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- PDB-7cd3: Crystal structure of the S103F mutant of Bacillus subtilis (natto... -

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Basic information

Entry
Database: PDB / ID: 7cd3
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 / YjgF/YER057c/UK114 family / Endoribonuclease L-PSP / RutC-like superfamily
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

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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
E: YabJ protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,88829
Polymers68,6385
Non-polymers2,25024
Water2,378132
1
A: YabJ protein
B: YabJ protein
C: YabJ protein
D: YabJ protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,60022
Polymers54,9114
Non-polymers1,68918
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13180 Å2
ΔGint-160 kcal/mol
Surface area18160 Å2
MethodPISA
2
E: YabJ protein
hetero molecules

E: YabJ protein
hetero molecules

E: YabJ protein
hetero molecules

E: YabJ protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,15328
Polymers54,9114
Non-polymers2,24224
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_556-x,y,-z+11
crystal symmetry operation4_556x,-y,-z+11
Buried area14590 Å2
ΔGint-219 kcal/mol
Surface area16570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.896, 108.598, 118.474
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein
YabJ protein


Mass: 13727.664 Da / Num. of mol.: 5 / 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
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 132 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.31 Å3/Da / Density % sol: 46.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 3.5
Details: 1.8 M ammonium sulfate, 1 mM zinc acetate, 0.1 M citric acid buffer pH 3.5

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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 19, 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: 37727 / % possible obs: 99.7 % / Redundancy: 9.3 % / Biso Wilson estimate: 33 Å2 / Rmerge(I) obs: 0.114 / Rpim(I) all: 0.038 / Χ2: 1.057 / Net I/σ(I): 12.4
Reflection shellResolution: 2.1→2.16 Å / Redundancy: 8 % / Rmerge(I) obs: 0.608 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 3711 / Rpim(I) all: 0.225 / Χ2: 1.244 / % possible all: 99.9

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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→80.05 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.92 / SU B: 6.27 / SU ML: 0.16 / Cross valid method: THROUGHOUT / ESU R: 0.225 / ESU R Free: 0.199 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25321 1950 5.3 %RANDOM
Rwork0.1944 ---
obs0.19753 35062 99.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 39.042 Å2
Baniso -1Baniso -2Baniso -3
1--1.19 Å20 Å20 Å2
2--0.02 Å20 Å2
3---1.17 Å2
Refinement stepCycle: 1 / Resolution: 2.1→80.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4443 0 134 132 4709
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0194655
X-RAY DIFFRACTIONr_bond_other_d0.0020.024288
X-RAY DIFFRACTIONr_angle_refined_deg1.5781.9716302
X-RAY DIFFRACTIONr_angle_other_deg0.9639981
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8055572
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.67225.817208
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.47415761
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.6491510
X-RAY DIFFRACTIONr_chiral_restr0.0910.2735
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215084
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02862
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_it2.7523.7532294
X-RAY DIFFRACTIONr_mcbond_other2.743.7512293
X-RAY DIFFRACTIONr_mcangle_it4.2785.6092861
X-RAY DIFFRACTIONr_mcangle_other4.285.6112862
X-RAY DIFFRACTIONr_scbond_it3.2564.2192359
X-RAY DIFFRACTIONr_scbond_other3.2544.2192359
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.1466.1663440
X-RAY DIFFRACTIONr_long_range_B_refined8.14845.5825017
X-RAY DIFFRACTIONr_long_range_B_other8.14845.5815015
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 128 -
Rwork0.278 2583 -
obs--99.82 %

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