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- PDB-5mq9: Crystal structure of Rae1 (YacP) from Bacillus subtilis (W164L mutant) -

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Basic information

Entry
Database: PDB / ID: 5mq9
TitleCrystal structure of Rae1 (YacP) from Bacillus subtilis (W164L mutant)
ComponentsUncharacterized protein YacP
KeywordsTRANSLATION / B. subtilis / RNA maturation and decay / endonuclease / peptide toxin
Function / homologyNYN/PIN ribonuclease, YacP-like / YacP-like NYN domain / Uncharacterized protein YacP
Function and homology information
Biological speciesBacillus subtilis subsp. subtilis str. 168 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 3.174 Å
AuthorsPiton, J. / Gilet, L. / Pellegrini, O. / Leroy, M. / Figaro, S. / Condon, C.
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 1.2Oct 16, 2019Group: Data collection / Category: reflns_shell
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
B: Uncharacterized protein YacP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,1185
Polymers41,8302
Non-polymers2883
Water66737
1
A: Uncharacterized protein YacP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1073
Polymers20,9151
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Uncharacterized protein YacP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,0112
Polymers20,9151
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.700, 63.950, 138.430
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: 20914.822 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Gene: yacP, BSU00970 / Plasmid: pet28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P37574
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / 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: 3.05 Å3/Da / Density % sol: 59.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.8 / Details: 0.05 M sodium acetate, 2M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 1.3051 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jul 8, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.3051 Å / Relative weight: 1
ReflectionResolution: 3.17→20 Å / Num. obs: 9099 / % possible obs: 100 % / Redundancy: 3.6 % / Biso Wilson estimate: 68.77 Å2 / Net I/σ(I): 12.11

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
SCALAdata scaling
autoSHARPphasing
RefinementMethod to determine structure: SIRAS / Resolution: 3.174→19.996 Å / SU ML: 0.52 / Cross valid method: THROUGHOUT / σ(F): 1.32 / Phase error: 33.86 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.3202 420 4.62 %RANDOM
Rwork0.2809 ---
obs0.2828 9096 99.91 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.174→19.996 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2449 0 15 37 2501
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032488
X-RAY DIFFRACTIONf_angle_d0.4983361
X-RAY DIFFRACTIONf_dihedral_angle_d17.211511
X-RAY DIFFRACTIONf_chiral_restr0.038388
X-RAY DIFFRACTIONf_plane_restr0.002436
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1741-3.6310.38811300.31642850X-RAY DIFFRACTION100
3.631-4.56570.32311440.26832846X-RAY DIFFRACTION100
4.5657-19.99610.28911460.27252980X-RAY DIFFRACTION100

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