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- PDB-5mq8: Crystal structure of Rae1 (YacP) from Bacillus subtilis -

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Basic information

Entry
Database: PDB / ID: 5mq8
TitleCrystal structure of Rae1 (YacP) from Bacillus subtilis
ComponentsUncharacterized protein YacP
KeywordsTRANSLATION / B. subtilis / RNA maturation and decay / endonuclease / peptide toxin
Function / homologyNYN/PIN ribonuclease, YacP-like / YacP-like NYN domain / mRNA catabolic process / RNA endonuclease activity / ribosome binding / Hydrolases; Acting on ester bonds / Ribosome-associated endoribonuclease 1
Function and homology information
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsPiton, J. / Gilet, L. / Pellegrini, O. / Leroy, M. / Figaro, S. / Condon, C.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research AgencysubtilNA2 France
CitationJournal: EMBO J. / Year: 2017
Title: Rae1/YacP, a new endoribonuclease involved in ribosome-dependent mRNA decay in Bacillus subtilis.
Authors: Leroy, M. / Piton, J. / Gilet, L. / Pellegrini, O. / Proux, C. / Coppee, J.Y. / Figaro, S. / Condon, C.
History
DepositionDec 20, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 19, 2017Provider: repository / Type: Initial release
Revision 1.1May 10, 2017Group: Database references
Revision 1.2Sep 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Uncharacterized protein YacP
D: Uncharacterized protein YacP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,0683
Polymers41,9762
Non-polymers921
Water3,063170
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4440 Å2
ΔGint-22 kcal/mol
Surface area17670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.628, 83.669, 95.729
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 Uncharacterized protein YacP


Mass: 20987.873 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Strain: 168 / Gene: yacP, BSU00970
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P37574
#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.: 170 / 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: 2.56 Å3/Da / Density % sol: 51.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Protein at 6 mg/mL in 0.07 M Tris-HCl pH 6.5, 5.2% PEG 8000, 35% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 22, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 2.25→25 Å / Num. obs: 21060 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 2 % / Biso Wilson estimate: 45.91 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.03017 / Net I/σ(I): 17.77
Reflection shellResolution: 2.25→2.33 Å / Redundancy: 2 % / Rmerge(I) obs: 0.2897 / Mean I/σ(I) obs: 2.68 / CC1/2: 0.844 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.25→23.87 Å / Cor.coef. Fo:Fc: 0.9331 / Cor.coef. Fo:Fc free: 0.9177 / SU R Cruickshank DPI: 0.266 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.281 / SU Rfree Blow DPI: 0.205 / SU Rfree Cruickshank DPI: 0.203
RfactorNum. reflection% reflectionSelection details
Rfree0.2394 1081 5.13 %RANDOM
Rwork0.2066 ---
obs0.2083 21060 99.99 %-
Displacement parametersBiso mean: 47.14 Å2
Baniso -1Baniso -2Baniso -3
1--2.3994 Å20 Å20 Å2
2---5.5549 Å20 Å2
3---7.9543 Å2
Refine analyzeLuzzati coordinate error obs: 0.314 Å
Refinement stepCycle: 1 / Resolution: 2.25→23.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2808 0 6 170 2984
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0092859HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.973849HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1073SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes86HARMONIC2
X-RAY DIFFRACTIONt_gen_planes404HARMONIC5
X-RAY DIFFRACTIONt_it2859HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.53
X-RAY DIFFRACTIONt_other_torsion18.83
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion376SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3300SEMIHARMONIC4
LS refinement shellResolution: 2.25→2.36 Å / Total num. of bins used: 11
RfactorNum. reflection% reflection
Rfree0.2789 132 4.81 %
Rwork0.2184 2612 -
all0.2212 2744 -
obs--100 %

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