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- PDB-5z9z: The C-terminal RRM domain of Arabidopsis SMALL RNA DEGRADING NUCL... -

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Basic information

Entry
Database: PDB / ID: 5z9z
TitleThe C-terminal RRM domain of Arabidopsis SMALL RNA DEGRADING NUCLEASE 1 (E329A/E330A/E332A)
ComponentsSmall RNA degrading nuclease 1
KeywordsRNA BINDING PROTEIN / RNA Recognition Motif
Function / homology
Function and homology information


3'-5'-exoribonuclease activity involved in mature miRNA 3'-end processing / miRNA catabolic process / miRNA binding / exonuclease activity / 3'-5' exonuclease activity / 3'-5'-RNA exonuclease activity / Hydrolases; Acting on ester bonds / nucleus
Similarity search - Function
RNA exonuclease 1-like, exonuclease domain / : / Exonuclease / Exonuclease, RNase T/DNA polymerase III / EXOIII / RNA-binding domain superfamily / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Nucleotide-binding alpha-beta plait domain superfamily
Similarity search - Domain/homology
CITRATE ANION / Small RNA degrading nuclease 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.049 Å
AuthorsChen, J. / Liu, L. / You, C. / Gu, J. / Ruan, W. / Zhang, L. / Cao, C. / Gan, J. / Huang, Y. / Chen, X. / Ma, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of ChinaNSFC 31230041 China
CitationJournal: Nat Commun / Year: 2018
Title: Structural and biochemical insights into small RNA 3' end trimming by Arabidopsis SDN1.
Authors: Chen, J. / Liu, L. / You, C. / Gu, J. / Ruan, W. / Zhang, L. / Gan, J. / Cao, C. / Huang, Y. / Chen, X. / Ma, J.
History
DepositionFeb 5, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 27, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 3, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Small RNA degrading nuclease 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,8923
Polymers11,5141
Non-polymers3782
Water1,33374
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area480 Å2
ΔGint-0 kcal/mol
Surface area6610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.132, 65.620, 74.730
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-635-

HOH

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Components

#1: Protein Small RNA degrading nuclease 1


Mass: 11513.741 Da / Num. of mol.: 1 / Fragment: C-terminal RRM domain, UNP residues 309-409 / Mutation: E329A,E330A,E332A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: SDN1, At3g50100, F3A4.180 / Production host: Escherichia coli (E. coli)
References: UniProt: A3KPE8, Hydrolases; Acting on ester bonds
#2: Chemical ChemComp-FLC / CITRATE ANION / Citric acid


Mass: 189.100 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H5O7
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 74 / 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: 2.17 Å3/Da / Density % sol: 43.37 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / Details: PEG 3350, ammonium citrate

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.987 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 11, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.049→34.96 Å / Num. obs: 6556 / % possible obs: 99.56 % / Redundancy: 13.7 % / Net I/σ(I): 29.4
Reflection shellResolution: 2.05→2.12 Å

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-20000.98.699adata collection
PHENIX(1.10.1_2155: ???)model building
PHENIX1.8.2_1309phasing
HKL-20000.98.699adata reduction
HKL-20000.98.699adata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.049→34.851 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 22.81
RfactorNum. reflection% reflection
Rfree0.227 649 9.93 %
Rwork0.178 --
obs0.1807 6539 98.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.049→34.851 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms780 0 26 74 880
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003817
X-RAY DIFFRACTIONf_angle_d0.5791101
X-RAY DIFFRACTIONf_dihedral_angle_d14.42496
X-RAY DIFFRACTIONf_chiral_restr0.044123
X-RAY DIFFRACTIONf_plane_restr0.002141
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0493-2.20750.26331180.18921113X-RAY DIFFRACTION96
2.2075-2.42960.28211340.18871171X-RAY DIFFRACTION100
2.4296-2.78110.26611330.18981169X-RAY DIFFRACTION100
2.7811-3.50330.22361270.17541196X-RAY DIFFRACTION100
3.5033-34.85630.2031370.16161241X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.5540.15870.30940.28360.41190.71840.08150.2139-0.08640.0858-0.11720.186-0.0574-0.11510.02010.10160.04320.00590.13140.00090.120210.92222.689841.3711
20.707-0.4596-0.32471.43620.03791.15950.0056-0.1416-0.0670.2025-0.13280.26030.0544-0.0804-0.08160.111-0.01350.01090.0809-0.00760.081519.456715.342448.8117
30.7778-0.37080.43420.2068-0.08570.92560.04580.37210.4051-0.2209-0.1563-0.108-0.27160.1667-0.15260.1608-0.00910.0350.20050.00620.179723.175324.600737.1337
41.7092-0.18040.94211.1817-0.68111.2320.1528-0.3187-0.24190.06580.05210.19950.0432-0.19950.16270.09480.01280.01350.1340.00730.125.617517.165142.287
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 308 through 320 )
2X-RAY DIFFRACTION2chain 'A' and (resid 321 through 361 )
3X-RAY DIFFRACTION3chain 'A' and (resid 362 through 383 )
4X-RAY DIFFRACTION4chain 'A' and (resid 384 through 408 )

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