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- PDB-9fw1: UMG-SP3 amidase from uncultured bacterium in complex with PMSF -

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Basic information

Entry
Database: PDB / ID: 9fw1
TitleUMG-SP3 amidase from uncultured bacterium in complex with PMSF
ComponentsUMG-SP3 amidase
KeywordsHYDROLASE / Amidase / PMSF / urethane degrading / plastic recycling
Function / homologyphenylmethanesulfonic acid
Function and homology information
Biological speciesuncultured bacterium (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.18 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 28, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)91,9888
Polymers91,2592
Non-polymers7296
Water1,38777
1
A: UMG-SP3 amidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,9944
Polymers45,6291
Non-polymers3643
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: UMG-SP3 amidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,9944
Polymers45,6291
Non-polymers3643
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.863, 90.863, 278.919
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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-PMS / phenylmethanesulfonic acid


Mass: 172.202 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C7H8O3S
Source: (gene. exp.) uncultured bacterium (environmental samples)
Production host: Escherichia coli K-12 (bacteria)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 3.16 Å3/Da / Density % sol: 61.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Bis-Tris pH 7, 3.8 M Ammonium acetate

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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: P13 (MX1) / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 6, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.18→47.54 Å / Num. obs: 40047 / % possible obs: 96.8 % / Redundancy: 2 % / CC1/2: 0.995 / Rmerge(I) obs: 0.04759 / Rpim(I) all: 0.04759 / Rrim(I) all: 0.0673 / Net I/σ(I): 18.69
Reflection shellResolution: 2.18→2.259 Å / Rmerge(I) obs: 0.4475 / Num. unique obs: 168 / CC1/2: 0.632 / Rpim(I) all: 0.4475 / Rrim(I) all: 0.6328

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.18→47.54 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2376 1990 4.97 %
Rwork0.1836 --
obs0.1863 40038 64.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.18→47.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6408 0 20 77 6505
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0126550
X-RAY DIFFRACTIONf_angle_d1.2428938
X-RAY DIFFRACTIONf_dihedral_angle_d6.664938
X-RAY DIFFRACTIONf_chiral_restr0.0551034
X-RAY DIFFRACTIONf_plane_restr0.0181174
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.18-2.240.40150.3063108X-RAY DIFFRACTION3
2.24-2.30.4158120.2798350X-RAY DIFFRACTION8
2.3-2.360.3082450.2533885X-RAY DIFFRACTION21
2.36-2.440.3139800.2611204X-RAY DIFFRACTION30
2.44-2.530.2936930.25131562X-RAY DIFFRACTION38
2.53-2.630.2967930.26532008X-RAY DIFFRACTION48
2.63-2.750.31351330.26092739X-RAY DIFFRACTION65
2.75-2.890.33942020.24223860X-RAY DIFFRACTION93
2.89-3.070.3092060.23184213X-RAY DIFFRACTION100
3.07-3.310.24812290.21254190X-RAY DIFFRACTION100
3.31-3.640.24352100.18494240X-RAY DIFFRACTION100
3.64-4.170.212030.1443848X-RAY DIFFRACTION90
4.17-5.250.17512580.12634269X-RAY DIFFRACTION100
5.25-47.540.19492210.15574572X-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)
10.2501-0.1449-0.46680.89550.2220.8770.0349-0.0323-0.2411-0.07970.03510.45010.166-0.6852-0.00250.2431-0.1505-0.06450.46680.08490.3958-34.2949-41.327210.9233
20.6921-0.3340.01130.6254-0.22241.9663-0.0736-0.06680.05580.01390.14480.0688-0.1295-0.1685-0.02420.1949-0.1231-0.01930.0790.02760.1692-17.0266-33.280118.5773
32.38250.26720.13991.9432-1.01512.7647-0.1975-0.0266-0.1065-0.00370.207-0.363-0.01250.4855-0.06170.0917-0.0173-0.00520.224-0.05860.1133-0.6154-35.108432.7632
41.26240.2508-0.0690.4298-0.21911.5988-0.05460.020.093-0.06670.0453-0.0685-0.45980.0489-0.06390.2507-0.104-0.00520.12470.00140.1802-10.2738-25.189416.4177
51.0538-0.70490.26720.8383-0.26190.0865-0.1164-0.23640.18680.09670.0580.0178-0.1435-0.1498-0.11710.19370.1931-0.03250.4128-0.05480.2421-22.6645-19.626868.5506
60.76440.17710.2320.9902-0.0121.8044-0.0841-0.24070.08140.05430.0232-0.0609-0.0709-0.04980.03070.07160.08030.01230.26050.02180.144-14.9055-28.422860.3245
70.8135-0.1254-0.15911.16-0.17361.8164-0.064-0.1367-0.0349-0.09320.06980.15990.071-0.31610.04740.12230.0234-0.01110.25710.03120.1755-23.6088-33.921649.59
81.02230.1671-0.46390.5114-0.28561.69170.0554-0.1111-0.20460.02870.01260.28520.6433-0.58110.20460.5476-0.24270.09820.40840.06150.4332-32.3133-53.916856.2207
91.93670.8297-0.86082.9783-0.58862.35150.0109-0.0144-0.51790.18540.0845-0.47980.65250.44660.03420.41560.1783-0.03750.27170.01890.2753-4.5193-51.082547.6306
106.48970.4158-2.32532.9635-0.20182.9567-0.08920.216-0.3159-0.02790.11920.01920.6326-0.2433-0.0750.29730.0163-0.0370.18130.03940.1537-16.5771-50.298738.2675
111.83570.424-0.90661.24540.36691.1129-0.0471-0.4088-0.39190.21770.03950.01890.7308-0.2179-0.04310.3607-0.00470.02830.28460.11380.246-19.4491-49.526360.8577
121.80820.3121-1.40931.3256-0.11231.11180.0217-0.04250.03430.10750.03580.22690.1894-0.65680.07290.2417-0.11940.02180.52450.09230.2507-31.7497-40.912556.4023
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 81 )
2X-RAY DIFFRACTION2chain 'A' and (resid 82 through 292 )
3X-RAY DIFFRACTION3chain 'A' and (resid 293 through 344 )
4X-RAY DIFFRACTION4chain 'A' and (resid 345 through 439 )
5X-RAY DIFFRACTION5chain 'B' and (resid 2 through 45 )
6X-RAY DIFFRACTION6chain 'B' and (resid 46 through 199 )
7X-RAY DIFFRACTION7chain 'B' and (resid 200 through 251 )
8X-RAY DIFFRACTION8chain 'B' and (resid 252 through 292 )
9X-RAY DIFFRACTION9chain 'B' and (resid 293 through 321 )
10X-RAY DIFFRACTION10chain 'B' and (resid 322 through 344 )
11X-RAY DIFFRACTION11chain 'B' and (resid 345 through 405 )
12X-RAY DIFFRACTION12chain 'B' and (resid 406 through 439 )

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