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- PDB-8xtb: Crystal structure of a novel PU plastic degradation urethanase UM... -

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Basic information

Entry
Database: PDB / ID: 8xtb
TitleCrystal structure of a novel PU plastic degradation urethanase UMG-SP2 from uncultured bacterium in complex with ligand
Componentsumgsp2
KeywordsHYDROLASE / PU / degradation / mutant
Function / homology:
Function and homology information
Biological speciesuncultured bacterium (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsCong, L. / Li, Z.S. / Zheng, Z.R. / Han, X. / Wei, R. / Liu, W.D. / Uwe, B.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Crystal structure of a novel PU plastic degradation urethanase UMG-SP2 mutant from uncultured bacterium
Authors: Cong, L. / Li, Z.S. / Zheng, Z.R. / Han, X. / Wei, R. / Liu, W.D. / Uwe, B.
History
DepositionJan 10, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jan 15, 2025Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2025Group: Data collection / Category: reflns / Item: _reflns.number_obs

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: umgsp2
B: umgsp2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,5374
Polymers94,0882
Non-polymers4492
Water3,621201
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2420 Å2
ΔGint-7 kcal/mol
Surface area30330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.936, 84.936, 275.819
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 umgsp2


Mass: 47044.090 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) uncultured bacterium (environmental samples)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
#2: Chemical ChemComp-A1D5H / 4-oxidanylbutyl ~{N}-(4-aminophenyl)carbamate


Mass: 224.256 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H16N2O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 201 / 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: 2.64 Å3/Da / Density % sol: 53.47 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 1.26M (NH4)2SO4, 0.1M HEPES pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.979183 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 16, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979183 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. obs: 43036 / % possible obs: 99.9 % / Redundancy: 17 % / CC1/2: 0.995 / Net I/av σ(I): 10.2 / Net I/σ(I): 7.68
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique obsCC1/2% possible allRmerge(I) obs
2.35-2.516.22.2129050.69699.6
2.5-2.67120940.840.917
2.67-2.88112640.909
2.88-3.15104450.96
3.15-3.5293720.976
3.52-4.0782750.99
4.07-4.9770210.992
4.97-6.9954290.992
6.99-5030220.996

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.35→19.23 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2425 2143 5 %
Rwork0.2066 --
obs0.2083 42847 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.35→19.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6404 0 32 201 6637
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036568
X-RAY DIFFRACTIONf_angle_d0.6178954
X-RAY DIFFRACTIONf_dihedral_angle_d7.21942
X-RAY DIFFRACTIONf_chiral_restr0.0431034
X-RAY DIFFRACTIONf_plane_restr0.0061178
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.440.33032090.29043977X-RAY DIFFRACTION100
2.44-2.540.3232100.26443981X-RAY DIFFRACTION100
2.54-2.650.27422100.26174005X-RAY DIFFRACTION100
2.65-2.790.31742120.25034013X-RAY DIFFRACTION100
2.79-2.960.31472110.25094019X-RAY DIFFRACTION100
2.96-3.190.26962120.2444033X-RAY DIFFRACTION100
3.19-3.510.24392150.21844072X-RAY DIFFRACTION100
3.51-4.010.22972160.18924097X-RAY DIFFRACTION100
4.02-5.040.19762180.16544147X-RAY DIFFRACTION100
5.04-19.230.20642300.17734360X-RAY DIFFRACTION100

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