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- PDB-7y0l: SulE-S209A -

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Basic information

Entry
Database: PDB / ID: 7y0l
TitleSulE-S209A
ComponentsAlpha/beta fold hydrolase
KeywordsHYDROLASE / complex / mutant
Function / homology
Function and homology information


Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases / hydrolase activity
Similarity search - Function
: / Alpha/beta hydrolase family / Alpha/beta hydrolase fold-1 / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
Chem-1MM / Alpha/beta fold hydrolase
Similarity search - Component
Biological speciesHansschlegelia zhihuaiae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.29 Å
AuthorsLiu, B. / Ran, T. / He, J. / Wang, W.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31970096 China
CitationJournal: Nat Commun / Year: 2023
Title: Crystal structures of herbicide-detoxifying esterase reveal a lid loop affecting substrate binding and activity.
Authors: Liu, B. / Wang, W. / Qiu, J. / Huang, X. / Qiu, S. / Bao, Y. / Xu, S. / Ruan, L. / Ran, T. / He, J.
History
DepositionJun 5, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 2, 2023Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alpha/beta fold hydrolase
B: Alpha/beta fold hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,5429
Polymers82,3192
Non-polymers1,2237
Water16,736929
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9330 Å2
ΔGint-25 kcal/mol
Surface area24470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.219, 139.863, 58.101
Angle α, β, γ (deg.)90.000, 101.600, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Alpha/beta fold hydrolase / Putative hydrolase


Mass: 41159.301 Da / Num. of mol.: 2 / Mutation: S209A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hansschlegelia zhihuaiae (bacteria) / Gene: EK403_17710 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: G9I933, Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases
#2: Chemical ChemComp-1MM / METHYL 2-[({[(4-METHOXY-6-METHYL-1,3,5-TRIAZIN-2-YL)AMINO]CARBONYL}AMINO)SULFONYL]BENZOATE / METSULFURON METHYL


Mass: 381.364 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H15N5O6S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 929 / 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: 2.48 Å3/Da / Density % sol: 50.33 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9789 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 29, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 1.29→50 Å / Num. obs: 193359 / % possible obs: 96.7 % / Redundancy: 6.6 % / CC1/2: 0.993 / Net I/σ(I): 28.5
Reflection shellResolution: 1.29→1.31 Å / Num. unique obs: 9349 / CC1/2: 0.925 / Rpim(I) all: 0.241 / % possible all: 93.4

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Processing

Software
NameVersionClassification
PHENIX1.16refinement
HKL-2000data reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4Q34

4q34


Resolution: 1.29→36.07 Å / Cross valid method: FREE R-VALUE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1672 --
Rwork0.1542 --
obs-193246 96.49 %
Displacement parametersBiso mean: 18.23 Å2
Refinement stepCycle: LAST / Resolution: 1.29→36.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5481 0 82 929 6492
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00685863
X-RAY DIFFRACTIONf_angle_d0.97787991
X-RAY DIFFRACTIONf_chiral_restr0.0896828
X-RAY DIFFRACTIONf_plane_restr0.00781060
X-RAY DIFFRACTIONf_dihedral_angle_d17.26623433

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