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- PDB-8gp0: crystal structure of SulE -

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Basic information

Entry
Database: PDB / ID: 8gp0
Titlecrystal structure of SulE
ComponentsAlpha/beta fold hydrolase
KeywordsHYDROLASE / SulE / wild type
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
CITRIC ACID / Alpha/beta fold hydrolase
Similarity search - Component
Biological speciesHansschlegelia zhihuaiae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.46 Å
AuthorsLiu, B. / Ran, T. / wang, W. / He, J.
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
DepositionAug 25, 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)83,1959
Polymers82,3512
Non-polymers8457
Water16,087893
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8870 Å2
ΔGint-28 kcal/mol
Surface area24540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.373, 139.194, 57.913
Angle α, β, γ (deg.)90.000, 101.290, 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: 41175.301 Da / Num. of mol.: 2
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, Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 893 / 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: 2.47 Å3/Da / Density % sol: 50.12 %
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: BL19U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 29, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.46→50 Å / Num. obs: 131514 / % possible obs: 99 % / Redundancy: 6.5 % / CC1/2: 0.99 / Rpim(I) all: 0.037 / Net I/σ(I): 20.78
Reflection shellResolution: 1.46→1.49 Å / Redundancy: 4.6 % / Num. unique obs: 4799 / CC1/2: 0.874 / Rpim(I) all: 0.204

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Processing

Software
NameVersionClassification
PHENIXv1.16refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7YD2

7yd2


Resolution: 1.46→47.37 Å / Cross valid method: FREE R-VALUE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1693 --
Rwork0.152 --
obs-131303 95.17 %
Displacement parametersBiso mean: 19.76 Å2
Refinement stepCycle: LAST / Resolution: 1.46→47.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5472 0 56 893 6421
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075733
X-RAY DIFFRACTIONf_angle_d0.87617801
X-RAY DIFFRACTIONf_chiral_restr0.0888813
X-RAY DIFFRACTIONf_plane_restr0.0061032
X-RAY DIFFRACTIONf_dihedral_angle_d16.52243354

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