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- PDB-7cd4: Crystal structure of the S103F mutant of Bacillus subtilis (natto... -

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Basic information

Entry
Database: PDB / ID: 7cd4
TitleCrystal structure of the S103F mutant of Bacillus subtilis (natto) YabJ protein.
ComponentsYabJ protein
KeywordsUNKNOWN FUNCTION / Mutant / Homotetramer
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
Biological speciesBacillus subtilis subsp. natto (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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
DepositionJun 18, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 3, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: YabJ protein
B: YabJ protein
C: YabJ protein
D: YabJ protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,74421
Polymers54,9114
Non-polymers83317
Water3,459192
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8920 Å2
ΔGint-235 kcal/mol
Surface area19570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.101, 85.506, 106.537
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
YabJ protein


Mass: 13727.664 Da / Num. of mol.: 4 / Mutation: S103F
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

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Non-polymers , 5 types, 209 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER


Mass: 209.240 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 192 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationY

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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: 2.68 Å3/Da / Density % sol: 54.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 13.5 % PEG 3350, 1 mM zinc acetate, 0.2 M magnesium chloride, 0.1 M Bis-Tris buffer pH 5.5

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 9, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→100 Å / Num. obs: 34597 / % possible obs: 99.3 % / Redundancy: 13.9 % / Biso Wilson estimate: 26 Å2 / Rmerge(I) obs: 0.109 / Χ2: 1.037 / Net I/σ(I): 15.9
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 13.3 % / Rmerge(I) obs: 0.684 / Mean I/σ(I) obs: 3 / Num. unique obs: 3375 / Χ2: 1.184 / % possible all: 98.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5Y6U

5y6u


Resolution: 2.1→66.68 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.94 / SU B: 4.593 / SU ML: 0.118 / Cross valid method: THROUGHOUT / ESU R: 0.184 / ESU R Free: 0.164 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2254 1729 5 %RANDOM
Rwork0.18498 ---
obs0.18693 32822 99.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 34.553 Å2
Baniso -1Baniso -2Baniso -3
1-0.41 Å20 Å20 Å2
2--1.58 Å20 Å2
3----1.99 Å2
Refinement stepCycle: 1 / Resolution: 2.1→66.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3573 0 30 192 3795
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0193658
X-RAY DIFFRACTIONr_bond_other_d0.0020.023393
X-RAY DIFFRACTIONr_angle_refined_deg1.4271.9544964
X-RAY DIFFRACTIONr_angle_other_deg0.92737896
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8135457
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.87325.783166
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.40215611
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.88158
X-RAY DIFFRACTIONr_chiral_restr0.0910.2572
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214071
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02689
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_it2.1673.3211840
X-RAY DIFFRACTIONr_mcbond_other2.1663.321839
X-RAY DIFFRACTIONr_mcangle_it3.4914.9632293
X-RAY DIFFRACTIONr_mcangle_other3.4914.9642294
X-RAY DIFFRACTIONr_scbond_it2.6013.6661818
X-RAY DIFFRACTIONr_scbond_other2.5983.6661818
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.2535.3632671
X-RAY DIFFRACTIONr_long_range_B_refined6.02439.9933977
X-RAY DIFFRACTIONr_long_range_B_other6.0239.9673971
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.102→2.156 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 133 -
Rwork0.266 2331 -
obs--97.08 %

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