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- PDB-8goy: SulE P44R -

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Basic information

Entry
Database: PDB / ID: 8goy
TitleSulE P44R
ComponentsAlpha/beta fold hydrolase
KeywordsHYDROLASE / SulE P44R
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-JV6 / Alpha/beta fold hydrolase
Similarity search - Component
Biological speciesHansschlegelia zhihuaiae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.784 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
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

Downloads & links

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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)83,2257
Polymers82,4712
Non-polymers7555
Water10,665592
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7910 Å2
ΔGint-29 kcal/mol
Surface area24900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.353, 139.450, 58.125
Angle α, β, γ (deg.)90.000, 101.670, 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: 41235.379 Da / Num. of mol.: 2 / Mutation: P44R
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.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-JV6 / 5-[(4,6-dimethoxypyrimidin-2-yl)carbamoylsulfamoyl]-1-methyl-pyrazole-4-carboxylic acid


Mass: 386.341 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H14N6O7S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 592 / 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: 50.23 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: PEG 4000

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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 PILATUS3 6M / Detector: PIXEL / Date: Sep 30, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.78→47.31 Å / Num. obs: 74840 / % possible obs: 98.3 % / Redundancy: 6.3 % / CC1/2: 0.997 / Net I/σ(I): 11.7
Reflection shellResolution: 1.78→1.82 Å / Num. unique obs: 3200 / CC1/2: 0.572

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Processing

Software
NameVersionClassification
PHENIXv1.16refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4Q34

4q34


Resolution: 1.784→47.31 Å / Cross valid method: FREE R-VALUE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1853 --
Rwork0.1585 --
obs-74772 98.44 %
Displacement parametersBiso mean: 19.42 Å2
Refinement stepCycle: LAST / Resolution: 1.784→47.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5479 0 50 592 6121
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00725737
X-RAY DIFFRACTIONf_angle_d0.91767801
X-RAY DIFFRACTIONf_chiral_restr0.0688811
X-RAY DIFFRACTIONf_plane_restr0.00591029
X-RAY DIFFRACTIONf_dihedral_angle_d15.96953356

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