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- PDB-7yd2: SulE_P44R_S209A -

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Basic information

Entry
Database: PDB / ID: 7yd2
TitleSulE_P44R_S209A
ComponentsAlpha/beta fold hydrolase
KeywordsHYDROLASE / complex
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-CIE / Chem-IJC / Alpha/beta fold hydrolase
Similarity search - Component
Biological speciesHansschlegelia zhihuaiae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.61 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
DepositionJul 3, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 19, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 2, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)84,22412
Polymers82,4392
Non-polymers1,78510
Water12,142674
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8910 Å2
ΔGint-62 kcal/mol
Surface area24710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.310, 140.260, 58.190
Angle α, β, γ (deg.)90.000, 101.710, 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

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Protein , 1 types, 2 molecules AB

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


Mass: 41219.379 Da / Num. of mol.: 2 / Mutation: P44R,S209A
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

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Non-polymers , 6 types, 684 molecules

#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 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-IJC / 2-[(4-chloranyl-6-methoxy-pyrimidin-2-yl)carbamoylsulfamoyl]benzoic acid


Mass: 386.768 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H11ClN4O6S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-CIE / 2-[[[[(4-CHLORO-6-METHOXY-2-PYRIMIDINYL)AMINO]CARBONYL]AMINO]SULFONYL]BENZOIC ACID ETHYL ESTER / CHLORIMURON ETHYL


Mass: 414.821 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H15ClN4O6S / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 674 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.49 Å3/Da / Density % sol: 50.54 %
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: BL17U / Wavelength: 0.979183 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 13, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979183 Å / Relative weight: 1
ReflectionResolution: 1.61→70.13 Å / Num. obs: 102138 / % possible obs: 98.8 % / Redundancy: 6.3 % / CC1/2: 0.997 / Rpim(I) all: 0.031 / Net I/σ(I): 14.6
Reflection shellResolution: 1.61→1.65 Å / Num. unique obs: 7066 / CC1/2: 0.898 / Rpim(I) all: 0.192

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Processing

Software
NameVersionClassification
PHENIXv1.16refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7Y0L

7y0l


Resolution: 1.61→47.3 Å / Cross valid method: FREE R-VALUE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1812 --
Rwork0.1646 --
obs-102066 98.74 %
Displacement parametersBiso mean: 24.51 Å2
Refinement stepCycle: LAST / Resolution: 1.61→47.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5470 0 113 674 6257
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00745767
X-RAY DIFFRACTIONf_angle_d1.02977841
X-RAY DIFFRACTIONf_chiral_restr0.0734809
X-RAY DIFFRACTIONf_plane_restr0.00621031
X-RAY DIFFRACTIONf_dihedral_angle_d16.72923348

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