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- PDB-8yrc: Chlorinated YabJ from Staphylococcus aureus -

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Basic information

Entry
Database: PDB / ID: 8yrc
TitleChlorinated YabJ from Staphylococcus aureus
ComponentsTranslation initiation inhibitor homologue
KeywordsSTRUCTURAL PROTEIN / ribonuclease / stress-response protein
Function / homologyRidA, conserved site / Uncharacterized protein family UPF0076 signature. / RidA family / YjgF/YER057c/UK114 family / Endoribonuclease L-PSP / RutC-like superfamily / OXYGEN ATOM / Translation initiation inhibitor homologue
Function and homology information
Biological speciesStaphylococcus aureus subsp. aureus Mu50 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsJeong, C. / Kim, H.J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2024
Title: YabJ from Staphylococcus aureus entraps chlorides within its pocket.
Authors: Jeong, C. / Kim, H.J.
History
DepositionMar 21, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 24, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Translation initiation inhibitor homologue
B: Translation initiation inhibitor homologue
C: Translation initiation inhibitor homologue
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,9046
Polymers42,8293
Non-polymers743
Water1,51384
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6210 Å2
ΔGint-58 kcal/mol
Surface area14740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.690, 75.350, 52.830
Angle α, β, γ (deg.)90.00, 103.05, 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.: 3
Source method: isolated from a genetically manipulated source
Details: MKIINTTRLPEALGPYSHATVVNGMVYTSGQIPLNVDGKIVSADVQAQTKQVLENLKVVL EEAGSDLNSVAKATIFIKDMNDFQKINEVYGQYFNEHKPARSCVEVARLPKDVKVEIELV SKIKEL
Source: (gene. exp.) Staphylococcus aureus subsp. aureus Mu50 (bacteria)
Gene: SAV0497 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0H3JTJ5
#2: Chemical ChemComp-O / OXYGEN ATOM / Oxygen


Mass: 15.999 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 84 / 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: 2.34 Å3/Da / Density % sol: 47.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 25% (w/v) PEG3350 and 100 mM Tris/HCl, pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: May 4, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.7→35.95 Å / Num. obs: 46373 / % possible obs: 97.6 % / Redundancy: 1.8 % / CC1/2: 0.99 / Net I/σ(I): 10.3
Reflection shellResolution: 1.7→1.73 Å / Num. unique obs: 2847 / CC1/2: 0.36

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5YU2

5yu2


Resolution: 1.7→32.51 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.967 / SU B: 1.896 / SU ML: 0.065 / Cross valid method: THROUGHOUT / ESU R: 0.026 / ESU R Free: 0.025 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2092 2041 4.8 %RANDOM
Rwork0.1829 ---
obs0.21645 40321 97.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.531 Å2
Baniso -1Baniso -2Baniso -3
1-12.69 Å20 Å2-1.56 Å2
2---5.44 Å20 Å2
3----7.25 Å2
Refinement stepCycle: 1 / Resolution: 1.7→32.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2904 0 3 84 2991
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0132947
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172860
X-RAY DIFFRACTIONr_angle_refined_deg1.8421.6393987
X-RAY DIFFRACTIONr_angle_other_deg1.3671.5796673
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8215373
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.10525.263133
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.25115559
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.23159
X-RAY DIFFRACTIONr_chiral_restr0.0920.2402
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.023220
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02507
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_it3.3933.7691495
X-RAY DIFFRACTIONr_mcbond_other3.3873.7671494
X-RAY DIFFRACTIONr_mcangle_it4.3895.6441864
X-RAY DIFFRACTIONr_mcangle_other4.395.6461865
X-RAY DIFFRACTIONr_scbond_it4.484.2011452
X-RAY DIFFRACTIONr_scbond_other4.4784.2031453
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.3176.112123
X-RAY DIFFRACTIONr_long_range_B_refined7.28144.8043098
X-RAY DIFFRACTIONr_long_range_B_other7.29344.7633085
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree1.032 168 -
Rwork1.007 2750 -
obs--91.3 %

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