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- PDB-7qzp: Identification and characterization of an RRM-containing, ELAV-li... -

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Basic information

Entry
Database: PDB / ID: 7qzp
TitleIdentification and characterization of an RRM-containing, ELAV-like, RNA binding protein in Acinetobacter Baumannii
ComponentsHypothetical RNA binding protein from Acinetobacter baumannii
KeywordsRNA BINDING PROTEIN / RNA / Acinetobacter / RRM / HUR
Function / homology: / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily / RNA binding / RRM domain-containing protein
Function and homology information
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsCiani, C. / Perez-Rafols, A. / Bonomo, I. / Micaelli, M. / Esposito, A. / Zucal, C. / Belli, R. / D'Agostino, V.G. / Bianconi, I. / Calderone, V. ...Ciani, C. / Perez-Rafols, A. / Bonomo, I. / Micaelli, M. / Esposito, A. / Zucal, C. / Belli, R. / D'Agostino, V.G. / Bianconi, I. / Calderone, V. / Cerofolini, L. / Fragai, M. / Provenzani, A.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
H2020 Marie Curie Actions of the European CommissionH2020-MSCA-ITN-2018European Union
CitationJournal: Biomolecules / Year: 2022
Title: Identification and Characterization of an RRM-Containing, RNA Binding Protein in Acinetobacter baumannii .
Authors: Ciani, C. / Perez-Rafols, A. / Bonomo, I. / Micaelli, M. / Esposito, A. / Zucal, C. / Belli, R. / D'Agostino, V.G. / Bianconi, I. / Calderone, V. / Cerofolini, L. / Massidda, O. / Whalen, M. ...Authors: Ciani, C. / Perez-Rafols, A. / Bonomo, I. / Micaelli, M. / Esposito, A. / Zucal, C. / Belli, R. / D'Agostino, V.G. / Bianconi, I. / Calderone, V. / Cerofolini, L. / Massidda, O. / Whalen, M.B. / Fragai, M. / Provenzani, A.
History
DepositionJan 31, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 13, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2022Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
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

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Assembly

Deposited unit
A: Hypothetical RNA binding protein from Acinetobacter baumannii


Theoretical massNumber of molelcules
Total (without water)10,9751
Polymers10,9751
Non-polymers00
Water81145
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area4650 Å2
Unit cell
Length a, b, c (Å)69.560, 69.560, 32.460
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number80
Space group name H-MI41

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Components

#1: Protein Hypothetical RNA binding protein from Acinetobacter baumannii


Mass: 10975.097 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Gene: HMPREF0022_00746 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A828SWT5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 1.79 Å3/Da / Density % sol: 31.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 0.1 M sodium acetate trihydrate, 3 M sodium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: BRUKER D8 QUEST / Wavelength: 1.5418 Å
DetectorType: Bruker PHOTON III / Detector: PIXEL / Date: Mar 2, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.65→19 Å / Num. obs: 8220 / % possible obs: 87.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.7 % / CC1/2: 0.99 / Rsym value: 0.079 / Net I/σ(I): 18.76
Reflection shellResolution: 1.65→1.75 Å / Mean I/σ(I) obs: 1.7 / Num. unique obs: 857 / CC1/2: 0.53 / Rsym value: 0.85

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Processing

Software
NameVersionClassification
PHENIX1.20rc1_4392refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1fxl

1fxl


Resolution: 1.65→18.87 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 31.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.23 411 5 %
Rwork0.2122 7803 -
obs0.2131 8214 87.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 106.02 Å2 / Biso mean: 36.745 Å2 / Biso min: 16.47 Å2
Refinement stepCycle: final / Resolution: 1.65→18.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms601 0 0 46 647
Biso mean---36.72 -
Num. residues----78
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.65-1.890.2685990.26791889198864
1.89-2.380.24721520.22982879303197
2.39-18.870.22091600.200630353195100
Refinement TLS params.Method: refined / Origin x: 31.3397 Å / Origin y: 25.2325 Å / Origin z: -7.0562 Å
111213212223313233
T0.19 Å2-0.0321 Å2-0.0155 Å2-0.2232 Å2-0.0026 Å2--0.1877 Å2
L4.1903 °20.3817 °2-0.3457 °2-4.0087 °2-0.278 °2--1.6959 °2
S0.0597 Å °-0.2113 Å °0.0735 Å °0.278 Å °-0.065 Å °-0.395 Å °-0.105 Å °0.3988 Å °0.016 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA19 - 96
2X-RAY DIFFRACTION1allS1 - 64

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