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- PDB-7c43: The crystal structure of Trypanosoma brucei RNase D : AMP complex -

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Basic information

Entry
Database: PDB / ID: 7c43
TitleThe crystal structure of Trypanosoma brucei RNase D : AMP complex
ComponentsCCHC-type domain-containing protein
KeywordsHYDROLASE / Trypanosoma brucei / RNase D / guide RNA degradation / RNA BINDING PROTEIN / AMP
Function / homology
Function and homology information


PET complex / nucleobase-containing compound metabolic process / 3'-5'-RNA exonuclease activity / nucleic acid binding / nucleotide 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
ADENOSINE MONOPHOSPHATE / : / CCHC-type domain-containing protein
Similarity search - Component
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 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 14, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 7, 2021Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CCHC-type domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,5746
Polymers38,9861
Non-polymers5885
Water46826
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area890 Å2
ΔGint-18 kcal/mol
Surface area15070 Å2
Unit cell
Length a, b, c (Å)49.730, 77.730, 99.301
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: 38986.012 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: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / 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: 2.46 Å3/Da / Density % sol: 50.03 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 0.1 M Bis-Tris pH 5.5, 30% PEG 3350

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 10, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.3→61.21 Å / Num. obs: 17294 / % possible obs: 97.4 % / Redundancy: 8.4 % / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.023 / Rrim(I) all: 0.074 / Χ2: 0.91 / Net I/σ(I): 8.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.3-2.384.80.27915940.8850.1220.3070.89991.6
2.38-2.485.20.27216520.9210.1170.2980.88995.4
2.48-2.596.30.2416830.9470.0950.2590.91596.6
2.59-2.737.40.21816930.970.080.2330.90197.5
2.73-2.98.20.16417150.9890.0570.1740.91998.3
2.9-3.128.80.11817500.9940.040.1250.93998.4
3.12-3.439.30.08517370.9970.0270.0890.90798.5
3.43-3.9311.30.06417690.9980.0190.0670.93899.2
3.93-4.9510.90.05118020.9980.0160.0540.85799.5
4.95-3011.20.05318990.9980.0160.0560.92299

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-3000data scaling
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
HKL2Mapphasing
RefinementMethod to determine structure: SAD / Resolution: 2.3→61.21 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.902 / SU B: 6.586 / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.31 / ESU R Free: 0.231 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2424 808 5.1 %RANDOM
Rwork0.1999 ---
obs0.2021 15127 89.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 102.72 Å2 / Biso mean: 32.742 Å2 / Biso min: 14.27 Å2
Baniso -1Baniso -2Baniso -3
1-0.75 Å20 Å20 Å2
2---0.06 Å2-0 Å2
3----0.69 Å2
Refinement stepCycle: final / Resolution: 2.3→61.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2292 0 27 26 2345
Biso mean--42.38 29.18 -
Num. residues----295
LS refinement shellResolution: 2.3→2.358 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.23 36 -
Rwork0.233 726 -
obs--59.25 %

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