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- PDB-1w0h: Crystallographic structure of the nuclease domain of 3'hExo, a DE... -

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Basic information

Entry
Database: PDB / ID: 1w0h
TitleCrystallographic structure of the nuclease domain of 3'hExo, a DEDDh family member, bound to rAMP
Components3'-5' EXONUCLEASE ERI1
KeywordsHYDROLASE / NUCLEASE DOMAIN / NUCLEASE / EXONUCLEASE
Function / homology
Function and homology information


histone pre-mRNA stem-loop binding / rRNA 3'-end processing / exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / histone pre-mRNA 3'end processing complex / regulatory ncRNA-mediated gene silencing / Major pathway of rRNA processing in the nucleolus and cytosol / 3'-5' exonuclease activity / ribosome binding / 3'-5'-RNA exonuclease activity / Hydrolases; Acting on ester bonds ...histone pre-mRNA stem-loop binding / rRNA 3'-end processing / exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / histone pre-mRNA 3'end processing complex / regulatory ncRNA-mediated gene silencing / Major pathway of rRNA processing in the nucleolus and cytosol / 3'-5' exonuclease activity / ribosome binding / 3'-5'-RNA exonuclease activity / Hydrolases; Acting on ester bonds / rRNA binding / nucleolus / metal ion binding / nucleus / cytoplasm
Similarity search - Function
: / SAP domain superfamily / Exonuclease / SAP domain / SAP motif profile. / Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation / SAP domain / Exonuclease, RNase T/DNA polymerase III / EXOIII / Ribonuclease H-like superfamily/Ribonuclease H ...: / SAP domain superfamily / Exonuclease / SAP domain / SAP motif profile. / Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation / SAP domain / 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
ADENOSINE MONOPHOSPHATE / 3'-5' exoribonuclease 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.59 Å
AuthorsCheng, Y. / Patel, D.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: Crystallographic Structure of the Nuclease Domain of 3'Hexo, a Deddh Family Member, Bound to Ramp
Authors: Cheng, Y. / Patel, D.
History
DepositionJun 4, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 30, 2004Provider: repository / Type: Initial release
Revision 1.1Jun 2, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 3'-5' EXONUCLEASE ERI1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5504
Polymers24,1551
Non-polymers3963
Water6,684371
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)101.600, 101.600, 100.400
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-2155-

HOH

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Components

#1: Protein 3'-5' EXONUCLEASE ERI1 / ERI-1 HOMOLOG / PROTEIN 3'HEXO


Mass: 24154.641 Da / Num. of mol.: 1 / Fragment: NUCLEASE DOMAIN, RESIDUES 122-321
Source method: isolated from a genetically manipulated source
Details: RAMP / Source: (gene. exp.) HOMO SAPIENS (human) / Description: SYNTHETIC GENE / Plasmid: PGBO / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q8IV48, Hydrolases; Acting on ester bonds
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 371 / Source method: isolated from a natural source / Formula: H2O
Compound detailsRNA EXONUCLEASE THAT BINDS TO THE 3' END OF HISTONE MRNAS WITH A POSSIBLE ROLE IN THEIR DEGRADATION.

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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: 3.1 Å3/Da / Density % sol: 60.28 %
Crystal growpH: 5.6 / Details: pH 5.60

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.964
DetectorDate: Apr 20, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.964 Å / Relative weight: 1
ReflectionResolution: 1.59→20 Å / Num. obs: 40933 / % possible obs: 99.5 % / Redundancy: 18.1 % / Rmerge(I) obs: 0.134 / Net I/σ(I): 20.6
Reflection shellRmerge(I) obs: 0.504 / Mean I/σ(I) obs: 5.4 / % possible all: 100

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Processing

SoftwareName: REFMAC / Classification: refinement
RefinementMethod to determine structure: OTHER / Resolution: 1.59→20 Å / SU B: 1.228 / SU ML: 0.044 / Cross valid method: THROUGHOUT / ESU R: 0.074 / ESU R Free: 0.077
RfactorNum. reflection% reflectionSelection details
Rfree0.202 2063 5 %RANDOM
Rwork0.168 ---
obs0.17 38822 99.29 %-
Displacement parametersBiso mean: 17.4 Å2
Baniso -1Baniso -2Baniso -3
1-0.26 Å20.13 Å20 Å2
2--0.26 Å20 Å2
3----0.4 Å2
Refinement stepCycle: LAST / Resolution: 1.59→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1642 0 25 371 2038

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