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- PDB-3krn: Crystal Structure of C. elegans cell-death-related nuclease 5(CRN-5) -

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Basic information

Entry
Database: PDB / ID: 3krn
TitleCrystal Structure of C. elegans cell-death-related nuclease 5(CRN-5)
ComponentsProtein C14A4.5, confirmed by transcript evidence
KeywordsHYDROLASE / RNase PH domain / homodimer / exosome / cell-death-related DNase
Function / homologyGHMP Kinase, N-terminal domain / Ribosomal Protein S5; domain 2 / 2-Layer Sandwich / Alpha Beta / :
Function and homology information
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.918 Å
AuthorsYang, C.-C. / Wang, Y.-T. / Hsiao, Y.-Y. / Doudeva, L.G. / Chow, S.Y. / Yuan, H.S.
CitationJournal: Rna / Year: 2010
Title: Structural and biochemical characterization of CRN-5 and Rrp46: an exosome component participating in apoptotic DNA degradation
Authors: Yang, C.-C. / Wang, Y.-T. / Hsiao, Y.-Y. / Doudeva, L.G. / Kuo, P.-H. / Chow, S.Y. / Yuan, H.S.
History
DepositionNov 19, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 26, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein C14A4.5, confirmed by transcript evidence
B: Protein C14A4.5, confirmed by transcript evidence


Theoretical massNumber of molelcules
Total (without water)48,2172
Polymers48,2172
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1900 Å2
ΔGint-12 kcal/mol
Surface area18330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.954, 44.837, 65.507
Angle α, β, γ (deg.)90.00, 100.65, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Protein C14A4.5, confirmed by transcript evidence / Cell death-related nuclease 5 / CRN-5


Mass: 24108.326 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Plasmid: pQE-70 / Production host: Escherichia coli (E. coli)
References: UniProt: Q17952, Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters

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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: 1.85 Å3/Da / Density % sol: 33.67 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1M Tris-HCl, 0.2M NaCl, 25% PEG 3350, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 102 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 13, 2008
RadiationMonochromator: LN2-cooled, fixed-exit double crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.9→50 Å / Num. obs: 3235 / % possible obs: 97.7 % / Observed criterion σ(I): 1 / Redundancy: 3.1 % / Biso Wilson estimate: 66.08 Å2 / Rmerge(I) obs: 0.071 / Rsym value: 0.091 / Net I/σ(I): 13.8 / Num. measured all: 9991
Reflection shellResolution: 3.9→4.04 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.197 / Mean I/σ(I) obs: 5.25 / Num. unique all: 305 / Rsym value: 0.267 / % possible all: 91.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
BALBESphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2NN6, chain D

2nn6


Resolution: 3.918→26.505 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.627 / SU ML: 0.54 / Isotropic thermal model: overall / σ(F): 1.38 / Phase error: 41.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3564 227 7.06 %RANDOM
Rwork0.3065 2990 --
obs0.3101 3217 97.19 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 76.401 Å2 / ksol: 0.318 e/Å3
Displacement parametersBiso max: 264.89 Å2 / Biso mean: 87.869 Å2 / Biso min: 11.83 Å2
Baniso -1Baniso -2Baniso -3
1-12.196 Å20 Å242.279 Å2
2---27.233 Å20 Å2
3---15.037 Å2
Refinement stepCycle: LAST / Resolution: 3.918→26.505 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2575 0 0 0 2575
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052614
X-RAY DIFFRACTIONf_angle_d0.9893522
X-RAY DIFFRACTIONf_chiral_restr0.066407
X-RAY DIFFRACTIONf_plane_restr0.006448
X-RAY DIFFRACTIONf_dihedral_angle_d18.856907
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.9178-4.93080.30711060.27571455X-RAY DIFFRACTION95
4.9308-26.50550.39751210.32771535X-RAY DIFFRACTION99

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