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- PDB-8sut: Crystal structure of YisK from Bacillus subtilis in complex with ... -

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Basic information

Entry
Database: PDB / ID: 8sut
TitleCrystal structure of YisK from Bacillus subtilis in complex with reaction product 4-Hydroxy-2-oxoglutaric acid
ComponentsFumarylacetoacetate hydrolase family protein
KeywordsHYDROLASE / fumarylacetoacetate hydrolase / decarboxylase / elongasome
Function / homologyFumarylacetoacetase-like, C-terminal / Fumarylacetoacetase-like, C-terminal domain superfamily / Fumarylacetoacetate (FAA) hydrolase family / isomerase activity / hydrolase activity / Chem-IO9 / : / Fumarylacetoacetate hydrolase family protein
Function and homology information
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsKrieger, I.V. / Chemelewski, V. / Guo, T. / Sperber, A. / Herman, J. / Sacchettini, J.C.
Funding support United States, 1items
OrganizationGrant numberCountry
Welch FoundationA-0015 United States
CitationJournal: J.Bacteriol. / Year: 2024
Title: Bacillus subtilis YisK possesses oxaloacetate decarboxylase activity and exhibits Mbl-dependent localization.
Authors: Guo, T. / Sperber, A.M. / Krieger, I.V. / Duan, Y. / Chemelewski, V.R. / Sacchettini, J.C. / Herman, J.K.
History
DepositionMay 13, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 1, 2023Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: 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.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 7, 2024Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fumarylacetoacetate hydrolase family protein
B: Fumarylacetoacetate hydrolase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,5356
Polymers69,1012
Non-polymers4344
Water2,666148
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3400 Å2
ΔGint-30 kcal/mol
Surface area23640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.686, 93.983, 124.981
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 Fumarylacetoacetate hydrolase family protein


Mass: 34550.441 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: B4122_0586 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0D6X359
#2: Chemical ChemComp-IO9 / (2~{R})-2-oxidanyl-4-oxidanylidene-pentanedioic acid


Mass: 162.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H6O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 148 / 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: 2.37 Å3/Da / Density % sol: 48.12 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / Details: 0.2 M Mg-acetate and 20% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 120 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.97934 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 12, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.93→47.04 Å / Num. obs: 47426 / % possible obs: 98.2 % / Redundancy: 4.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.035 / Net I/σ(I): 12.4
Reflection shellResolution: 1.93→1.98 Å / Rmerge(I) obs: 1.5 / Num. unique obs: 2885 / CC1/2: 0.259 / Rpim(I) all: 0.921

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Processing

Software
NameVersionClassification
REFMAC2000refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.93→47.04 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.953 / SU B: 5.829 / SU ML: 0.149 / Cross valid method: THROUGHOUT / ESU R: 0.156 / ESU R Free: 0.148 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2299 1998 4.2 %RANDOM
Rwork0.18295 ---
obs0.18491 45270 97.7 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.623 Å2
Baniso -1Baniso -2Baniso -3
1-1.7 Å20 Å20 Å2
2---0.79 Å20 Å2
3----0.91 Å2
Refinement stepCycle: LAST / Resolution: 1.93→47.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4662 0 24 148 4834
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0174780
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164512
X-RAY DIFFRACTIONr_angle_refined_deg1.361.8556445
X-RAY DIFFRACTIONr_angle_other_deg0.4541.57210576
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.1385.169623
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.94310886
X-RAY DIFFRACTIONr_chiral_restr0.0670.2730
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025320
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02848
X-RAY DIFFRACTIONr_mcbond_it5.6944.3992411
X-RAY DIFFRACTIONr_mcbond_other5.6944.3992411
X-RAY DIFFRACTIONr_mcangle_it6.9526.5863009
X-RAY DIFFRACTIONr_mcangle_other6.9526.5873010
X-RAY DIFFRACTIONr_scbond_it8.4185.2922369
X-RAY DIFFRACTIONr_scbond_other8.375.2882364
X-RAY DIFFRACTIONr_scangle_other11.2657.5573436
X-RAY DIFFRACTIONr_long_range_B_refined12.87654.7425011
X-RAY DIFFRACTIONr_long_range_B_other12.89554.6964988
LS refinement shellResolution: 1.93→1.98 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.346 118 -
Rwork0.378 2682 -
obs--79.12 %

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