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- PDB-7c42: The crystal structure of Trypanosoma brucei RNase D -

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Basic information

Entry
Database: PDB / ID: 7c42
TitleThe crystal structure of Trypanosoma brucei RNase D
ComponentsCCHC-type domain-containing protein
KeywordsHYDROLASE / Trypanosoma brucei / RNase D / guide RNA degradation / RNA BINDING PROTEIN
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
CCHC-type domain-containing protein
Similarity search - Component
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 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
Revision 1.1Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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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)39,1173
Polymers38,9861
Non-polymers1312
Water4,414245
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area15150 Å2
Unit cell
Length a, b, c (Å)50.929, 77.451, 101.544
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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 245 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.58 Å3/Da / Density % sol: 52.34 %
Description: The entry contains friedel pairs in F_plus/minus columns and I_plus/minus columns
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: BL17U / Wavelength: 0.9793 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 30, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.998→30 Å / Num. obs: 42575 / % possible obs: 98.8 % / Redundancy: 10.2 % / Biso Wilson estimate: 21.93 Å2 / Rmerge(I) obs: 0.116 / Rpim(I) all: 0.036 / Rrim(I) all: 0.121 / Χ2: 0.926 / Net I/σ(I): 9.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2-2.077.30.62225240.8330.2140.660.91192.5
2.07-2.158.10.51526770.9020.1730.5450.94397.5
2.15-2.259.10.41427060.9520.1350.4370.96799
2.25-2.379.80.32327690.9740.1040.340.95499.7
2.37-2.529.60.2727370.9810.0890.2850.92699.9
2.52-2.7111.40.21427680.9890.0660.2240.924100
2.71-2.9911.60.14727890.9910.0450.1540.91499.9
2.99-3.4211.60.10127920.9960.0310.1060.854100
3.42-4.3111.60.0828330.9960.0240.0840.80899.9
4.31-3011.90.129740.9920.030.1051.0699.9

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL2Mapphasing
RefinementMethod to determine structure: SAD / Resolution: 2→29.497 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 21.87 / Stereochemistry target values: ML
Details: The entry contains friedel pairs in F_plus/minus columns and I_plus/minus columns
RfactorNum. reflection% reflection
Rfree0.2152 3475 8.16 %
Rwork0.1761 39100 -
obs0.1793 42575 81.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 118.61 Å2 / Biso mean: 27.1226 Å2 / Biso min: 9.06 Å2
Refinement stepCycle: final / Resolution: 2→29.497 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2271 0 2 245 2518
Biso mean--20.4 33.3 -
Num. residues----293
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062317
X-RAY DIFFRACTIONf_angle_d0.7633139
X-RAY DIFFRACTIONf_chiral_restr0.048357
X-RAY DIFFRACTIONf_plane_restr0.005405
X-RAY DIFFRACTIONf_dihedral_angle_d8.761392
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2-2.02590.2773610.203165934
2.0259-2.05480.2657650.226878540
2.0548-2.08550.2691810.197888146
2.0855-2.1180.2741860.200596450
2.118-2.15280.2417960.2213109157
2.1528-2.18990.28121010.1987114960
2.1899-2.22970.24411100.2016126065
2.2297-2.27250.23261210.1985135370
2.2725-2.31890.22131360.1937142674
2.3189-2.36930.25161350.1897153379
2.3693-2.42440.24951400.2001158282
2.4244-2.4850.24611490.1915165387
2.485-2.55220.25471550.2005179291
2.5522-2.62720.24021630.1856180696
2.6272-2.71190.26631720.1897190098
2.7119-2.80880.22931740.18231921100
2.8088-2.92120.21681730.19171919100
2.9212-3.0540.22921730.1781927100
3.054-3.21480.18661690.18041940100
3.2148-3.4160.22231660.1761928100
3.416-3.67930.20681760.15821924100
3.6793-4.04870.17731670.14681922100
4.0487-4.63260.15861740.14661937100
4.6326-5.82920.22221600.15791933100
5.8292-29.4970.19141720.1827191599

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