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- PDB-7c45: The crystal structure of Trypanosoma brucei RNase D complex with ... -

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Basic information

Entry
Database: PDB / ID: 7c45
TitleThe crystal structure of Trypanosoma brucei RNase D complex with RNA U12
Components
  • CCHC-type domain-containing protein
  • RNA (5'-R(*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
KeywordsRNA BINDING PROTEIN/RNA / Trypanosoma brucei / RNase D / guide RNA degradation / RNA BINDING PROTEIN / RNA U12 / RNA BINDING PROTEIN-RNA complex
Function / homology
Function and homology information


PET complex / nucleobase-containing compound metabolic process / 3'-5'-RNA exonuclease activity / nucleic acid binding / mitochondrion / zinc ion binding
Similarity search - Function
3'-5' exonuclease / 3'-5' exonuclease / 3'-5' exonuclease domain / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / Ribonuclease H superfamily / Ribonuclease H-like superfamily
Similarity search - Domain/homology
RNA / RNA (> 10) / CCHC-type domain-containing protein
Similarity search - Component
Biological speciesTrypanosoma brucei brucei (eukaryote)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.769 Å
AuthorsGao, Y.Q. / Gan, J.H.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2019FY101500 China
CitationJournal: Nucleic Acids Res. / Year: 2021
Title: Structural basis for guide RNA trimming by RNase D ribonuclease in Trypanosoma brucei.
Authors: Gao, Y. / Liu, H. / Zhang, C. / Su, S. / Chen, Y. / Chen, X. / Li, Y. / Shao, Z. / Zhang, Y. / Shao, Q. / Li, J. / Huang, Z. / Ma, J. / Gan, J.
History
DepositionMay 15, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 7, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CCHC-type domain-containing protein
D: RNA (5'-R(*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2676
Polymers37,0562
Non-polymers2114
Water4,053225
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2700 Å2
ΔGint-55 kcal/mol
Surface area14800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.449, 65.843, 99.914
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein CCHC-type domain-containing protein / RNase D


Mass: 33427.359 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei brucei (strain 927/4 GUTat10.1) (eukaryote)
Strain: 927/4 GUTat10.1 / Gene: Tb09.211.3670 / Production host: Escherichia coli (E. coli) / References: UniProt: Q38DE2
#2: RNA chain RNA (5'-R(*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')


Mass: 3629.032 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 225 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.97 Å3/Da / Density % sol: 37.65 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / Details: 0.2 M Sodium acetate trihydrate, 20% PEG 3350

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 29, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.769→50 Å / Num. obs: 28011 / % possible obs: 95.2 % / Redundancy: 4.1 % / Biso Wilson estimate: 18.93 Å2 / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.043 / Rrim(I) all: 0.09 / Χ2: 0.915 / Net I/σ(I): 5.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.77-1.833.90.47325800.7870.2650.546190.2
1.83-1.914.10.38826810.8510.2110.4441.01892.8
1.91-1.994.10.31527870.8720.1720.361.00495.6
1.99-2.140.24527540.9110.1380.2831.02195.4
2.1-2.234.20.1828540.9450.0990.2070.99997.9
2.23-2.44.20.13728620.9650.0760.1580.97698.4
2.4-2.644.10.10728300.9780.060.1240.91696.2
2.64-3.034.30.07728610.9890.0410.0880.84597.1
3.03-3.814.20.04928560.9950.0270.0560.76595.4
3.81-5040.03629460.9950.020.0410.64193.4

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Processing

Software
NameVersionClassification
HKL-3000data scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
HKL2Mapphasing
RefinementMethod to determine structure: SAD / Resolution: 1.769→36.84 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2212 1356 5.04 %
Rwork0.1925 25565 -
obs0.194 26921 91.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 85.45 Å2 / Biso mean: 22.2613 Å2 / Biso min: 13.77 Å2
Refinement stepCycle: final / Resolution: 1.769→36.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2262 197 4 225 2688
Biso mean--18.84 26.81 -
Num. residues----305
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082522
X-RAY DIFFRACTIONf_angle_d0.9893458
X-RAY DIFFRACTIONf_chiral_restr0.056410
X-RAY DIFFRACTIONf_plane_restr0.006411
X-RAY DIFFRACTIONf_dihedral_angle_d19.2891499
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.7692-1.83250.28171230.2317215079
1.8325-1.90580.29751120.2304232184
1.9058-1.99260.26341420.2159242788
1.9926-2.09760.27481380.2147248091
2.0976-2.2290.2181380.2047265596
2.229-2.40110.24691310.2082267697
2.4011-2.64260.23131170.2086269996
2.6426-3.02490.23341620.203269397
3.0249-3.81040.20531360.1752271095
3.8104-36.840.17931570.164275493
Refinement TLS params.Method: refined / Origin x: 15.5865 Å / Origin y: -5.6245 Å / Origin z: -11.48 Å
111213212223313233
T0.1661 Å20.0014 Å20.0153 Å2-0.1781 Å20.0244 Å2--0.1883 Å2
L0.2102 °20.147 °20.3261 °2-0.5495 °20.4562 °2--0.8558 °2
S0.0364 Å °-0.0194 Å °-0.0332 Å °0.0222 Å °0.0041 Å °-0.0598 Å °0.0185 Å °0.0214 Å °-0.0438 Å °
Refinement TLS groupSelection details: all

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