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- PDB-9fvf: UMG-SP3 amidase from uncultured bacterium -

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Basic information

Entry
Database: PDB / ID: 9fvf
TitleUMG-SP3 amidase from uncultured bacterium
ComponentsAmidase UMG-SP3
KeywordsHYDROLASE / amidase / urethane degradation / plastic recycling
Function / homologyChem-PG6
Function and homology information
Biological speciesuncultured bacterium (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.32 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
DepositionJun 27, 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: Amidase UMG-SP3
B: Amidase UMG-SP3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,8136
Polymers91,2592
Non-polymers5554
Water1,00956
1
A: Amidase UMG-SP3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0884
Polymers45,6291
Non-polymers4583
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Amidase UMG-SP3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,7262
Polymers45,6291
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.707, 90.707, 278.114
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 Amidase UMG-SP3


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-PG6 / 1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE


Mass: 266.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O6
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / 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: 2.42 Å3/Da / Density % sol: 54.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Hepes pH 7.5 4 M Ammonium Acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.87313 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Sep 15, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87313 Å / Relative weight: 1
ReflectionResolution: 2.32→47.42 Å / Num. obs: 50769 / % possible obs: 99.49 % / Redundancy: 2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.03706 / Rpim(I) all: 0.03706 / Rrim(I) all: 0.05242 / Net I/σ(I): 15.86
Reflection shellResolution: 2.32→2.408 Å / Rmerge(I) obs: 0.6449 / Mean I/σ(I) obs: 1.25 / Num. unique obs: 4908 / CC1/2: 0.684 / Rpim(I) all: 0.6449 / Rsym value: 0.9121 / % possible all: 98.46

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
pointlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.32→47.42 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2497 2404 4.74 %
Rwork0.188 --
obs0.1908 50769 99.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.32→47.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6393 0 33 56 6482
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0116554
X-RAY DIFFRACTIONf_angle_d1.1418935
X-RAY DIFFRACTIONf_dihedral_angle_d6.869943
X-RAY DIFFRACTIONf_chiral_restr0.0551035
X-RAY DIFFRACTIONf_plane_restr0.0111173
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.32-2.370.3861300.32412736X-RAY DIFFRACTION98
2.37-2.420.35761600.31182760X-RAY DIFFRACTION99
2.42-2.480.31371360.28452787X-RAY DIFFRACTION100
2.48-2.540.31971390.27362792X-RAY DIFFRACTION100
2.54-2.610.36361300.26422817X-RAY DIFFRACTION100
2.61-2.690.35681410.25742802X-RAY DIFFRACTION99
2.69-2.770.30851490.25912781X-RAY DIFFRACTION99
2.77-2.870.32421270.24332816X-RAY DIFFRACTION99
2.87-2.990.27781400.21512840X-RAY DIFFRACTION100
2.99-3.120.26841520.20612820X-RAY DIFFRACTION100
3.12-3.290.24741420.20712815X-RAY DIFFRACTION100
3.29-3.50.29491460.20772862X-RAY DIFFRACTION100
3.5-3.770.24771360.16822849X-RAY DIFFRACTION99
3.77-4.140.22121390.15322892X-RAY DIFFRACTION100
4.14-4.740.20751570.13292892X-RAY DIFFRACTION100
4.74-5.970.18381310.15592968X-RAY DIFFRACTION100
5.97-47.420.20941490.1583136X-RAY DIFFRACTION100
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)
12.5236-0.4192-0.83181.09720.51741.096-0.09370.3079-0.2566-0.0867-0.05930.49360.1321-1.04770.07460.4841-0.0486-0.08350.8575-0.01110.6386-33.6402-38.10617.0296
21.2219-0.25250.08581.2045-0.3082.31540.0414-0.1762-0.2378-0.0430.02470.33680.5467-0.7045-0.04940.3976-0.1635-0.03660.59060.00270.4925-24.2739-43.404514.0527
31.57971.038-0.16441.1950.69941.8349-0.0169-0.1734-0.24550.2205-0.0873-0.00280.4836-0.10520.11480.4818-0.04660.02190.44490.02190.5479-16.0653-37.870922.5862
42.2278-0.6262-0.26631.00680.0122.5111-0.03790.04690.0791-0.01660.06570.5275-0.2735-0.78010.00490.47320.0338-0.03170.74550.00180.6345-26.5056-29.109525.0483
51.77390.07580.0612.75280.71654.3115-0.12270.07680.468-0.11130.1096-0.0988-1.5246-0.06350.04040.9136-0.0548-0.06810.40260.00870.5565-11.163-13.76818.1747
61.80530.55410.12191.8117-0.27522.6019-0.2271-0.06610.13360.43720.1795-0.613-0.59570.4060.02760.6164-0.1289-0.05380.6196-0.00890.5259-2.7331-25.004127.7655
73.5672-0.02090.66033.4038-1.96712.8286-0.3457-0.2896-0.1840.09590.3656-0.5387-0.16890.4259-0.0260.5402-0.0434-0.00240.6007-0.01910.4475-1.241-35.563335.3202
81.13150.25250.32561.69160.35133.6443-0.04090.04280.0991-0.1104-0.0288-0.0747-0.64440.0520.06250.4614-0.0567-0.04680.41350.02140.4688-10.4428-25.189716.4397
91.13590.19580.28241.57960.20823.0047-0.0967-0.1713-0.01680.0604-0.00190.14040.0983-0.50410.09460.30450.05120.01980.60110.02740.4199-20.1708-30.838759.3057
101.0187-0.1261-1.57493.18990.1873.287-0.16110.1111-0.40030.21870.1107-0.2070.878-0.0103-0.00660.75270.00360.00580.52790.05550.5545-10.4214-50.219843.6074
111.2880.6727-0.40161.40130.89511.7846-0.0099-0.3772-0.21250.2766-0.01870.18070.6152-0.66710.02470.6069-0.14560.04270.74890.07240.5383-23.8963-45.749159.6156
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 45 )
2X-RAY DIFFRACTION2chain 'A' and (resid 46 through 166 )
3X-RAY DIFFRACTION3chain 'A' and (resid 167 through 213 )
4X-RAY DIFFRACTION4chain 'A' and (resid 214 through 242 )
5X-RAY DIFFRACTION5chain 'A' and (resid 243 through 279 )
6X-RAY DIFFRACTION6chain 'A' and (resid 280 through 308 )
7X-RAY DIFFRACTION7chain 'A' and (resid 309 through 344 )
8X-RAY DIFFRACTION8chain 'A' and (resid 345 through 439 )
9X-RAY DIFFRACTION9chain 'B' and (resid 2 through 292 )
10X-RAY DIFFRACTION10chain 'B' and (resid 293 through 344 )
11X-RAY DIFFRACTION11chain 'B' and (resid 345 through 439 )

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