFRACTION98.334934358
2.1632-2.7250.1860188401121430.1856381518472959X-RAY DIFFRACTION98.6327503975
2.725-2.80.1981538585121260.19812520X-RAY DIFFRACTION82.7909887359
Refinement TLS params.Method: refined / Origin x: 79.2987867651 Å / Origin y: 0.666036948163 Å / Origin z: 41.8795882323 Å
111213212223313233
T0.0214922856441 Å2-0.00776716574685 Å2-0.00264439627206 Å2-0.027940296381 Å20.00221075256778 Å2--0.0400536659064 Å2
L1.37159993344 °2-0.271856075028 °20.0566944427467 °2-1.39123061457 °2-0.0708927221804 °2--1.80396521618 °2
S-0.0356856785345 Å °0.00246621617988 Å °0.0392896101715 Å °0.0267066672801 Å °-0.028269279166 Å °-0.132455424534 Å °-0.0761003853795 Å °0.117348676186 Å °0.0371544328151 Å °
Refinement TLS groupSelection details: all

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