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- PDB-1yvu: Crystal structure of A. aeolicus Argonaute -

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Basic information

Entry
Database: PDB / ID: 1yvu
TitleCrystal structure of A. aeolicus Argonaute
Componentshypothetical protein aq_1447
KeywordsRNA BINDING PROTEIN / GENE REGULATION / RNase H fold
Function / homology
Function and homology information


regulatory ncRNA-mediated post-transcriptional gene silencing / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / miRNA binding / RNA endonuclease activity / single-stranded RNA binding / DNA binding / metal ion binding / cytoplasm
Similarity search - Function
PAZ domain fold / PAZ domain superfamily / Aquifex aeolicus argonaute, PAZ domain / PAZ domain / Piwi domain / Piwi domain profile. / Piwi domain / Piwi / PAZ domain superfamily / PAZ domain profile. ...PAZ domain fold / PAZ domain superfamily / Aquifex aeolicus argonaute, PAZ domain / PAZ domain / Piwi domain / Piwi domain profile. / Piwi domain / Piwi / PAZ domain superfamily / PAZ domain profile. / PAZ domain / Response regulator / Ribonuclease H-like superfamily/Ribonuclease H / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Roll / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.9 Å
AuthorsYuan, Y.R. / Pei, Y. / Ma, J.B. / Kuryavyi, V. / Zhadina, M. / Meister, G. / Chen, H.Y. / Dauter, Z. / Tuschl, T. / Patel, D.J.
CitationJournal: Mol.Cell / Year: 2005
Title: Crystal structure of A. aeolicus Argonaute provides unique perspectives into the mechanism of guide strand-mediated mRNA cleavage
Authors: Yuan, Y.R. / Pei, Y. / Ma, J.B. / Kuryavyi, V. / Zhadina, M. / Meister, G. / Chen, H.Y. / Dauter, Z. / Tuschl, T. / Patel, D.J.
History
DepositionFeb 16, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 9, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: hypothetical protein aq_1447
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,5862
Polymers83,5461
Non-polymers401
Water1,24369
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.150, 100.679, 115.217
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein hypothetical protein aq_1447


Mass: 83545.750 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Strain: VF5 / Plasmid: pET28b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O67434
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / 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: 2.188 Å3/Da / Density % sol: 42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: PEG 550MME, calcium chloride, cacodylate, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
31
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-ID-B / Wavelength: 0.9788, 0.9790, 0.95
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 22, 2004
RadiationMonochromator: 360 degree swapping with 0.5 degree oscillation
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97881
20.9791
30.951
ReflectionResolution: 2.9→23.9 Å / Num. obs: 15291 / % possible obs: 99.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.6 % / Biso Wilson estimate: 60.7 Å2 / Rmerge(I) obs: 0.111 / Rsym value: 0.111
Reflection shellResolution: 2.9→3 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.472 / % possible all: 98.6

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Processing

Software
NameVersionClassification
X-PLOR3.851refinement
HKL-2000data reduction
SCALEPACKdata scaling
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.9→23.9 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.298 747 4.9 %RANDOM
Rwork0.208 ---
all0.216 15921 --
obs0.208 15291 89.3 %-
Displacement parametersBiso mean: 47.3 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.54 Å0.39 Å
Refinement stepCycle: LAST / Resolution: 2.9→23.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5670 0 1 69 5740
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.017
X-RAY DIFFRACTIONx_angle_deg2
X-RAY DIFFRACTIONx_dihedral_angle_d25.6
X-RAY DIFFRACTIONx_improper_angle_d1.89
X-RAY DIFFRACTIONx_mcbond_it3.951.5
X-RAY DIFFRACTIONx_mcangle_it5.952
X-RAY DIFFRACTIONx_scbond_it5.562
X-RAY DIFFRACTIONx_scangle_it7.972.5
LS refinement shellResolution: 2.9→3.08 Å / Rfactor Rfree error: 0.033 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.343 109 5.5 %
Rwork0.26 1886 -
obs--71.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CNS_PROTEIN_REP.PARAMCNS_PROTEIN.TOP
X-RAY DIFFRACTION2CNS_WATER_REP.PARAMCNS_WATER.TOP
X-RAY DIFFRACTION3CNS_ION.PARAMCNS_ION.TOP

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