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- PDB-3da5: Crystal Structure of Piwi/Argonaute/Zwille(PAZ) domain from Therm... -

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Basic information

Entry
Database: PDB / ID: 3da5
TitleCrystal Structure of Piwi/Argonaute/Zwille(PAZ) domain from Thermococcus thioreducens
ComponentsArgonaute
KeywordsRNA BINDING PROTEIN / PAZ domain / RNA binding / SH3-like barrel
Function / homologyCathepsin B; Chain A - #180 / Argonaute PAZ domain, archaea / PAZ domain / PAZ domain superfamily / Cathepsin B; Chain A / Alpha-Beta Complex / Alpha Beta / Argonaute
Function and homology information
Biological speciesThermococcus thioreducens (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.94 Å
AuthorsHughes, R.C. / Ng, J.D.
CitationJournal: to be published
Title: Crystal Structure of Piwi/Argonaute/Zwille(PAZ) domain from Thermococcus thioreducens
Authors: Hughes, R.C. / Ng, J.D.
History
DepositionMay 28, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 29, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Argonaute
B: Argonaute


Theoretical massNumber of molelcules
Total (without water)30,8712
Polymers30,8712
Non-polymers00
Water37821
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.392, 60.896, 66.447
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Argonaute /


Mass: 15435.667 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus thioreducens (archaea) / Strain: OGL-20 / Gene: Ago-PAZ / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: D0VWU1*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 21 / 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: 1.88 Å3/Da / Density % sol: 34.47 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 8.5
Details: Dioxane, PEG8000, pH 8.5, vapor diffusion, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 1, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.94→44.9 Å / Num. obs: 14536 / % possible obs: 81.1 % / Observed criterion σ(F): 1.7 / Observed criterion σ(I): 3 / Redundancy: 4.9 % / Biso Wilson estimate: 32.7 Å2 / Rmerge(I) obs: 0.046 / Rsym value: 0.046 / Net I/σ(I): 30.7
Reflection shellResolution: 1.94→2.01 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 3.23 / Num. unique all: 1048 / Rsym value: 0.32 / % possible all: 59.4

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.22 Å44.9 Å
Translation2.22 Å44.9 Å

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Processing

Software
NameVersionClassificationNB
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1U04

1u04


Resolution: 1.94→44.9 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.936 / SU B: 5.393 / SU ML: 0.158 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.274 / ESU R Free: 0.217 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.267 730 5 %RANDOM
Rwork0.216 ---
obs0.218 14511 81.13 %-
all-17886 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 34.363 Å2
Baniso -1Baniso -2Baniso -3
1-0.32 Å20 Å20 Å2
2--0.7 Å20 Å2
3----1.03 Å2
Refinement stepCycle: LAST / Resolution: 1.94→44.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2016 0 0 21 2037
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0222073
X-RAY DIFFRACTIONr_bond_other_d0.0010.021420
X-RAY DIFFRACTIONr_angle_refined_deg1.7721.952817
X-RAY DIFFRACTIONr_angle_other_deg0.99133447
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.1835240
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.24823.981108
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.915344
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.261513
X-RAY DIFFRACTIONr_chiral_restr0.1150.2295
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022286
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02430
X-RAY DIFFRACTIONr_nbd_refined0.2380.2382
X-RAY DIFFRACTIONr_nbd_other0.1990.21396
X-RAY DIFFRACTIONr_nbtor_refined0.1880.21000
X-RAY DIFFRACTIONr_nbtor_other0.090.21045
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1220.247
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0090.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.240.226
X-RAY DIFFRACTIONr_symmetry_vdw_other0.250.257
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2730.25
X-RAY DIFFRACTIONr_mcbond_it1.4591.51261
X-RAY DIFFRACTIONr_mcbond_other0.3181.5476
X-RAY DIFFRACTIONr_mcangle_it2.27621964
X-RAY DIFFRACTIONr_scbond_it2.9443965
X-RAY DIFFRACTIONr_scangle_it4.4194.5853
LS refinement shellResolution: 1.94→1.988 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 47 -
Rwork0.262 704 -
all-751 -
obs--57.28 %

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