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- PDB-4r1j: Crystal structure of Arc1p-C -

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Basic information

Entry
Database: PDB / ID: 4r1j
TitleCrystal structure of Arc1p-C
ComponentsGU4 nucleic-binding protein 1
KeywordsRNA BINDING PROTEIN / EMAP / tRNA binding / tRNA
Function / homology
Function and homology information


methionyl glutamyl tRNA synthetase complex / glutamyl-tRNA aminoacylation / tyrosine-tRNA ligase activity / methionyl-tRNA aminoacylation / tRNA aminoacylation for protein translation / phosphatidylinositol-3-phosphate binding / phosphatidylinositol-3,5-bisphosphate binding / enzyme activator activity / cytoplasmic stress granule / tRNA binding / cytoplasm
Similarity search - Function
tRNA-binding domain / Putative tRNA binding domain / tRNA-binding domain profile. / Glutathione S-transferase, C-terminal domain superfamily / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
tRNA-aminoacylation cofactor ARC1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsAltegoer, F. / Bange, G.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2015
Title: A Synthetic Adenylation-Domain-Based tRNA-Aminoacylation Catalyst.
Authors: Giessen, T.W. / Altegoer, F. / Nebel, A.J. / Steinbach, R.M. / Bange, G. / Marahiel, M.A.
History
DepositionAug 6, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 18, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 11, 2015Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GU4 nucleic-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,1472
Polymers22,0551
Non-polymers921
Water4,810267
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.658, 49.961, 82.941
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein GU4 nucleic-binding protein 1 / G4p1 protein / P42 / Protein ARC1


Mass: 22055.178 Da / Num. of mol.: 1 / Fragment: unp residues 201-376
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: ARC1, G4P1, YGL105W, G3085 / Production host: Escherichia coli (E. coli) / References: UniProt: P46672
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 267 / 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: 2 Å3/Da / Density % sol: 38.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.1M MES, pH 6.0, 10 % v/v glycerol, 30 % w/v PEG 600 and 5 % w/v PEG 1000, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97871 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 28, 2014
RadiationMonochromator: Single crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97871 Å / Relative weight: 1
ReflectionResolution: 1.4→42.8 Å / Num. obs: 35696 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 13.3
Reflection shellResolution: 1.4→1.48 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 3 / % possible all: 99.1

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Processing

Software
NameVersionClassification
DNAdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FL0

1fl0


Resolution: 1.4→42.796 Å / SU ML: 0.12 / σ(F): 0 / Phase error: 20.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2013 1687 4.85 %RANDOM
Rwork0.1768 ---
obs0.178 34792 97.41 %-
all-0 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.4→42.796 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1370 0 6 267 1643
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061416
X-RAY DIFFRACTIONf_angle_d1.1481910
X-RAY DIFFRACTIONf_dihedral_angle_d12.041549
X-RAY DIFFRACTIONf_chiral_restr0.078207
X-RAY DIFFRACTIONf_plane_restr0.005251
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3994-1.44050.26911120.24392538X-RAY DIFFRACTION91
1.4405-1.4870.27581390.21672649X-RAY DIFFRACTION95
1.487-1.54020.23641330.20542662X-RAY DIFFRACTION96
1.5402-1.60190.20661370.18922697X-RAY DIFFRACTION96
1.6019-1.67480.2161540.1762687X-RAY DIFFRACTION97
1.6748-1.76310.20051130.17672768X-RAY DIFFRACTION98
1.7631-1.87350.1961460.17242768X-RAY DIFFRACTION99
1.8735-2.01820.2021600.17332776X-RAY DIFFRACTION99
2.0182-2.22130.21611350.16592814X-RAY DIFFRACTION99
2.2213-2.54270.19691550.17942846X-RAY DIFFRACTION100
2.5427-3.20330.18471520.18262871X-RAY DIFFRACTION100
3.2033-42.81640.18951510.16293029X-RAY DIFFRACTION100

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