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- PDB-7jly: Crystal Structure of RNA Binding Protein PG1 -

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Basic information

Entry
Database: PDB / ID: 7jly
TitleCrystal Structure of RNA Binding Protein PG1
ComponentsRNA-binding protein
KeywordsRNA BINDING PROTEIN / P. Gingivalis-1
Function / homology
Function and homology information


RNA binding / metal ion binding
Similarity search - Function
: / : / 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
Similarity search - Domain/homology
ACETATE ION / RNA-binding protein
Similarity search - Component
Biological speciesPorphyromonas gingivalis W83 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.73 Å
AuthorsMusayev, F.N. / Scarsdale, J.N. / Belvin, B.R. / Lewis, J.P.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R21 DE023745 United States
CitationJournal: To be published
Title: High Resolution Structure of RNA Binding Protein PG1
Authors: Musayev, F.N. / Belvin, B.R. / Scarsdale, J.N. / Lewis, J.P.
History
DepositionJul 30, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 28, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: 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: RNA-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,6183
Polymers11,5191
Non-polymers992
Water2,090116
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.128, 40.128, 83.676
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-302-

HOH

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Components

#1: Protein RNA-binding protein


Mass: 11518.844 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porphyromonas gingivalis W83 (bacteria)
Strain: ATCC BAA-308 / W83 / Gene: PG_0627 / Plasmid: pET30a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q7MWI3
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.69 Å3/Da / Density % sol: 27.28 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 0.1M MES, pH6.0, 22% PEG 8000, 0.2M Ca Acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jul 29, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.73→34.76 Å / Num. obs: 8483 / % possible obs: 98.4 % / Redundancy: 17.57 % / Biso Wilson estimate: 21.63 Å2 / Rmerge(I) obs: 0.074 / Rrim(I) all: 0.076 / Χ2: 0.92 / Net I/σ(I): 22.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRrim(I) allΧ2% possible all
1.73-1.7914.590.3496.77760.3621.293.7
1.79-1.8617.750.2838.78220.2911.1397.4
1.86-1.9517.580.23410.48220.2411.0597.9
1.95-2.0517.730.17413.78430.1790.9797.8
2.05-2.1817.720.13816.98350.1420.9298.5
2.18-2.3517.340.1218.88430.1230.8899.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation1.73 Å34.75 Å
Translation1.73 Å34.75 Å

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Processing

Software
NameVersionClassification
d*TREK9.9.8.6 W9RSSIdata reduction
d*TREK9.9.8.6 W9RSSIdata scaling
PHASER2.8.2phasing
PHENIX1.9_1692refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4zka

4zka


Resolution: 1.73→34.752 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 24.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2113 400 4.72 %
Rwork0.1778 8083 -
obs0.1794 8483 98.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 71.42 Å2 / Biso mean: 24.2292 Å2 / Biso min: 14.41 Å2
Refinement stepCycle: final / Resolution: 1.73→34.752 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms676 0 5 116 797
Biso mean--29.4 29.76 -
Num. residues----83
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007695
X-RAY DIFFRACTIONf_angle_d0.969932
X-RAY DIFFRACTIONf_chiral_restr0.04698
X-RAY DIFFRACTIONf_plane_restr0.003129
X-RAY DIFFRACTIONf_dihedral_angle_d13.335271
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.7303-1.98070.28631340.2009258397
1.9807-2.49540.21141370.1904265699
2.4954-34.750.19461290.16772844100

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