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- PDB-7cd2: Crystal structure of the S103F mutant of Bacillus subtilis (natto... -

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Basic information

Entry
Database: PDB / ID: 7cd2
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: 2.7 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 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
D: YabJ protein
E: YabJ protein
F: YabJ protein
G: YabJ protein
H: YabJ protein
I: YabJ protein
J: YabJ protein
K: YabJ protein
L: YabJ protein
M: YabJ protein
N: YabJ protein
O: YabJ protein
P: YabJ protein
Q: YabJ protein
R: YabJ protein
S: YabJ protein
T: YabJ protein


Theoretical massNumber of molelcules
Total (without water)274,55320
Polymers274,55320
Non-polymers00
Water00
1
A: YabJ protein
B: YabJ protein
C: YabJ protein
D: YabJ protein


Theoretical massNumber of molelcules
Total (without water)54,9114
Polymers54,9114
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6240 Å2
ΔGint-34 kcal/mol
Surface area19120 Å2
MethodPISA
2
E: YabJ protein
F: YabJ protein
G: YabJ protein
H: YabJ protein


Theoretical massNumber of molelcules
Total (without water)54,9114
Polymers54,9114
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6020 Å2
ΔGint-34 kcal/mol
Surface area18690 Å2
MethodPISA
3
I: YabJ protein
J: YabJ protein
K: YabJ protein
L: YabJ protein


Theoretical massNumber of molelcules
Total (without water)54,9114
Polymers54,9114
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6160 Å2
ΔGint-29 kcal/mol
Surface area18630 Å2
MethodPISA
4
M: YabJ protein
N: YabJ protein
O: YabJ protein
P: YabJ protein


Theoretical massNumber of molelcules
Total (without water)54,9114
Polymers54,9114
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6240 Å2
ΔGint-31 kcal/mol
Surface area18760 Å2
MethodPISA
5
Q: YabJ protein
R: YabJ protein
S: YabJ protein
T: YabJ protein


Theoretical massNumber of molelcules
Total (without water)54,9114
Polymers54,9114
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6110 Å2
ΔGint-33 kcal/mol
Surface area18670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.984, 96.121, 263.314
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
YabJ protein


Mass: 13727.664 Da / Num. of mol.: 20 / 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
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: 2.23 Å3/Da / Density % sol: 44.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 25% PEG 4000, 0.45 M ammonium acetate, 0.1 M sodium acetate buffer pH 4.2

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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: Jun 23, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→150 Å / Num. obs: 62923 / % possible obs: 93.3 % / Redundancy: 11.8 % / Biso Wilson estimate: 42.2 Å2 / Rmerge(I) obs: 0.115 / Χ2: 1.207 / Net I/σ(I): 15.5
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 11.5 % / Rmerge(I) obs: 0.733 / Mean I/σ(I) obs: 3.1 / Num. unique obs: 6046 / Χ2: 1.397 / % possible all: 91.3

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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: 2.7→39.912 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.892 / SU B: 16.258 / SU ML: 0.323 / Cross valid method: THROUGHOUT / ESU R Free: 0.415 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27701 3166 5 %RANDOM
Rwork0.18581 ---
obs0.19046 59674 93.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 54.087 Å2
Baniso -1Baniso -2Baniso -3
1-0.16 Å20 Å20 Å2
2---1.09 Å20 Å2
3---0.93 Å2
Refinement stepCycle: 1 / Resolution: 2.7→39.912 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16838 0 0 0 16838
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.01917182
X-RAY DIFFRACTIONr_bond_other_d0.0020.0215925
X-RAY DIFFRACTIONr_angle_refined_deg2.1381.95223307
X-RAY DIFFRACTIONr_angle_other_deg1.156337051
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.13652149
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.74225.993806
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.382152924
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.4691540
X-RAY DIFFRACTIONr_chiral_restr0.1180.22687
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02119219
X-RAY DIFFRACTIONr_gen_planes_other0.0020.023257
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_it5.5135.3248647
X-RAY DIFFRACTIONr_mcbond_other5.515.3238646
X-RAY DIFFRACTIONr_mcangle_it8.2467.95610779
X-RAY DIFFRACTIONr_mcangle_other8.2457.95610780
X-RAY DIFFRACTIONr_scbond_it5.6685.7028535
X-RAY DIFFRACTIONr_scbond_other5.6675.7028535
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.3968.36312528
X-RAY DIFFRACTIONr_long_range_B_refined11.04662.25118253
X-RAY DIFFRACTIONr_long_range_B_other11.04662.25518254
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.704→2.774 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.475 217 -
Rwork0.317 4145 -
obs--87.94 %

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