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- PDB-5y5r: Crystal structure of a novel Pyrethroid Hydrolase PytH with BIF -

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Basic information

Entry
Database: PDB / ID: 5y5r
TitleCrystal structure of a novel Pyrethroid Hydrolase PytH with BIF
ComponentsPyrethroid hydrolase
KeywordsHYDROLASE / PytH
Function / homology
Function and homology information


jasmonic acid metabolic process / methyl salicylate esterase activity / salicylic acid metabolic process
Similarity search - Function
Methylesterase/Alpha-hydroxynitrile lyase / Alpha/beta hydrolase family / Epoxide hydrolase-like / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
Chem-8NL / Pyrethroid hydrolase
Similarity search - Component
Biological speciesSphingobium faniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.899 Å
AuthorsXu, D.Q. / Ran, T.T. / Wang, W.W.
CitationJournal: To Be Published
Title: Structure and Catalytic Mechanism of a Novel Pyrethroid Hydrolase from Sphingobium faniae JZ-2
Authors: Xu, D.Q. / Ran, T.T. / He, J. / Wang, W.W.
History
DepositionAug 9, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 15, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pyrethroid hydrolase
B: Pyrethroid hydrolase
C: Pyrethroid hydrolase
D: Pyrethroid hydrolase
E: Pyrethroid hydrolase
F: Pyrethroid hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)191,74418
Polymers188,6306
Non-polymers3,11412
Water8,485471
1
A: Pyrethroid hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9573
Polymers31,4381
Non-polymers5192
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Pyrethroid hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9573
Polymers31,4381
Non-polymers5192
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Pyrethroid hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9573
Polymers31,4381
Non-polymers5192
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Pyrethroid hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9573
Polymers31,4381
Non-polymers5192
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Pyrethroid hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9573
Polymers31,4381
Non-polymers5192
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Pyrethroid hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9573
Polymers31,4381
Non-polymers5192
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)168.857, 168.857, 123.864
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

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Components

#1: Protein
Pyrethroid hydrolase


Mass: 31438.330 Da / Num. of mol.: 6 / Fragment: UNP residues 2-280
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sphingobium faniae (bacteria) / Gene: pytH / Production host: Escherichia coli (E. coli) / References: UniProt: D0VUS3
#2: Chemical
ChemComp-8NL / (2-methyl-3-phenyl-phenyl)methyl (1~{S})-3-[(~{E})-2-chloranyl-3,3,3-tris(fluoranyl)prop-1-enyl]-2,2-dimethyl-cyclopropane-1-carboxylate


Mass: 422.868 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C23H22ClF3O2
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 471 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.34 Å3/Da / Density % sol: 47.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.7 / Details: Ammonium Sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 15, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.899→20 Å / Num. obs: 139606 / % possible obs: 99.3 % / Redundancy: 14.9 % / Net I/σ(I): 7.91
Reflection shellResolution: 1.9→2.01 Å / Redundancy: 14.1 % / Mean I/σ(I) obs: 1.18 / Num. unique obs: 41697 / % possible all: 96.1

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Processing

Software
NameVersionClassification
PHENIX(dev_2247: ???)refinement
XDSdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.899→19.913 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 36.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.322 7012 5.02 %
Rwork0.2732 --
obs0.2756 139583 99.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.899→19.913 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11367 0 204 471 12042
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01111917
X-RAY DIFFRACTIONf_angle_d1.46116353
X-RAY DIFFRACTIONf_dihedral_angle_d16.8967053
X-RAY DIFFRACTIONf_chiral_restr0.0751819
X-RAY DIFFRACTIONf_plane_restr0.012178
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8988-1.92030.36972050.37293679X-RAY DIFFRACTION84
1.9203-1.94290.45882160.39874410X-RAY DIFFRACTION100
1.9429-1.96660.4012470.35674377X-RAY DIFFRACTION100
1.9666-1.99150.37732190.35834410X-RAY DIFFRACTION100
1.9915-2.01760.37562170.34754382X-RAY DIFFRACTION100
2.0176-2.04530.39252360.3584390X-RAY DIFFRACTION100
2.0453-2.07440.4272370.36794406X-RAY DIFFRACTION100
2.0744-2.10540.41362250.36014401X-RAY DIFFRACTION100
2.1054-2.13820.42442450.35334414X-RAY DIFFRACTION100
2.1382-2.17320.39042250.33124394X-RAY DIFFRACTION100
2.1732-2.21070.36132250.33134416X-RAY DIFFRACTION100
2.2107-2.25080.40962110.3394441X-RAY DIFFRACTION100
2.2508-2.29410.36972410.34364400X-RAY DIFFRACTION100
2.2941-2.34080.3932120.32444434X-RAY DIFFRACTION100
2.3408-2.39160.3872330.31484404X-RAY DIFFRACTION100
2.3916-2.44720.36422290.31774430X-RAY DIFFRACTION100
2.4472-2.50820.36312700.3134354X-RAY DIFFRACTION100
2.5082-2.57590.37882350.30444424X-RAY DIFFRACTION100
2.5759-2.65160.34072430.29334455X-RAY DIFFRACTION100
2.6516-2.73690.32132370.27474405X-RAY DIFFRACTION100
2.7369-2.83450.32982390.28974459X-RAY DIFFRACTION100
2.8345-2.94760.34222130.29814467X-RAY DIFFRACTION100
2.9476-3.08130.35452510.29074439X-RAY DIFFRACTION100
3.0813-3.24310.33672390.27374457X-RAY DIFFRACTION100
3.2431-3.44530.29982640.26094461X-RAY DIFFRACTION100
3.4453-3.70980.29972470.23494453X-RAY DIFFRACTION100
3.7098-4.08020.27772310.23194508X-RAY DIFFRACTION100
4.0802-4.6640.27052490.20494535X-RAY DIFFRACTION100
4.664-5.85130.23622210.21094600X-RAY DIFFRACTION100
5.8513-19.91440.22962500.19924766X-RAY DIFFRACTION100

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