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- PDB-3cm5: Crystal structure of Cell-Death Related Nuclease 4 (CRN-4) bound ... -

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Basic information

Entry
Database: PDB / ID: 3cm5
TitleCrystal structure of Cell-Death Related Nuclease 4 (CRN-4) bound with Mn
ComponentsCell death-related nuclease 4
KeywordsHYDROLASE / APOPTOSIS / apoptotic nuclease / 3'-5' exonuclease / DEDD family
Function / homology
Function and homology information


DNA nuclease activity / exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / apoptotic DNA fragmentation / DNA catabolic process / RNA catabolic process / RNA nuclease activity / 3'-5' exonuclease activity / DNA endonuclease activity / single-stranded DNA binding / 3'-5'-RNA exonuclease activity ...DNA nuclease activity / exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / apoptotic DNA fragmentation / DNA catabolic process / RNA catabolic process / RNA nuclease activity / 3'-5' exonuclease activity / DNA endonuclease activity / single-stranded DNA binding / 3'-5'-RNA exonuclease activity / Hydrolases; Acting on ester bonds / metal ion binding / cytoplasm
Similarity search - Function
: / : / Exonuclease / Exonuclease, RNase T/DNA polymerase III / EXOIII / Ribonuclease H-like superfamily/Ribonuclease H / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily / Ribonuclease H-like superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / 3'-5' exonuclease crn-4
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.81 Å
AuthorsHsiao, Y.-Y. / Yuan, H.S.
CitationJournal: Mol.Cell.Biol. / Year: 2009
Title: Crystal structure of CRN-4: implications for domain function in apoptotic DNA degradation
Authors: Hsiao, Y.-Y. / Nakagawa, A. / Shi, Z. / Mitani, S. / Xue, D. / Yuan, H.S.
History
DepositionMar 21, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 30, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cell death-related nuclease 4
B: Cell death-related nuclease 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,4266
Polymers71,1852
Non-polymers2414
Water1,45981
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Cell death-related nuclease 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7133
Polymers35,5931
Non-polymers1202
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Cell death-related nuclease 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7133
Polymers35,5931
Non-polymers1202
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)125.132, 165.432, 64.589
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Cell death-related nuclease 4 / CRN-4


Mass: 35592.629 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Strain: Bristol N2 / Gene: crn-4 / Plasmid: pGEX-4T-2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS
References: UniProt: Q10905, Hydrolases; Acting on ester bonds
#2: Chemical ChemComp-ZN / ZINC ION


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


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / 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: 4.7 Å3/Da / Density % sol: 73.81 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 5% isopropanal, 0.1M HEPES pH 7.5, 10% PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 0.999 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 6, 2007
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. obs: 30689 / % possible obs: 92.2 % / Observed criterion σ(I): 3 / Redundancy: 3.8 % / Rsym value: 0.062 / Net I/σ(I): 20.5
Reflection shellResolution: 2.81→2.88 Å / Redundancy: 3.8 % / Num. unique all: 2850 / Rsym value: 0.424 / % possible all: 81

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3CG7

3cg7


Resolution: 2.81→30 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.912 / SU B: 10.523 / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.423 / ESU R Free: 0.288 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23877 1564 5.1 %RANDOM
Rwork0.20126 ---
obs0.20314 29078 91.72 %-
all-30642 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.919 Å2
Baniso -1Baniso -2Baniso -3
1--1.92 Å20 Å20 Å2
2--2.16 Å20 Å2
3----0.24 Å2
Refine analyzeLuzzati coordinate error obs: 0.382 Å
Refinement stepCycle: LAST / Resolution: 2.81→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4792 0 4 81 4877
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0224902
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4431.9476642
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4415586
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.70624.08250
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.01915850
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7351534
X-RAY DIFFRACTIONr_chiral_restr0.1070.2722
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023766
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2260.22384
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.320.23437
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1320.2188
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1930.230
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0660.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9721.53000
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.29324776
X-RAY DIFFRACTIONr_scbond_it1.79432130
X-RAY DIFFRACTIONr_scangle_it2.8164.51866
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.81→2.882 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.346 106 -
Rwork0.335 1811 -
obs--81.06 %

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