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- PDB-9fz1: UMG-SP3 amidase from uncultured bacterium in complex with 4,4'-MDA -

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Basic information

Entry
Database: PDB / ID: 9fz1
TitleUMG-SP3 amidase from uncultured bacterium in complex with 4,4'-MDA
ComponentsUMG-SP3
KeywordsHYDROLASE / amidase / urethane bond / 4 / 4'-MDA / plastic recycling
Function / homology: / ACETATE ION
Function and homology information
Biological speciesuncultured bacterium (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsRotilio, L. / Morth, J.P.
Funding support Denmark, 1items
OrganizationGrant numberCountry
Novo Nordisk Foundation Denmark
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2025
Title: Structural and Functional Characterization of an Amidase Targeting a Polyurethane for Sustainable Recycling.
Authors: Rotilio, L. / Bayer, T. / Meinert, H. / Teixeira, L.M.C. / Johansen, M.B. / Sommerfeldt, A. / Petersen, A.R. / Sandahl, A. / Keller, M.B. / Holck, J. / Paiva, P. / Otzen, D.E. / Bornscheuer, ...Authors: Rotilio, L. / Bayer, T. / Meinert, H. / Teixeira, L.M.C. / Johansen, M.B. / Sommerfeldt, A. / Petersen, A.R. / Sandahl, A. / Keller, M.B. / Holck, J. / Paiva, P. / Otzen, D.E. / Bornscheuer, U.T. / Wei, R. / Fernandes, P.A. / Ramos, M.J. / Westh, P. / Morth, J.P.
History
DepositionJul 4, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 5, 2025Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2025Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UMG-SP3
B: UMG-SP3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,32613
Polymers91,2592
Non-polymers1,06711
Water6,305350
1
A: UMG-SP3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0646
Polymers45,6291
Non-polymers4345
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: UMG-SP3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,2627
Polymers45,6291
Non-polymers6336
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.642, 90.642, 277.711
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 UMG-SP3 / Amidase


Mass: 45629.453 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) uncultured bacterium (environmental samples)
Production host: Escherichia coli K-12 (bacteria)
#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-A1IHK / 4-[(4-aminophenyl)methyl]aniline


Mass: 198.264 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C13H14N2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 350 / 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: 3.13 Å3/Da / Density % sol: 60.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M HEPES pH 7.5; 4 M Ammonium acetate; 5 mM sodium malonate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 X CdTe 16M / Detector: PIXEL / Date: Dec 5, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2→64.76 Å / Num. obs: 50608 / % possible obs: 94.4 % / Redundancy: 2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.03768 / Rpim(I) all: 0.03768 / Rrim(I) all: 0.05328 / Net I/σ(I): 21.26
Reflection shellResolution: 2→2.072 Å / Num. unique obs: 1426 / CC1/2: 0.851

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→64.76 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2279 2553 5.05 %
Rwork0.1761 --
obs0.1787 50596 63.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→64.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6382 0 77 350 6809
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0116590
X-RAY DIFFRACTIONf_angle_d1.148980
X-RAY DIFFRACTIONf_dihedral_angle_d7.415939
X-RAY DIFFRACTIONf_chiral_restr0.0541035
X-RAY DIFFRACTIONf_plane_restr0.0111188
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.040.2514280.1847741X-RAY DIFFRACTION18
2.04-2.080.3084460.1972780X-RAY DIFFRACTION19
2.08-2.130.3148570.2045868X-RAY DIFFRACTION21
2.13-2.170.2667560.2251050X-RAY DIFFRACTION26
2.17-2.230.3314760.21681211X-RAY DIFFRACTION30
2.23-2.290.2779770.21541370X-RAY DIFFRACTION33
2.29-2.360.2697880.21681629X-RAY DIFFRACTION40
2.36-2.430.2899910.21471834X-RAY DIFFRACTION44
2.43-2.520.27631110.21512162X-RAY DIFFRACTION52
2.52-2.620.28641350.22942758X-RAY DIFFRACTION67
2.62-2.740.28082330.23233785X-RAY DIFFRACTION91
2.74-2.880.29362270.23114141X-RAY DIFFRACTION100
2.88-3.070.2642070.21664197X-RAY DIFFRACTION100
3.07-3.30.26722240.18554187X-RAY DIFFRACTION100
3.3-3.630.23222140.16784241X-RAY DIFFRACTION100
3.63-4.160.19732030.13944265X-RAY DIFFRACTION100
4.16-5.240.15742410.12354281X-RAY DIFFRACTION100
5.24-64.760.19762390.17064543X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.08220.4911-0.64430.9744-0.33453.1990.28150.08790.23040.0658-0.02690.113-0.5378-0.0104-0.01130.22270.0940.09290.14340.03690.221410.2222-24.931886.5601
22.41070.6677-1.14983.9197-0.80644.03260.210.0771-0.58570.1862-0.13810.23260.48070.0121-0.14880.27450.00220.01010.1479-0.050.20599.0965-44.6645104.4354
30.56250.1298-0.68160.9853-0.5381.67330.05140.0775-0.09380.0265-0.0625-0.01720.21860.47230.00960.18890.10910.00940.26860.00480.205618.001-39.626984.7639
43.266-0.4827-2.35841.74180.27853.02640.1425-0.2930.23470.0057-0.0474-0.0748-0.6620.9239-0.07740.2389-0.07470.00450.38770.01990.212224.7598-26.406988.449
51.20170.07130.19220.85110.17891.7781-0.064-0.25840.06110.02210.02610.0343-0.1634-0.26570.04110.14480.11520.03120.39890.06820.1696-16.9196-26.985659.9288
61.06440.0102-0.09220.32970.13361.3052-0.0736-0.2166-0.07550.1073-0.09960.4670.5941-0.93260.1540.4209-0.31210.06280.82750.2290.4644-34.2149-49.774856.4118
71.53770.8624-1.83241.9471-0.03523.09520.16510.1949-0.36650.13240.0529-0.12670.6826-0.2311-0.06910.3584-0.0002-0.03590.25610.11970.2683-14.4745-51.272843.9463
81.71390.5169-0.90211.48820.65581.12110.0429-0.4284-0.42510.31090.1213-0.02060.8466-0.3351-0.05160.468-0.06030.00230.46510.18790.3944-17.171-51.014963.7201
91.71710.228-0.84430.96250.01420.44310.0914-0.191-0.04490.0380.03250.2020.3874-0.50230.060.224-0.10480.03180.63660.13350.2617-29.1712-41.739255.5318
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 308 )
2X-RAY DIFFRACTION2chain 'A' and (resid 309 through 343 )
3X-RAY DIFFRACTION3chain 'A' and (resid 344 through 405 )
4X-RAY DIFFRACTION4chain 'A' and (resid 406 through 439 )
5X-RAY DIFFRACTION5chain 'B' and (resid 2 through 240 )
6X-RAY DIFFRACTION6chain 'B' and (resid 241 through 279 )
7X-RAY DIFFRACTION7chain 'B' and (resid 280 through 345 )
8X-RAY DIFFRACTION8chain 'B' and (resid 346 through 388 )
9X-RAY DIFFRACTION9chain 'B' and (resid 389 through 439 )

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