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- PDB-9je9: Crystal structure of a amidase that can hydrolase PU plastic -

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Basic information

Entry
Database: PDB / ID: 9je9
TitleCrystal structure of a amidase that can hydrolase PU plastic
ComponentsAmidase
KeywordsHYDROLASE / PU plastic / hydrolyse / degradation
Function / homology: / Amidase signature domain / Amidase signature (AS) superfamily / Amidase / endomembrane system / Amidase
Function and homology information
Biological speciesSphingomonas sp. TPD3009 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.41 Å
AuthorsLi, Z.S. / Fang, S.T. / Zheng, Z.R. / Xia, W. / Zhou, H.Y. / Li, W.S. / You, S. / Han, X. / Liu, W.D.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Acs Catalysis / Year: 2025
Title: Discovery and Engineering of a Urethanase for Enhanced Depolymerization of Polyurethane
Authors: Li, Z. / Fan, S. / Chen, Y. / Xia, W. / Zhou, H. / Zhou, X. / Qin, B. / Qin, H. / Dong, W. / Gu, Q. / Zhu, H. / Bornscheuer, U.T. / Wei, R. / Han, X. / Liu, W.
History
DepositionSep 2, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 9, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Amidase
B: Amidase


Theoretical massNumber of molelcules
Total (without water)98,3772
Polymers98,3772
Non-polymers00
Water1,802100
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)92.820, 92.820, 135.086
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein Amidase


Mass: 49188.332 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sphingomonas sp. TPD3009 (bacteria) / Gene: DC425_12480
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A2T7VCT5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 100 / 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: 2.96 Å3/Da / Density % sol: 58.41 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: Li2SO4, HEPES, PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.979183 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 20, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979183 Å / Relative weight: 1
ReflectionResolution: 2.41→92.82 Å / Num. obs: 43518 / % possible obs: 99 % / Redundancy: 2 % / CC1/2: 0.996 / Net I/σ(I): 5.5
Reflection shellResolution: 2.41→2.5 Å / Redundancy: 2 % / Mean I/σ(I) obs: 1.1 / Num. unique obs: 4625 / CC1/2: 0.326 / Χ2: 0.7

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Processing

Software
NameVersionClassification
PHENIX(1.21_5207: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.41→92.82 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2733 2054 4.73 %
Rwork0.2182 --
obs0.2207 43415 98.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.41→92.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6199 0 0 100 6299
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096393
X-RAY DIFFRACTIONf_angle_d1.4378726
X-RAY DIFFRACTIONf_dihedral_angle_d10.463898
X-RAY DIFFRACTIONf_chiral_restr0.08996
X-RAY DIFFRACTIONf_plane_restr0.0141167
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.41-2.50.36732200.33724166X-RAY DIFFRACTION100
2.5-2.60.35882250.31314149X-RAY DIFFRACTION100
2.6-2.720.35772160.30464137X-RAY DIFFRACTION100
2.72-2.860.3082100.28694175X-RAY DIFFRACTION100
2.86-3.040.32951900.2684186X-RAY DIFFRACTION100
3.04-3.280.30792030.25934193X-RAY DIFFRACTION100
3.28-3.610.29721850.2394189X-RAY DIFFRACTION100
3.61-4.130.30682090.22253738X-RAY DIFFRACTION90
4.13-5.20.21092020.18434207X-RAY DIFFRACTION100
5.2-92.820.24291940.17314221X-RAY DIFFRACTION99

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