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- PDB-6qy6: Crystal structure of the CCA-adding enzyme of a psychrophilic organism -

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Basic information

Entry
Database: PDB / ID: 6qy6
TitleCrystal structure of the CCA-adding enzyme of a psychrophilic organism
ComponentsCCA-adding enzyme
KeywordsRNA BINDING PROTEIN / tRNA maturation / tRNA nucleotidyltransferase / psychrophilic enzyme
Function / homology
Function and homology information


tRNA processing / nucleotidyltransferase activity / tRNA binding / nucleotide 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 ...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
ACETATE ION / PHOSPHATE ION / CCA-adding protein
Similarity search - Component
Biological speciesPlanococcus halocryophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
Authorsde Wijn, R. / Rollet, K. / 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 BiologyANR-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. / Wellner, K. / Betat, H. / Morl, M. / Sauter, C.
History
DepositionMar 8, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 25, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 16, 2020Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.2Nov 3, 2021Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_2 / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Jan 24, 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

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Assembly

Deposited unit
A: CCA-adding enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,9557
Polymers48,4981
Non-polymers4566
Water4,288238
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS, gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1260 Å2
ΔGint-11 kcal/mol
Surface area18920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.031, 70.031, 291.590
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


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-30(+) / Details (production host): pET-30 Ek/LIC / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A1C7DQ98, CCA tRNA nucleotidyltransferase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


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


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 238 / 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: 3.62 Å3/Da / Density % sol: 65.98 % / Description: bipyramid
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: protein solution at 4.5 mg/mL in 50 mM Tris-HCl pH7.5, 200 mM NaCl, 5 mM MgCl2; reservoir solution: 100 mM Sodium acetate; pH 4.5 1 M di-Ammonium hydrogen phosphate
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: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 68555 / % possible obs: 99.9 % / Redundancy: 13 % / Biso Wilson estimate: 44.8 Å2 / CC1/2: 1 / Rrim(I) all: 0.074 / Net I/σ(I): 19.5
Reflection shellResolution: 1.8→1.91 Å / Redundancy: 12.9 % / Mean I/σ(I) obs: 0.66 / Num. unique obs: 10787 / CC1/2: 0.59 / Rrim(I) all: 2.648 / % possible all: 99.3

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDS20160617data reduction
XSCALE20160617data scaling
PHENIX1.13_2998phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MIV

1miv


Resolution: 1.8→39.926 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 27.6
RfactorNum. reflection% reflection
Rfree0.2321 3420 5 %
Rwork0.207 --
obs0.2083 68408 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.8→39.926 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3043 0 29 238 3310
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073125
X-RAY DIFFRACTIONf_angle_d0.7944211
X-RAY DIFFRACTIONf_dihedral_angle_d14.9221169
X-RAY DIFFRACTIONf_chiral_restr0.051468
X-RAY DIFFRACTIONf_plane_restr0.004531
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.82570.51471310.47692496X-RAY DIFFRACTION96
1.8257-1.8530.50171410.47532650X-RAY DIFFRACTION99
1.853-1.88190.50291400.42312657X-RAY DIFFRACTION100
1.8819-1.91280.44511410.36562665X-RAY DIFFRACTION100
1.9128-1.94580.34031400.34182684X-RAY DIFFRACTION100
1.9458-1.98120.40231390.31192656X-RAY DIFFRACTION100
1.9812-2.01930.31591400.27172644X-RAY DIFFRACTION100
2.0193-2.06050.31051410.26252712X-RAY DIFFRACTION100
2.0605-2.10530.26981400.24962643X-RAY DIFFRACTION100
2.1053-2.15430.28781410.24212679X-RAY DIFFRACTION100
2.1543-2.20810.29961420.24362686X-RAY DIFFRACTION100
2.2081-2.26780.27531410.24582689X-RAY DIFFRACTION100
2.2678-2.33450.25281430.22852709X-RAY DIFFRACTION100
2.3345-2.40990.23761420.21542696X-RAY DIFFRACTION100
2.4099-2.4960.27811400.21612680X-RAY DIFFRACTION100
2.496-2.59590.21931430.21612712X-RAY DIFFRACTION100
2.5959-2.7140.25641430.2112706X-RAY DIFFRACTION100
2.714-2.85710.24131430.21422720X-RAY DIFFRACTION100
2.8571-3.0360.23851440.21482748X-RAY DIFFRACTION100
3.036-3.27040.23711440.21852728X-RAY DIFFRACTION100
3.2704-3.59930.22621460.20512767X-RAY DIFFRACTION100
3.5993-4.11960.18971490.17362816X-RAY DIFFRACTION100
4.1196-5.18850.17251470.15722813X-RAY DIFFRACTION100
5.1885-39.93620.20391590.18153032X-RAY DIFFRACTION100

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