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- PDB-5yu2: Structure of Ribonuclease YabJ -

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Basic information

Entry
Database: PDB / ID: 5yu2
TitleStructure of Ribonuclease YabJ
ComponentsTranslation initiation inhibitor homologue
KeywordsGENE REGULATION / SAV0497 / YabJ / ribonuclease
Function / homology
Function and homology information


RidA, conserved site / Uncharacterized protein family UPF0076 signature. / RidA family / YjgF/YER057c/UK114 family / Endoribonuclease L-PSP / RutC-like / RutC-like superfamily / 60s Ribosomal Protein L30; Chain: A; / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Translation initiation inhibitor homologue
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsKim, H.J. / Kwon, A.R. / Lee, B.J.
Funding support Korea, Republic Of, 3items
OrganizationGrant numberCountry
National Research Foundation (Korea)2015R1A2A1A05001894 Korea, Republic Of
National Research Foundation (Korea)2014K1A3A1A19067618 Korea, Republic Of
National Research Foundation (Korea)2010-0025488 Korea, Republic Of
CitationJournal: Biosci. Rep. / Year: 2018
Title: A novel chlorination-induced ribonuclease YabJ fromStaphylococcus aureus.
Authors: Kim, H.J. / Kwon, A.R. / Lee, B.J.
History
DepositionNov 20, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 26, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 31, 2018Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Nov 22, 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: Translation initiation inhibitor homologue
B: Translation initiation inhibitor homologue
C: Translation initiation inhibitor homologue
D: Translation initiation inhibitor homologue
E: Translation initiation inhibitor homologue
F: Translation initiation inhibitor homologue


Theoretical massNumber of molelcules
Total (without water)85,6586
Polymers85,6586
Non-polymers00
Water8,989499
1
A: Translation initiation inhibitor homologue
B: Translation initiation inhibitor homologue
C: Translation initiation inhibitor homologue


Theoretical massNumber of molelcules
Total (without water)42,8293
Polymers42,8293
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5930 Å2
ΔGint-33 kcal/mol
Surface area15120 Å2
MethodPISA
2
D: Translation initiation inhibitor homologue
E: Translation initiation inhibitor homologue
F: Translation initiation inhibitor homologue


Theoretical massNumber of molelcules
Total (without water)42,8293
Polymers42,8293
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5880 Å2
ΔGint-38 kcal/mol
Surface area14200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.118, 83.216, 89.358
Angle α, β, γ (deg.)90.00, 94.29, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Translation initiation inhibitor homologue


Mass: 14276.385 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (strain Mu50 / ATCC 700699) (bacteria)
Strain: Mu50 / ATCC 700699 / Gene: SAV0497 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0H3JTJ5
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 499 / 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: 2.04 Å3/Da / Density % sol: 39.69 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 25% (w/v) PEG 3350, 100 mM Tris/HCl, pH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 7, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 65604 / % possible obs: 99.1 % / Redundancy: 2.1 % / Net I/σ(I): 42.6
Reflection shellResolution: 1.75→1.78 Å / % possible all: 95.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
MxDCdata collection
HKL-2000data scaling
MOLREP11.4.06phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1QD9

1qd9


Resolution: 1.75→46.99 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.954 / SU B: 2.416 / SU ML: 0.077 / Cross valid method: THROUGHOUT / ESU R: 0.113 / ESU R Free: 0.112 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20206 3325 4.8 %RANDOM
Rwork0.15968 ---
obs0.16181 65604 99.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 24.614 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.75→46.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5820 0 0 499 6319
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0195920
X-RAY DIFFRACTIONr_bond_other_d0.0020.025758
X-RAY DIFFRACTIONr_angle_refined_deg1.8881.9768014
X-RAY DIFFRACTIONr_angle_other_deg1.058313435
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.965752
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.16226.356247
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.703151125
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4491518
X-RAY DIFFRACTIONr_chiral_restr0.1220.2958
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0216466
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021000
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.4172.2063002
X-RAY DIFFRACTIONr_mcbond_other2.4152.2053001
X-RAY DIFFRACTIONr_mcangle_it3.4223.2953744
X-RAY DIFFRACTIONr_mcangle_other3.4223.2963745
X-RAY DIFFRACTIONr_scbond_it3.2342.6092918
X-RAY DIFFRACTIONr_scbond_other3.232.6092918
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.9763.7474266
X-RAY DIFFRACTIONr_long_range_B_refined6.44227.6666471
X-RAY DIFFRACTIONr_long_range_B_other6.2627.2386351
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.748→1.793 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.266 236 -
Rwork0.228 4726 -
obs--97.43 %

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