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- PDB-6ibp: Structure of a psychrophilic CCA-adding enzyme at room temperatur... -

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Basic information

Entry
Database: PDB / ID: 6ibp
TitleStructure of a psychrophilic CCA-adding enzyme at room temperature in ChipX microfluidic device
ComponentsCCA-adding enzymeCCA tRNA nucleotidyltransferase
KeywordsRNA BINDING PROTEIN / tRNA maturation / tRNA nucleotidyltransferase / ChipX / psychrophilic enzyme
Function / homology
Function and homology information


RNA 3'-end processing / tRNA processing / nucleotidyltransferase activity / nucleotide binding / RNA binding / metal ion binding
Similarity search - Function
Serum Albumin; Chain A, Domain 1 - #80 / CCA-adding enzyme, C-terminal / tRNA nucleotidyltransferase domain 2 putative / tRNA nucleotidyltransferase/poly(A) polymerase, RNA and SrmB- binding domain / Probable RNA and SrmB- binding site of polymerase A / Poly A polymerase, head domain / Poly A polymerase head domain / Serum Albumin; Chain A, Domain 1 / Beta Polymerase, domain 2 / Beta Polymerase; domain 2 ...Serum Albumin; Chain A, Domain 1 - #80 / CCA-adding enzyme, C-terminal / tRNA nucleotidyltransferase domain 2 putative / tRNA nucleotidyltransferase/poly(A) polymerase, RNA and SrmB- binding domain / Probable RNA and SrmB- binding site of polymerase A / Poly A polymerase, head domain / Poly A polymerase head domain / Serum Albumin; Chain A, Domain 1 / Beta Polymerase, domain 2 / Beta Polymerase; domain 2 / Nucleotidyltransferase superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesPlanococcus halocryophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.536 Å
Authorsde Wijn, R. / Hennig, O. / Rollet, K. / Bluhm, A. / Betat, H. / Moerl, M. / Lorber, B. / Sauter, C.
Funding support France, 2items
OrganizationGrant numberCountry
French National Research AgencyANR-10-LABX-0036_NETRNA France
French National Research AgencyANR-11-LABX-0057_MITOCROSS France
CitationJournal: Iucrj / Year: 2019
Title: A simple and versatile microfluidic device for efficient biomacromolecule crystallization and structural analysis by serial crystallography.
Authors: de Wijn, R. / Hennig, O. / Roche, J. / Engilberge, S. / Rollet, K. / Fernandez-Millan, P. / Brillet, K. / Betat, H. / Morl, M. / Roussel, A. / Girard, E. / Mueller-Dieckmann, C. / Fox, G.C. ...Authors: de Wijn, R. / Hennig, O. / Roche, J. / Engilberge, S. / Rollet, K. / Fernandez-Millan, P. / Brillet, K. / Betat, H. / Morl, M. / Roussel, A. / Girard, E. / Mueller-Dieckmann, C. / Fox, G.C. / Olieric, V. / Gavira, J.A. / Lorber, B. / Sauter, C.
History
DepositionNov 30, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 29, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: 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: CCA-adding enzyme


Theoretical massNumber of molelcules
Total (without water)48,4981
Polymers48,4981
Non-polymers00
Water1629
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area18620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.500, 71.500, 293.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein CCA-adding enzyme / CCA tRNA nucleotidyltransferase


Mass: 48498.266 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Planococcus halocryophilus (bacteria) / Gene: BBI08_05760 / Plasmid: pET-30b(+) / Details (production host): pET-30 Ek/LIC / Production host: Escherichia coli BL21(DE3)
References: UniProt: A0A1C7DQ98, CCA tRNA nucleotidyltransferase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 3.9 Å3/Da / Density % sol: 68.3 % / Description: bipyramids
Crystal growTemperature: 293 K / Method: counter-diffusion / pH: 7.5
Details: protein solution at 5.5 mg/mL in 50 mM Tris-HCl pH 7.5, 200 mM NaCl, 5 mM MgCl2; reservoir solution: 30% (m/v) PEG3350, 200 mM ammonium chloride pH 6.6. Crystallization and crystallographic ...Details: protein solution at 5.5 mg/mL in 50 mM Tris-HCl pH 7.5, 200 mM NaCl, 5 mM MgCl2; reservoir solution: 30% (m/v) PEG3350, 200 mM ammonium chloride pH 6.6. Crystallization and crystallographic analysis were performed using the ChipX microfluidic device.
PH range: 6.6-7.5

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Data collection

DiffractionMean temperature: 293 K / Ambient temp details: in situ / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Dec 9, 2016
RadiationMonochromator: Bartels Monochromator with dual channel cut crystals
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.536→46 Å / Num. obs: 23922 / % possible obs: 90.6 % / Redundancy: 7.5 % / Biso Wilson estimate: 57.4 Å2 / CC1/2: 0.987 / Rmerge(I) obs: 0.176 / Rrim(I) all: 0.189 / Net I/σ(I): 8.1
Reflection shellResolution: 2.536→2.6 Å / Redundancy: 6 % / Rmerge(I) obs: 1.16 / Num. unique obs: 1598 / CC1/2: 0.55 / Rrim(I) all: 1.26 / % possible all: 84.6

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998)refinement
XDS20180808data reduction
XSCALE20180808data scaling
PHENIX(1.13_2998)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MIV

1miv


Resolution: 2.536→45.397 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.14
Details: The structure was refined using data collected on five crystals at room temperature
RfactorNum. reflection% reflectionSelection details
Rfree0.2144 1180 5 %RANDOM
Rwork0.188 ---
obs0.1893 23583 89.34 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 60.05 Å2
Refinement stepCycle: LAST / Resolution: 2.536→45.397 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2989 0 0 9 2998
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093047
X-RAY DIFFRACTIONf_angle_d0.9634111
X-RAY DIFFRACTIONf_dihedral_angle_d16.8291146
X-RAY DIFFRACTIONf_chiral_restr0.06461
X-RAY DIFFRACTIONf_plane_restr0.005517
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.536-2.65140.36031210.31492300X-RAY DIFFRACTION75
2.6514-2.79110.32241450.28992747X-RAY DIFFRACTION90
2.7911-2.9660.30141500.25122813X-RAY DIFFRACTION91
2.966-3.19490.28321470.24632828X-RAY DIFFRACTION92
3.1949-3.51630.25111500.20852861X-RAY DIFFRACTION92
3.5163-4.02490.21381530.17592905X-RAY DIFFRACTION92
4.0249-5.06990.15211540.14392966X-RAY DIFFRACTION93
5.0699-45.4040.18291600.1622983X-RAY DIFFRACTION88

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