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- PDB-8ivn: crystal structure of SulE mutant -

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Basic information

Entry
Database: PDB / ID: 8ivn
Titlecrystal structure of SulE mutant
ComponentsAlpha/beta fold hydrolase
KeywordsHYDROLASE / Complex / SulE / 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 / L(+)-TARTARIC ACID / Alpha/beta fold hydrolase
Similarity search - Component
Biological speciesHansschlegelia zhihuaiae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsLiu, B. / He, J. / Ran, T. / 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
DepositionMar 28, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 2, 2023Provider: repository / Type: Initial release

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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)83,8139
Polymers82,1842
Non-polymers1,6287
Water15,331851
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9510 Å2
ΔGint-20 kcal/mol
Surface area24960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.230, 139.730, 58.150
Angle α, β, γ (deg.)90.000, 101.420, 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


Mass: 41092.234 Da / Num. of mol.: 2 / Mutation: S209A,H333A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hansschlegelia zhihuaiae (bacteria) / Gene: EK403_17710 / Production host: Escherichia coli (E. coli) / References: UniProt: G9I933
#2: Chemical ChemComp-1MM / METHYL 2-[({[(4-METHOXY-6-METHYL-1,3,5-TRIAZIN-2-YL)AMINO]CARBONYL}AMINO)SULFONYL]BENZOATE / METSULFURON METHYL / Metsulfuron-methyl


Mass: 381.364 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C14H15N5O6S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-TLA / L(+)-TARTARIC ACID / Tartaric acid


Mass: 150.087 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O6 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 851 / 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: 50.45 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: PEG

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 1, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.5→42.03 Å / Num. obs: 126161 / % possible obs: 98.9 % / Redundancy: 6 % / CC1/2: 0.992 / Rpim(I) all: 0.04 / Net I/σ(I): 16.4
Reflection shellResolution: 1.5→1.54 Å / Num. unique obs: 8460 / CC1/2: 0.698 / Rpim(I) all: 0.395

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Processing

Software
NameVersionClassification
PHENIXv1.16refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8GOL

8gol


Resolution: 1.5→40.78 Å / Cross valid method: FREE R-VALUE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1797 --
Rwork0.1635 --
obs-126085 98.8 %
Displacement parametersBiso mean: 17.94 Å2
Refinement stepCycle: LAST / Resolution: 1.5→40.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5466 0 110 851 6427
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00895765
X-RAY DIFFRACTIONf_angle_d1.01067842
X-RAY DIFFRACTIONf_chiral_restr0.0736813
X-RAY DIFFRACTIONf_plane_restr0.0061034
X-RAY DIFFRACTIONf_dihedral_angle_d16.60533356

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