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- PDB-3cm6: Crystal structure of cell-death related nuclease 4 (CRN-4) bound ... -

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Basic information

Entry
Database: PDB / ID: 3cm6
TitleCrystal structure of cell-death related nuclease 4 (CRN-4) bound with Er
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 / 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
ERBIUM (III) ION / Cell death-related nuclease 4
Similarity search - Component
Biological speciesCaenorhabditis elegans (unknown)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 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

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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)71,6516
Polymers71,1852
Non-polymers4654
Water2,774154
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)35,8253
Polymers35,5931
Non-polymers2332
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)35,8253
Polymers35,5931
Non-polymers2332
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)130.279, 157.795, 65.244
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 (unknown) / 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-ER3 / ERBIUM (III) ION / Erbium


Mass: 167.259 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Er
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 154 / 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: 4.71 Å3/Da / Density % sol: 73.89 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2M sodium formate, 20% PEG 3350, pH 7.5, 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: 2.6→30 Å / Num. all: 43224 / Num. obs: 43082 / % possible obs: 99.8 % / Observed criterion σ(I): 3 / Redundancy: 4.9 % / Rsym value: 0.077 / Net I/σ(I): 19.6
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 5.1 % / Num. unique all: 4240 / Rsym value: 0.436 / % possible all: 100

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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: 2.6→30 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.884 / SU B: 8.124 / SU ML: 0.176 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.296 / ESU R Free: 0.247 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26516 2119 5 %RANDOM
Rwork0.22484 ---
all-42080 --
obs-39961 99.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.791 Å2
Baniso -1Baniso -2Baniso -3
1--2.05 Å20 Å20 Å2
2--2.61 Å20 Å2
3----0.56 Å2
Refine analyzeLuzzati coordinate error obs: 0.367 Å
Refinement stepCycle: LAST / Resolution: 2.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4806 0 4 154 4964
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0224916
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.321.9476661
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1475588
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.50124.104251
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.32715852
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3271534
X-RAY DIFFRACTIONr_chiral_restr0.1020.2724
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023778
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2150.22211
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3140.23371
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1690.2204
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1790.222
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1660.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7251.53026
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.27324791
X-RAY DIFFRACTIONr_scbond_it1.69732162
X-RAY DIFFRACTIONr_scangle_it2.74.51870
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.368 145 -
Rwork0.301 2904 -
obs--99.97 %

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