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- PDB-5y51: Crystal structure of PytH_H230A -

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Basic information

Entry
Database: PDB / ID: 5y51
TitleCrystal structure of PytH_H230A
ComponentsPyrethroid hydrolase
KeywordsHYDROLASE
Function / homologyMethylesterase/Alpha-hydroxynitrile lyase / Alpha/beta hydrolase family / Epoxide hydrolase-like / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold / hydrolase activity / Pyrethroid hydrolase
Function and homology information
Biological speciesSphingobium faniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsXu, D.Q. / Ran, T.T. / He, J. / Wang, W.W.
Funding support China, 1items
OrganizationGrant numberCountry
State's Key Project of Research and Development Plan2016YFD0801102 China
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 6, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 8, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)186,83412
Polymers186,2586
Non-polymers5766
Water59433
1
A: Pyrethroid hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1392
Polymers31,0431
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Pyrethroid hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1392
Polymers31,0431
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Pyrethroid hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1392
Polymers31,0431
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Pyrethroid hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1392
Polymers31,0431
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Pyrethroid hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1392
Polymers31,0431
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Pyrethroid hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1392
Polymers31,0431
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)168.375, 168.375, 123.858
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: 31042.998 Da / Num. of mol.: 6 / Mutation: H230A
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-SO4 / SULFATE ION / Sulfate


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


Mass: 18.015 Da / Num. of mol.: 33 / Source method: isolated from a natural source / Formula: H2O

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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: 2.36 Å3/Da / Density % sol: 47.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / 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: Oct 15, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. obs: 75180 / % possible obs: 95.4 % / Observed criterion σ(I): 1.9 / Redundancy: 7.7 % / Net I/σ(I): 8
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 7.7 % / Mean I/σ(I) obs: 1.9 / Num. unique obs: 11027 / % possible all: 97

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Processing

Software
NameVersionClassification
PHENIX(dev_2247: ???)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→19.816 Å / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 36.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.33 3779 5.04 %
Rwork0.269 --
obs0.272 74982 94.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→19.816 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11351 0 30 33 11414
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01111678
X-RAY DIFFRACTIONf_angle_d1.14515989
X-RAY DIFFRACTIONf_dihedral_angle_d18.5556995
X-RAY DIFFRACTIONf_chiral_restr0.0591801
X-RAY DIFFRACTIONf_plane_restr0.0092129
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.32910.45721420.35432637X-RAY DIFFRACTION97
2.3291-2.35970.45871290.35212667X-RAY DIFFRACTION97
2.3597-2.39190.43191550.34482614X-RAY DIFFRACTION96
2.3919-2.42610.40481200.33612683X-RAY DIFFRACTION96
2.4261-2.46220.39931410.31822666X-RAY DIFFRACTION97
2.4622-2.50060.39091230.30542656X-RAY DIFFRACTION96
2.5006-2.54150.35231530.30442633X-RAY DIFFRACTION96
2.5415-2.58530.37191560.31422631X-RAY DIFFRACTION96
2.5853-2.63220.34611640.31782615X-RAY DIFFRACTION96
2.6322-2.68270.40771310.38852593X-RAY DIFFRACTION94
2.6827-2.73730.44871390.32562611X-RAY DIFFRACTION96
2.7373-2.79660.34171510.32372643X-RAY DIFFRACTION96
2.7966-2.86150.48631360.3292632X-RAY DIFFRACTION96
2.8615-2.93290.35791330.30662637X-RAY DIFFRACTION95
2.9329-3.01190.36741450.30572629X-RAY DIFFRACTION95
3.0119-3.10020.36861260.29992637X-RAY DIFFRACTION95
3.1002-3.19990.3751230.29562670X-RAY DIFFRACTION95
3.1999-3.31370.3581570.28712626X-RAY DIFFRACTION95
3.3137-3.44570.35211450.31192607X-RAY DIFFRACTION94
3.4457-3.60170.34541560.2742610X-RAY DIFFRACTION95
3.6017-3.79030.3121320.30232618X-RAY DIFFRACTION94
3.7903-4.02590.34371510.28472606X-RAY DIFFRACTION93
4.0259-4.33380.27931500.20932633X-RAY DIFFRACTION94
4.3338-4.76440.23581250.19622634X-RAY DIFFRACTION93
4.7644-5.44130.31111320.20632647X-RAY DIFFRACTION93
5.4413-6.8090.25591410.21052632X-RAY DIFFRACTION92
6.809-19.81630.1891230.16992736X-RAY DIFFRACTION90

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