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- PDB-8suu: Crystal structure of YisK from Bacillus subtilis in apo form -

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Basic information

Entry
Database: PDB / ID: 8suu
TitleCrystal structure of YisK from Bacillus subtilis in apo form
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 / : / Fumarylacetoacetate hydrolase family protein
Function and homology information
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.26 Å
AuthorsKrieger, I.V. / Chemelewski, V. / Guo, T. / Sperber, A. / Herman, J. / Sacchettini, J.C.
Funding support United States, 2items
OrganizationGrant numberCountry
Welch FoundationA-0015 United States
National Science Foundation (NSF, United States)1514629 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)69,2114
Polymers69,1012
Non-polymers1102
Water90150
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 area23440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.937, 93.768, 125.484
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-MN / MANGANESE (II) ION


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


Mass: 18.015 Da / Num. of mol.: 50 / 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: 2.47 Å3/Da / Density % sol: 50.25 %
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: 0.97 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 12, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.26→46.93 Å / Num. obs: 30609 / % possible obs: 100 % / Redundancy: 6.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.117 / Rpim(I) all: 0.07 / Net I/σ(I): 11.9
Reflection shellResolution: 2.26→2.32 Å / Rmerge(I) obs: 2.209 / Num. unique obs: 2217 / CC1/2: 0.298 / Rpim(I) all: 1.423

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Processing

Software
NameVersionClassification
REFMAC2000refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.26→46.93 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.937 / SU B: 26.289 / SU ML: 0.259 / Cross valid method: THROUGHOUT / ESU R: 0.324 / ESU R Free: 0.235 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.25478 1995 6.5 %RANDOM
Rwork0.21094 ---
obs0.21376 28549 99.92 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 64.315 Å2
Baniso -1Baniso -2Baniso -3
1--0.99 Å2-0 Å20 Å2
2--1.34 Å2-0 Å2
3----0.35 Å2
Refinement stepCycle: LAST / Resolution: 2.26→46.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4502 0 2 50 4554
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0174585
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164366
X-RAY DIFFRACTIONr_angle_refined_deg1.1411.8516180
X-RAY DIFFRACTIONr_angle_other_deg0.3851.5710226
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.1095.168596
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.40110856
X-RAY DIFFRACTIONr_chiral_restr0.0550.2704
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025072
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02820
X-RAY DIFFRACTIONr_mcbond_it1.773.1742319
X-RAY DIFFRACTIONr_mcbond_other1.773.1742319
X-RAY DIFFRACTIONr_mcangle_it2.8894.7552890
X-RAY DIFFRACTIONr_mcangle_other2.8884.7552891
X-RAY DIFFRACTIONr_scbond_it2.0893.4582266
X-RAY DIFFRACTIONr_scbond_other2.093.4582265
X-RAY DIFFRACTIONr_scangle_other3.3985.0813291
X-RAY DIFFRACTIONr_long_range_B_refined5.27339.8644742
X-RAY DIFFRACTIONr_long_range_B_other5.27139.8414740
LS refinement shellResolution: 2.26→2.319 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.391 139 -
Rwork0.393 2067 -
obs--99.91 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.3123-0.0427-0.42372.6763-0.0151.82530.0071-0.1346-0.00930.1896-0.065-0.0010.03050.06010.05790.3046-0.0216-0.00880.03240.0470.235-24.86.60817.202
21.5839-0.0096-0.30122.1726-0.80652.516-0.02990.176-0.1144-0.4531-0.06370.02120.4259-0.05650.09370.53570.00190.0120.0397-0.02470.3383-22.831-0.99-13.204
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 301
2X-RAY DIFFRACTION2B1 - 303

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