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- PDB-9fzw: Structure of Urethanase UMG-SP2 -

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Basic information

Entry
Database: PDB / ID: 9fzw
TitleStructure of Urethanase UMG-SP2
ComponentsUrethanase UMG-SP2
KeywordsHYDROLASE / urethanases / polyurethane / plastic degradation / polymer degradation / enzyme engineering
Biological speciesuncultured bacterium (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.59 Å
AuthorsSingh, P. / Lennartz, F. / Bornscheuer, U.T. / Wei, R. / Weber, G.
Funding support Germany, 1items
OrganizationGrant numberCountry
Helmholtz AssociationKA2-HSC-10 Germany
CitationJournal: Adv Sci / Year: 2025
Title: Structure-Guided Engineering of a Versatile Urethanase Improves Its Polyurethane Depolymerization Activity.
Authors: Li, Z. / Han, X. / Cong, L. / Singh, P. / Paiva, P. / Branson, Y. / Li, W. / Chen, Y. / Jaradat, D.M.M. / Lennartz, F. / Bayer, T. / Schmidt, L. / Garscha, U. / You, S. / Fernandes, P.A. / ...Authors: Li, Z. / Han, X. / Cong, L. / Singh, P. / Paiva, P. / Branson, Y. / Li, W. / Chen, Y. / Jaradat, D.M.M. / Lennartz, F. / Bayer, T. / Schmidt, L. / Garscha, U. / You, S. / Fernandes, P.A. / Ramos, M.J. / Bornscheuer, U.T. / Weber, G. / Wei, R. / Liu, W.
History
DepositionJul 6, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 21, 2025Provider: repository / Type: Initial release
Revision 1.1Dec 3, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Urethanase UMG-SP2
B: Urethanase UMG-SP2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,74913
Polymers91,7322
Non-polymers1,01711
Water5,080282
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5380 Å2
ΔGint-30 kcal/mol
Surface area30250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.770, 88.770, 276.440
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Urethanase UMG-SP2


Mass: 45865.848 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) uncultured bacterium (environmental samples)
Production host: Escherichia coli (E. coli)
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 282 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.97 Å3/Da / Density % sol: 58.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.5
Details: 0.2M ammonium sulfate, 0.1M HEPES, pH 7.5, 35% (w/v) Poly(acrylic acid sodium salt) 2100

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.918 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Apr 16, 2024
RadiationMonochromator: DCM Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 2.59→46.93 Å / Num. obs: 65635 / % possible obs: 100 % / Redundancy: 14.2 % / CC1/2: 0.978 / Net I/σ(I): 4.7
Reflection shellResolution: 2.59→2.75 Å / Num. unique obs: 10605 / CC1/2: 0.311

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Processing

Software
NameVersionClassification
PHENIX(1.21_5207: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.59→21.71 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2356 2092 3.19 %
Rwork0.2076 --
obs0.2086 65493 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.59→21.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6417 0 65 282 6764
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026603
X-RAY DIFFRACTIONf_angle_d0.5458989
X-RAY DIFFRACTIONf_dihedral_angle_d10.6832331
X-RAY DIFFRACTIONf_chiral_restr0.041036
X-RAY DIFFRACTIONf_plane_restr0.0051176
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.59-2.650.41091370.36194218X-RAY DIFFRACTION100
2.65-2.720.39151400.34954250X-RAY DIFFRACTION100
2.72-2.790.33091420.324241X-RAY DIFFRACTION100
2.79-2.870.36141430.31284213X-RAY DIFFRACTION100
2.87-2.960.33011380.29314237X-RAY DIFFRACTION100
2.96-3.070.30441370.27394222X-RAY DIFFRACTION100
3.07-3.190.29381420.25634220X-RAY DIFFRACTION100
3.19-3.340.30781370.2434209X-RAY DIFFRACTION100
3.34-3.510.24531410.21174208X-RAY DIFFRACTION100
3.51-3.730.23581390.18494240X-RAY DIFFRACTION100
3.73-4.020.21691380.16884231X-RAY DIFFRACTION100
4.02-4.420.16041390.15124232X-RAY DIFFRACTION100
4.42-5.050.16161360.15024221X-RAY DIFFRACTION100
5.05-6.340.19891440.17934236X-RAY DIFFRACTION100
6.34-21.710.1661390.15844223X-RAY DIFFRACTION100

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