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- PDB-9izt: Crystal structure of a PU hydrolysis enzyme Aes72 from Comamonas ... -

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Basic information

Entry
Database: PDB / ID: 9izt
TitleCrystal structure of a PU hydrolysis enzyme Aes72 from Comamonas acidovorans
ComponentsAcetyl esterase/lipase
KeywordsHYDROLASE / PU / Degradation / enzyme
Function / homology
Function and homology information


triacylglycerol lipase activity
Similarity search - Function
Lipase, GDXG, putative histidine active site / Lipolytic enzymes "G-D-X-G" family, putative histidine active site. / Lipase, GDXG, putative serine active site / Lipolytic enzymes "G-D-X-G" family, putative serine active site. / : / Alpha/beta hydrolase fold-3 / alpha/beta hydrolase fold / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
Acetyl esterase/lipase
Similarity search - Component
Biological speciesDelftia acidovorans (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsHan, X. / Li, Z.S. / Liu, J.W. / Liu, W.D. / Dong, W.L.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Crystal structure of a PU hydrolysis enzyme Aes72 from Comamonas acidovorans
Authors: Han, X. / Li, Z.S. / Liu, J.W. / Liu, W.D. / Dong, W.L.
History
DepositionAug 1, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Feb 4, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Acetyl esterase/lipase
B: Acetyl esterase/lipase


Theoretical massNumber of molelcules
Total (without water)65,3162
Polymers65,3162
Non-polymers00
Water11,115617
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1890 Å2
ΔGint-14 kcal/mol
Surface area21720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.161, 71.121, 101.579
Angle α, β, γ (deg.)90.00, 104.11, 90.00
Int Tables number5
Space group name H-MI121
Components on special symmetry positions
IDModelComponents
11A-381-

HOH

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Components

#1: Protein Acetyl esterase/lipase


Mass: 32658.043 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Sequence reference for Delftia acidovorans (80866) is not available in UniProt at the time of biocuration. Current sequence reference is from UniProt ID A0A1I2L9V0.
Source: (gene. exp.) Delftia acidovorans (bacteria) / Gene: SAMN04488025_10455
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A1I2L9V0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 617 / Source method: isolated from a natural source / Formula: H2O
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: 2.08 Å3/Da / Density % sol: 40.8 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.2 M Ammonium Acetate, 0.1 M tri-sodium Citrate dihydrate, 30% PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-X / Wavelength: 1.54056 Å
DetectorType: RIGAKU HyPix-Arc 150 / Detector: PIXEL / Date: Oct 10, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54056 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 48962 / % possible obs: 99 % / Redundancy: 7.6 % / CC1/2: 0.995 / Net I/σ(I): 11.19
Reflection shellResolution: 1.8→1.87 Å / Mean I/σ(I) obs: 1.6 / Num. unique obs: 4785 / CC1/2: 0.698

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Processing

Software
NameVersionClassification
PHENIX(1.21_5207: ???)refinement
CrystFELdata scaling
PHASERphasing
CrysalisProdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→29.64 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2151 2465 5.04 %
Rwork0.1739 --
obs0.176 48950 98.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→29.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4458 0 0 617 5075
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084686
X-RAY DIFFRACTIONf_angle_d1.6996372
X-RAY DIFFRACTIONf_dihedral_angle_d6.16646
X-RAY DIFFRACTIONf_chiral_restr0.067702
X-RAY DIFFRACTIONf_plane_restr0.015844
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.860.28692400.2354487X-RAY DIFFRACTION97
1.86-1.940.2612370.23084657X-RAY DIFFRACTION99
1.94-2.030.23922640.19634650X-RAY DIFFRACTION100
2.03-2.130.23932240.18314690X-RAY DIFFRACTION100
2.13-2.270.2282560.17694676X-RAY DIFFRACTION100
2.27-2.440.22012470.17164676X-RAY DIFFRACTION100
2.44-2.690.22352460.17624692X-RAY DIFFRACTION100
2.69-3.080.22182520.17724698X-RAY DIFFRACTION100
3.08-3.880.17642540.15634661X-RAY DIFFRACTION99
3.88-29.640.19162450.14794598X-RAY DIFFRACTION96

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