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- PDB-3bk1: Crystal Structure Analysis of RNase J -

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Basic information

Entry
Database: PDB / ID: 3bk1
TitleCrystal Structure Analysis of RNase J
ComponentsMetal dependent hydrolase
KeywordsHYDROLASE / RNase J / Endoribonuclease / 5'-3' Exoribonuclease / Metal dependent hydrolase / Metallo-beta-lactamase
Function / homology
Function and homology information


5'-3' RNA exonuclease activity / RNA endonuclease activity / rRNA processing / Hydrolases; Acting on ester bonds / RNA binding / zinc ion binding / identical protein binding / cytoplasm
Similarity search - Function
Ubiquitin-like (UB roll) - #580 / Metallo-hydrolase/oxidoreductase / Ribonuclease J, bacteria / Ribonuclease J, C-terminal / Ribonuclease J C-terminal domain / Ribonuclease J / Ribonuclease J, domain 2 / Beta-lactamase superfamily domain / Zn-dependent metallo-hydrolase, RNA specificity domain / Zn-dependent metallo-hydrolase RNA specificity domain ...Ubiquitin-like (UB roll) - #580 / Metallo-hydrolase/oxidoreductase / Ribonuclease J, bacteria / Ribonuclease J, C-terminal / Ribonuclease J C-terminal domain / Ribonuclease J / Ribonuclease J, domain 2 / Beta-lactamase superfamily domain / Zn-dependent metallo-hydrolase, RNA specificity domain / Zn-dependent metallo-hydrolase RNA specificity domain / Sugar transport proteins signature 1. / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase; Chain A / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Ubiquitin-like (UB roll) / 4-Layer Sandwich / Roll / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.33 Å
Authorsde la Sierra-Gallay, I.L. / Zig, L. / Putzer, H.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2008
Title: Structural insights into the dual activity of RNase J
Authors: de la Sierra-Gallay, I.L. / Zig, L. / Jamalli, A. / Putzer, H.
History
DepositionDec 5, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 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: Metal dependent hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,9098
Polymers63,3061
Non-polymers6037
Water3,423190
1
A: Metal dependent hydrolase
hetero molecules

A: Metal dependent hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,81816
Polymers126,6122
Non-polymers1,20614
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area7470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.830, 117.620, 230.490
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number22
Space group name H-MF222
Components on special symmetry positions
IDModelComponents
11A-1127-

HOH

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Components

#1: Protein Metal dependent hydrolase / RNase J


Mass: 63305.957 Da / Num. of mol.: 1 / Fragment: UNP residues 20-573
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB27 / Gene: TTC0775 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: Q72JJ7, Hydrolases
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 190 / 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: 2.62 Å3/Da / Density % sol: 53.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 2-4% PEG 4K, 0.02M ammonium sulfate, 0.1M Na-MES, pH5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 9, 2006
RadiationMonochromator: Double crystal, Si(111) or Si(311) and Toroidal mirror
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.33→59 Å / Num. obs: 28236 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.5 % / Biso Wilson estimate: 30.3 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 30.53
Reflection shellResolution: 2.33→2.4 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.171 / Mean I/σ(I) obs: 10.22 / Num. unique all: 2122 / % possible all: 88.5

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Processing

Software
NameVersionClassificationNB
CNS1.2refinement
PDB_EXTRACT3.004data extraction
MxCuBEdata collection
XDSdata reduction
XSCALEdata scaling
SHELXphasing
CNSphasing
RefinementMethod to determine structure: SAD / Resolution: 2.33→53.75 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 9593661 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.22 2801 9.9 %RANDOM
Rwork0.197 ---
obs0.197 28236 98.9 %-
all-28236 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 46.29 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 33.3 Å2
Baniso -1Baniso -2Baniso -3
1--10.78 Å20 Å20 Å2
2--9.03 Å20 Å2
3---1.75 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.24 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 2.33→53.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4315 0 29 190 4534
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d23.8
X-RAY DIFFRACTIONc_improper_angle_d0.91
X-RAY DIFFRACTIONc_mcbond_it2.041.5
X-RAY DIFFRACTIONc_mcangle_it2.762
X-RAY DIFFRACTIONc_scbond_it3.662
X-RAY DIFFRACTIONc_scangle_it4.242.5
LS refinement shellResolution: 2.33→2.48 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.269 437 9.9 %
Rwork0.22 3988 -
all-4425 -
obs--94.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2ion.paramwater.top
X-RAY DIFFRACTION3cis_peptide.paramligand_xplor_top.txt
X-RAY DIFFRACTION4water_rep.paramion.top
X-RAY DIFFRACTION5ligand_xplor_par.txt

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