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- PDB-31gl: Prescottella amidase, S181A mutant, diethyl toluene-2,4-dicarbama... -

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Basic information

Entry
Database: PDB / ID: 31gl
TitlePrescottella amidase, S181A mutant, diethyl toluene-2,4-dicarbamate soak
Componentsamidase
KeywordsHYDROLASE / Urethanase
Function / homology
Function and homology information


amidase / amidase activity
Similarity search - Function
Amidase / Amidase, conserved site / Amidases signature. / Amidase signature domain / Amidase signature (AS) superfamily / Amidase
Similarity search - Domain/homology
: / FORMIC ACID / amidase
Similarity search - Component
Biological speciesPrescottella equi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsBloch, Y. / Panneerselvam, S.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
H2020 Marie Curie Actions of the European Commission945405European Union
Citation
Journal: To Be Published
Title: Crystallographic exploration of a Prescottella sp. amidase as a model system for urethanase activity.
Authors: Bloch, Y. / Panneerselvam, S. / Schneider, T.R.
#1: Journal: Appl Microbiol Biotechnol / Year: 2006
Title: Isolation of a bacterium that degrades urethane compounds and characterization of its urethane hydrolase.
Authors: Akutsu-Shigeno, Y. / Adachi, Y. / Yamada, C. / Toyoshima, K. / Nomura, N. / Uchiyama, H. / Nakajima-Kambe, T.
History
DepositionJun 3, 2026Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 16, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: amidase
B: amidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,3679
Polymers101,8042
Non-polymers5637
Water24,6271367
1
A: amidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,3175
Polymers50,9021
Non-polymers4154
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: amidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,0504
Polymers50,9021
Non-polymers1483
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.662, 65.473, 67.556
Angle α, β, γ (deg.)101.23, 89.42, 110.83
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein amidase


Mass: 50901.906 Da / Num. of mol.: 2 / Mutation: S181A
Source method: isolated from a genetically manipulated source
Details: residues part of cloning and purification strategy residues His6tag residues + HRV 3C tag residues removed by proteolytic digest actual protein starts from residue 21 which is natively ...Details: residues part of cloning and purification strategy residues His6tag residues + HRV 3C tag residues removed by proteolytic digest actual protein starts from residue 21 which is natively residue 2 S181A mismatch is mutation in catalytic residue
Source: (gene. exp.) Prescottella equi (bacteria) / Strain: TB-60 / Gene: ABEU19_000766 / Plasmid: pET derived / Production host: Escherichia coli (E. coli) / Strain (production host): T7 Express lysY/Iq / References: UniProt: A0ABW9FQ31, amidase

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Non-polymers , 5 types, 1374 molecules

#2: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH2O2
#3: Chemical ChemComp-A1J91 / Diethyl toluene-2,4-dicarbamate / ethyl ~{N}-[3-(ethoxycarbonylamino)-4-methyl-phenyl]carbamate


Mass: 266.293 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H18N2O4
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1367 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.09 Å3/Da / Density % sol: 41.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 20% (w/v) PEG 3350, 200 mM Magnesium formate, 100 mM HEPES pH 7.4

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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: 0.8265 Å
DetectorType: DECTRIS EIGER2 X CdTe 16M / Detector: PIXEL / Date: Jan 26, 2026
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8265 Å / Relative weight: 1
ReflectionResolution: 1.005→49.744 Å / Num. obs: 230080 / % possible obs: 94 % / Redundancy: 8.8 % / Biso Wilson estimate: 9.96 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.038 / Rrim(I) all: 0.082 / Net I/σ(I): 14.1
Reflection shell

Num. unique obs: 11504 / Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsCC1/2Rpim(I) allRrim(I) all% possible all
3.428-49.7449.50.03949.80.9990.020.044100
1.005-1.1716.20.98720.640.6081.16666.2

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Processing

Software
NameVersionClassification
BUSTER2.10.4refinement
autoPROC2025-04-07data reduction
XDSJan 19, 2025 (BUILT 20250430)data reduction
STARANISO3.0.6 (20250212)data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.2→17.54 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.971 / SU R Cruickshank DPI: 0.039 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.038 / SU Rfree Blow DPI: 0.041 / SU Rfree Cruickshank DPI: 0.039
RfactorNum. reflection% reflectionSelection details
Rfree0.1494 10683 -RANDOM
Rwork0.1229 ---
obs0.1242 213049 79.5 %-
Displacement parametersBiso mean: 14.91 Å2
Baniso -1Baniso -2Baniso -3
1--0.9604 Å20.2619 Å2-0.2319 Å2
2--0.3317 Å20.0437 Å2
3---0.6287 Å2
Refine analyzeLuzzati coordinate error obs: 0.1 Å
Refinement stepCycle: LAST / Resolution: 1.2→17.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7112 0 35 1367 8514
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.01414878HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.7826931HARMONIC8
X-RAY DIFFRACTIONt_dihedral_angle_d4390SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes2525HARMONIC5
X-RAY DIFFRACTIONt_it14849HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion968SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies33HARMONIC1
X-RAY DIFFRACTIONt_ideal_dist_contact16424SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion6.25
X-RAY DIFFRACTIONt_other_torsion14.23
LS refinement shellResolution: 1.2→1.22 Å
RfactorNum. reflection% reflection
Rfree0.225 209 -
Rwork0.1869 --
obs0.1887 4261 33.2 %

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