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- PDB-6tvz: Structure of a psychrophilic CCA-adding enzyme crystallized in th... -

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Basic information

Entry
Database: PDB / ID: 6tvz
TitleStructure of a psychrophilic CCA-adding enzyme crystallized in the XtalController device
ComponentsCCA-adding enzymeCCA tRNA nucleotidyltransferase
KeywordsRNA BINDING PROTEIN / tRNA maturation / tRNA nucleotidyltransferase / 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
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 / Nucleotidyltransferase superfamily
Similarity search - Domain/homology
ACETATE ION / PHOSPHATE ION / CCA-adding protein
Similarity search - Component
Biological speciesPlanococcus halocryophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.28 Å
Authorsde Wijn, R. / Rollet, K. / Coudray, L. / Hennig, O. / Betat, H. / Moerl, M. / Lorber, B. / Sauter, C.
Funding support France, 3items
OrganizationGrant numberCountry
French National Research AgencyANR-10-LABX-0036_NETRNA France
French National Research AgencyANR-11-LABX-0057_MITOCROSS France
French National Research AgencyANR-10-LABX-0036_INRT France
CitationJournal: Crystals / Year: 2020
Title: Monitoring the Production of High Diffraction-Quality Crystals of Two Enzymes in Real Time Using In Situ Dynamic Light Scattering
Authors: de Wijn, R. / Rollet, K. / Engilberge, S. / McEwen, A.G. / Hennig, O. / Betat, H. / Moerl, M. / Riobe, F. / Maury, O. / Girard, E. / Benas, P. / Lorber, B. / Sauter, C.
History
DepositionJan 10, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 16, 2020Provider: 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

Downloads & links

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Assembly

Deposited unit
A: CCA-adding enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,0838
Polymers48,4981
Non-polymers5847
Water1,892105
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1440 Å2
ΔGint-15 kcal/mol
Surface area18700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.530, 70.530, 291.480
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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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 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1C7DQ98
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: PO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 105 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.74 Å3/Da / Density % sol: 67.4 % / Description: elongated tetragonal bipyramid
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: A 10 micoliter drop of CCA-adding enzyme stock solution at 5 mg/ml in 0.05 M HEPES-NaOH pH 7.5, 0.1 M NaCl was incubated in the XtalController instrument. The crystallization was triggered ...Details: A 10 micoliter drop of CCA-adding enzyme stock solution at 5 mg/ml in 0.05 M HEPES-NaOH pH 7.5, 0.1 M NaCl was incubated in the XtalController instrument. The crystallization was triggered by the gradual addition of crystallant solution (1 M diammonium phosphate, 0.1 M ammonium acetate pH 4.5).

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.9799 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 23, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9799 Å / Relative weight: 1
ReflectionResolution: 2.28→47.2 Å / Num. obs: 34470 / % possible obs: 0.995 % / Redundancy: 6.9 % / Biso Wilson estimate: 44.72 Å2 / CC1/2: 1 / Rpim(I) all: 0.034 / Rrim(I) all: 0.086 / Net I/σ(I): 15.5
Reflection shellResolution: 2.28→2.42 Å / Redundancy: 7 % / Num. unique obs: 5385 / CC1/2: 0.76 / Rpim(I) all: 0.448 / Rrim(I) all: 1.26 / % possible all: 98.5

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6QY6

6qy6


Resolution: 2.28→47.19 Å / SU ML: 0.4031 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.9338
RfactorNum. reflection% reflection
Rfree0.2573 1702 4.99 %
Rwork0.214 --
obs0.2162 34125 98.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 50.98 Å2
Refinement stepCycle: LAST / Resolution: 2.28→47.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2989 0 36 105 3130
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00863076
X-RAY DIFFRACTIONf_angle_d0.97364144
X-RAY DIFFRACTIONf_chiral_restr0.0593461
X-RAY DIFFRACTIONf_plane_restr0.0056519
X-RAY DIFFRACTIONf_dihedral_angle_d19.01911152
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.28-2.350.5251180.47072327X-RAY DIFFRACTION86.37
2.35-2.430.35261400.30682669X-RAY DIFFRACTION99.86
2.43-2.510.33211410.26212681X-RAY DIFFRACTION99.93
2.51-2.610.28191420.23982687X-RAY DIFFRACTION99.93
2.61-2.730.32551400.24462658X-RAY DIFFRACTION99.93
2.73-2.880.27481430.22342714X-RAY DIFFRACTION99.97
2.88-3.060.2551430.23332716X-RAY DIFFRACTION99.97
3.06-3.290.27071420.24062709X-RAY DIFFRACTION99.79
3.29-3.630.27211440.24392728X-RAY DIFFRACTION99.72
3.63-4.150.28151450.2232779X-RAY DIFFRACTION99.05
4.15-5.230.21081460.14962772X-RAY DIFFRACTION99.18
5.23-47.190.19021580.16872983X-RAY DIFFRACTION98.99
Refinement TLS params.Method: refined / Origin x: 40.6403073594 Å / Origin y: 37.0329519812 Å / Origin z: 54.0238436045 Å
111213212223313233
T0.254130817511 Å2-0.0166974169117 Å20.0129870581604 Å2-0.30859381964 Å2-0.0463621902006 Å2--0.278635569454 Å2
L0.0534118055859 °20.00609376945419 °2-0.0302289790587 °2-0.410890502721 °2-0.203546021458 °2--0.22647942827 °2
S0.0221777447193 Å °0.0549242844304 Å °0.0153868469873 Å °0.0509727742611 Å °-0.0798630803929 Å °0.0584311359007 Å °0.0444007962826 Å °0.0850100519738 Å °2.45598090771E-10 Å °
Refinement TLS groupSelection details: all

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