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- PDB-3cg7: Crystal structure of cell-death related nuclease 4 (CRN-4) -

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Basic information

Entry
Database: PDB / ID: 3cg7
TitleCrystal structure of cell-death related nuclease 4 (CRN-4)
ComponentsCell death-related nuclease 4
KeywordsHYDROLASE / APOPTOSIS / 3'-5' exonuclease / DEDDh / nuclease
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 / 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
Cell death-related nuclease 4
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 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 5, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 30, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)71,3164
Polymers71,1852
Non-polymers1312
Water3,117173
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1780 Å2
ΔGint-5 kcal/mol
Surface area26560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.474, 165.379, 64.263
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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 173 / 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: 2

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Sample preparation

CrystalDensity Matthews: 4.84 Å3/Da / Density % sol: 74.61 %
Crystal growTemperature: 277 K / pH: 7.5
Details: 0.2M sodium formate, 20% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 277K, pH 7.50

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSRRC BL13B110.999
SYNCHROTRONNSRRC BL13B120.978993,0.963960,0.979185
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDJul 1, 2006
ADSC QUANTUM 3152CCDSep 22, 2006
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SAGITALLY FOCUSED SI(111)SINGLE WAVELENGTHMx-ray1
2MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.9991
20.9789931
30.963961
40.9791851
ReflectionResolution: 2.5→30 Å / Num. obs: 45644 / % possible obs: 96.3 % / Observed criterion σ(I): 3 / Redundancy: 4.3 % / Rsym value: 0.052 / Net I/σ(I): 21.5
Reflection shellResolution: 2.5→2.56 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.426 / Mean I/σ(I) obs: 3.01 / Rsym value: 0.426 / % possible all: 88.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
SHELXSphasing
RefinementMethod to determine structure: MAD / Resolution: 2.5→30 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.914 / SU B: 14.373 / SU ML: 0.147 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.216 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24681 2301 5 %RANDOM
Rwork0.2061 ---
obs0.20816 43319 96.31 %-
all-45644 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 47.021 Å2
Baniso -1Baniso -2Baniso -3
1--1.44 Å20 Å20 Å2
2--1.4 Å20 Å2
3---0.04 Å2
Refine analyzeLuzzati coordinate error obs: 0.344 Å
Refinement stepCycle: LAST / Resolution: 2.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4822 0 2 173 4997
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0224933
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1451.9476684
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5155589
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.96124.111253
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.68115855
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1271534
X-RAY DIFFRACTIONr_chiral_restr0.0890.2725
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023794
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1980.22121
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3060.23394
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1430.2225
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1890.225
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1190.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6631.53042
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.15424800
X-RAY DIFFRACTIONr_scbond_it1.55832170
X-RAY DIFFRACTIONr_scangle_it2.4934.51884
X-RAY DIFFRACTIONr_rigid_bond_restr4.67835149
X-RAY DIFFRACTIONr_sphericity_free3.3883171
X-RAY DIFFRACTIONr_sphericity_bonded2.01134775
LS refinement shellResolution: 2.502→2.567 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.34 163 -
Rwork0.281 2896 -
obs--88.64 %

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