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- PDB-7oqx: Crystal structure of a psychrophilic CCA-adding enzyme in complex... -

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Basic information

Entry
Database: PDB / ID: 7oqx
TitleCrystal structure of a psychrophilic CCA-adding enzyme in complex with CMPcPP
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
Chem-2TM / ACETATE ION / PHOSPHATE ION / CCA-adding protein
Similarity search - Component
Biological speciesPlanococcus halocryophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsRollet, K. / de Wijn, R. / Bluhm, A. / Hennig, O. / Betat, H. / Moerl, M. / Lorber, B. / Sauter, C.
Funding support France, 2items
OrganizationGrant numberCountry
French National Research AgencyANR-10-LABX-0036_NETRNA France
French Infrastructure for Integrated Structural Biology (FRISBI)ANR-10-INSB-05 France
CitationJournal: Comput Struct Biotechnol J / Year: 2021
Title: CCA-addition in the cold: Structural characterization of the psychrophilic CCA-adding enzyme from the permafrost bacterium Planococcus halocryophilus .
Authors: de Wijn, R. / Rollet, K. / Ernst, F.G.M. / Wellner, K. / Betat, H. / Morl, M. / Sauter, C.
History
DepositionJun 4, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 3, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 24, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)49,79314
Polymers48,4981
Non-polymers1,29513
Water1,78399
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS, gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1770 Å2
ΔGint-12 kcal/mol
Surface area19560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.800, 69.800, 290.850
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

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Protein , 1 types, 1 molecules A

#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-30bEk/LIC / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1C7DQ98

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Non-polymers , 5 types, 112 molecules

#2: Chemical ChemComp-2TM / 5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]cytidine / CMPcPP


Mass: 481.184 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H18N3O13P3
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 99 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.66 Å3/Da / Density % sol: 66.37 % / Description: bipyramid
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: protein solution at 4.5 mg/mL in 50 mM Tris-HCl pH 7.5, 200 mM NaCl, 5 mM MgCl2; reservoir solution: 100 mM Sodium acetate; pH 4.5 1 M di-Ammonium hydrogen phosphate remarks : soaking 30 ...Details: protein solution at 4.5 mg/mL in 50 mM Tris-HCl pH 7.5, 200 mM NaCl, 5 mM MgCl2; reservoir solution: 100 mM Sodium acetate; pH 4.5 1 M di-Ammonium hydrogen phosphate remarks : soaking 30 seconds in a drop with 10 mM CMPcPP and reservoir solution + 20% glycerol
PH range: 4.5 - 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9786 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 9, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 37711 / % possible obs: 99.8 % / Redundancy: 25.7 % / Biso Wilson estimate: 50.85 Å2 / CC1/2: 0.99 / Rrim(I) all: 0.15 / Net I/av σ(I): 16.84 / Net I/σ(I): 16.84
Reflection shellResolution: 2.2→2.34 Å / Redundancy: 27.1 % / Mean I/σ(I) obs: 1.98 / Num. unique obs: 5903 / CC1/2: 0.786 / Rrim(I) all: 1.616 / % possible all: 99.3

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDS20200417data reduction
XSCALE20200417data scaling
PHENIX1.19.2_4158phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6QXN

6qxn


Resolution: 2.2→46.74 Å / SU ML: 0.2954 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.6168
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2424 1886 5 %
Rwork0.2055 35825 -
obs0.2073 37711 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 51.98 Å2
Refinement stepCycle: LAST / Resolution: 2.2→46.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3005 0 81 99 3185
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00823163
X-RAY DIFFRACTIONf_angle_d0.93034271
X-RAY DIFFRACTIONf_chiral_restr0.0575471
X-RAY DIFFRACTIONf_plane_restr0.0078532
X-RAY DIFFRACTIONf_dihedral_angle_d15.97971180
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.260.30131410.25962672X-RAY DIFFRACTION99.36
2.26-2.330.34411420.23942694X-RAY DIFFRACTION99.61
2.33-2.40.28921410.23232690X-RAY DIFFRACTION99.75
2.4-2.490.28891420.24112693X-RAY DIFFRACTION99.79
2.49-2.590.28231430.24482715X-RAY DIFFRACTION99.9
2.59-2.70.33741430.27652714X-RAY DIFFRACTION99.93
2.7-2.850.29241420.25462708X-RAY DIFFRACTION99.96
2.85-3.020.28581450.26052756X-RAY DIFFRACTION99.97
3.03-3.260.30341450.26542739X-RAY DIFFRACTION99.97
3.26-3.590.27951450.21662769X-RAY DIFFRACTION99.97
3.59-4.10.20511490.1712822X-RAY DIFFRACTION100
4.11-5.170.18541480.1472818X-RAY DIFFRACTION100
5.17-46.740.19521600.18853035X-RAY DIFFRACTION99.69

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