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- PDB-8zu4: Crystal Structure of Methyl parathion hydrolase mutant A127L/I145... -

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Basic information

Entry
Database: PDB / ID: 8zu4
TitleCrystal Structure of Methyl parathion hydrolase mutant A127L/I145L/Q272D/S279A/S304P
ComponentsMethyl parathion hydrolase
KeywordsHYDROLASE
Function / homology: / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / hydrolase activity / metal ion binding / Methyl parathion hydrolase
Function and homology information
Biological speciesPseudomonas sp. WBC-3 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.39 Å
AuthorsXu, F. / Fan, S.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)22078129 China
CitationJournal: To Be Published
Title: Crystal Structure of Methyl parathion hydrolase mutant A127L/I145L/Q272D/S279A/S304P
Authors: Xu, F. / Fan, S. / Li, Y.
History
DepositionJun 7, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jun 11, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Methyl parathion hydrolase
B: Methyl parathion hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,0296
Polymers62,7672
Non-polymers2624
Water11,602644
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4800 Å2
ΔGint-168 kcal/mol
Surface area22840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.233, 86.320, 58.800
Angle α, β, γ (deg.)90.00, 112.81, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Methyl parathion hydrolase


Mass: 31383.578 Da / Num. of mol.: 2 / Mutation: A127L,I145L,Q272D, S279A,S304P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas sp. WBC-3 (bacteria) / Gene: mpd / Production host: Escherichia coli (E. coli) / References: UniProt: Q841S6
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 644 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.38 Å3/Da / Density % sol: 48.24 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Bis-Tris pH 6.5, 28% w/v Polyethylene glycol monomethyl ether 2,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.9791 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 9, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.39→19.73 Å / Num. obs: 159152 / % possible obs: 74.5 % / Redundancy: 5.81 % / CC1/2: 0.999 / Rmerge(I) obs: 0.023 / Rrim(I) all: 0.033 / Net I/σ(I): 8.13
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
1.39-1.470.6746270.370.9531
1.47-1.570.57824620.6460.8181
1.57-1.70.20248470.9190.2851
1.7-1.860.09889130.9740.1391
1.86-2.080.06587930.9890.0921
2.08-2.390.04278300.9940.061
2.39-2.920.02761720.9970.0391
2.92-4.080.01942300.9980.0261
1.44-4.080.01922420.9980.0261

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.39→19.73 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.55 / Phase error: 28.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1979 3874 2.43 %
Rwork0.1667 --
obs0.1675 159152 68.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.39→19.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4418 0 4 644 5066
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_angle_d0.8236146
X-RAY DIFFRACTIONf_dihedral_angle_d13.8561628
X-RAY DIFFRACTIONf_chiral_restr0.08694
X-RAY DIFFRACTIONf_plane_restr0.007806
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.39-1.40.683750.4704114X-RAY DIFFRACTION1
1.4-1.420.3664170.3664429X-RAY DIFFRACTION20
1.42-1.440.4957260.4313847X-RAY DIFFRACTION20
1.44-1.460.4752270.46851290X-RAY DIFFRACTION20
1.46-1.480.424300.42231699X-RAY DIFFRACTION21
1.48-1.50.3469630.34692274X-RAY DIFFRACTION28
1.5-1.530.43680.40912623X-RAY DIFFRACTION33
1.53-1.550.3076940.30763259X-RAY DIFFRACTION40
1.55-1.580.303840.29993771X-RAY DIFFRACTION46
1.58-1.610.3425870.29764277X-RAY DIFFRACTION52
1.64-1.670.29331600.25745225X-RAY DIFFRACTION65
1.71-1.750.25231820.22776854X-RAY DIFFRACTION85
1.75-1.790.23131760.21927815X-RAY DIFFRACTION96
1.79-1.840.23921960.20257972X-RAY DIFFRACTION98
1.84-1.890.24762150.20168040X-RAY DIFFRACTION99
1.89-1.960.24221820.22637788X-RAY DIFFRACTION96
1.96-2.030.20012150.1758047X-RAY DIFFRACTION99
2.03-2.110.19541870.17927985X-RAY DIFFRACTION98
2.11-2.20.17511920.16418062X-RAY DIFFRACTION100
2.2-2.320.21982170.18187992X-RAY DIFFRACTION98
2.32-2.460.1932050.16998054X-RAY DIFFRACTION99
2.46-2.650.20881990.1688043X-RAY DIFFRACTION99
2.65-2.920.16371950.15858036X-RAY DIFFRACTION99
2.92-3.340.1912090.1388109X-RAY DIFFRACTION99
3.34-4.20.16631970.12958028X-RAY DIFFRACTION99

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