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- PDB-5y6u: Crystal structure of wild-type YabJ protein from Bacillus subtili... -

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Basic information

Entry
Database: PDB / ID: 5y6u
TitleCrystal structure of wild-type YabJ protein from Bacillus subtilis (natto).
ComponentsYabJ protein
KeywordsUNKNOWN FUNCTION / Homotrimer
Function / homology
Function and homology information


deaminase activity / metal ion binding / cytosol
Similarity search - Function
RidA, conserved site / Uncharacterized protein family UPF0076 signature. / RidA family / RutC-like / YjgF/YER057c/UK114 family / Endoribonuclease L-PSP / RutC-like superfamily / 60s Ribosomal Protein L30; Chain: A; / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETIC ACID / RidA family protein
Similarity search - Component
Biological speciesBacillus subtilis subsp. natto (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsFujimoto, Z. / Kishine, N. / Kimura, K.
CitationJournal: Biosci.Biotechnol.Biochem. / Year: 2021
Title: Tetramer formation of Bacillus subtilis YabJ protein that belongs to YjgF/YER057c/UK114 family.
Authors: Fujimoto, Z. / Hong, L.T.T. / Kishine, N. / Suzuki, N. / Kimura, K.
History
DepositionAug 15, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 15, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
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: YabJ protein
B: YabJ protein
C: YabJ protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,3639
Polymers41,0033
Non-polymers3606
Water9,944552
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5610 Å2
ΔGint-32 kcal/mol
Surface area14410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.767, 53.767, 203.941
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein YabJ protein


Mass: 13667.567 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. natto (strain BEST195) (bacteria)
Strain: BEST195 / Gene: yabJ, BSNT_00084 / Plasmid: pET22b(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: D4G3D4
#2: Chemical
ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H4O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 552 / 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: 2.08 Å3/Da / Density % sol: 40.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 22.5% PEG 3350, 0.45 M ammonium acetate, 0.1 M sodium acetate buffer pH 4.2

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 23, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→100 Å / Num. obs: 53138 / % possible obs: 100 % / Redundancy: 21.2 % / Biso Wilson estimate: 12 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 57.6
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 21.7 % / Rmerge(I) obs: 0.554 / Mean I/σ(I) obs: 6.6 / Num. unique obs: 2636 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1QD9

1qd9


Resolution: 1.5→46.56 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.959 / SU B: 1.166 / SU ML: 0.044 / Cross valid method: THROUGHOUT / ESU R: 0.076 / ESU R Free: 0.073 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18024 2699 5.1 %RANDOM
Rwork0.16059 ---
obs0.1616 50332 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 14.205 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20.01 Å20 Å2
2--0.01 Å20 Å2
3----0.05 Å2
Refinement stepCycle: 1 / Resolution: 1.5→46.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2856 0 24 552 3432
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0193007
X-RAY DIFFRACTIONr_bond_other_d0.0020.022803
X-RAY DIFFRACTIONr_angle_refined_deg1.1691.9544091
X-RAY DIFFRACTIONr_angle_other_deg1.11436548
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0265376
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.91225.802131
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.26515512
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.643156
X-RAY DIFFRACTIONr_chiral_restr0.0690.2478
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213352
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02546
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_it0.6021.2891510
X-RAY DIFFRACTIONr_mcbond_other0.6011.2871508
X-RAY DIFFRACTIONr_mcangle_it1.0671.9251877
X-RAY DIFFRACTIONr_mcangle_other1.0671.9261878
X-RAY DIFFRACTIONr_scbond_it0.6721.3831497
X-RAY DIFFRACTIONr_scbond_other0.6711.3831498
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.0962.042207
X-RAY DIFFRACTIONr_long_range_B_refined4.02117.7833529
X-RAY DIFFRACTIONr_long_range_B_other3.87817.3763469
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.204 188 -
Rwork0.201 3686 -
obs--99.28 %

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