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- PDB-7c4c: The crystal structure of Trypanosoma brucei RNase D : GMP complex -

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Basic information

Entry
Database: PDB / ID: 7c4c
TitleThe crystal structure of Trypanosoma brucei RNase D : GMP complex
ComponentsCCHC-type domain-containing protein
KeywordsRNA BINDING PROTEIN / Trypanosoma brucei / RNase D / guide RNA degradation / GMP
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
GUANOSINE-5'-MONOPHOSPHATE / : / CCHC-type domain-containing protein
Similarity search - Component
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.265 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 1.1Oct 16, 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)41,16117
Polymers38,9861
Non-polymers2,17516
Water73941
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-32 kcal/mol
Surface area17340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.169, 75.001, 101.409
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


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.: 6 / 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.: 6 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-5GP / GUANOSINE-5'-MONOPHOSPHATE


Mass: 363.221 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H14N5O8P / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.8 Å3/Da / Density % sol: 56.1 %
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: 2.25→30.15 Å / Num. obs: 20606 / % possible obs: 98.3 % / Redundancy: 7.3 % / Biso Wilson estimate: 26.6 Å2 / Rmerge(I) obs: 0.089 / Rpim(I) all: 0.032 / Rrim(I) all: 0.095 / Χ2: 0.903 / Net I/σ(I): 9.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.25-2.333.60.40519050.1740.2210.4660.78592.5
2.33-2.424.20.40419740.3040.2050.4570.82696.4
2.42-2.534.60.38919970.4550.1910.4370.85796.9
2.53-2.676.10.37120450.6360.1590.4060.90999.2
2.67-2.836.90.30120740.8680.120.3260.95599.3
2.83-3.057.50.22720660.9490.0840.2431.02799.6
3.05-3.3680.1520840.9850.0530.1591.04299.5
3.36-3.8510.10.0920850.9960.0290.0951.02799.7
3.85-4.8410.30.05821350.9980.0180.0610.85199.7
4.84-3010.80.0522410.9980.0150.0530.70899.5

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
HKL2Mapphasing
RefinementMethod to determine structure: SAD / Resolution: 2.265→30 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.5 / Phase error: 22.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2389 918 5.11 %
Rwork0.1922 17061 -
obs0.1946 17979 85.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 165.69 Å2 / Biso mean: 41.8257 Å2 / Biso min: 13.77 Å2
Refinement stepCycle: final / Resolution: 2.265→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2524 0 90 41 2655
Biso mean--71.87 34.15 -
Num. residues----332
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012662
X-RAY DIFFRACTIONf_angle_d0.943618
X-RAY DIFFRACTIONf_chiral_restr0.051404
X-RAY DIFFRACTIONf_plane_restr0.007456
X-RAY DIFFRACTIONf_dihedral_angle_d16.6831563
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.265-2.38430.2508400.2385100536
2.3843-2.53360.31971060.2477202973
2.5336-2.72910.2861400.2433263994
2.7291-3.00350.25621700.2262276199
3.0035-3.43760.23611600.20192793100
3.4376-4.32890.20161480.16242854100
4.3289-300.22651540.1629298099
Refinement TLS params.Method: refined / Origin x: -17.2869 Å / Origin y: 8.6059 Å / Origin z: -12.4793 Å
111213212223313233
T0.158 Å20.0032 Å2-0.024 Å2-0.1879 Å20.0169 Å2--0.2095 Å2
L0.5301 °20.4498 °2-0.6854 °2-0.4594 °2-0.273 °2--1.2156 °2
S-0.042 Å °0.0334 Å °0.2182 Å °-0.088 Å °0.0781 Å °0.0589 Å °0.0208 Å °-0.038 Å °-0.047 Å °
Refinement TLS groupSelection details: all

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