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- PDB-30zo: Prescottella amidase inhibited by PMSF -

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Basic information

Entry
Database: PDB / ID: 30zo
TitlePrescottella amidase inhibited by PMSF
Componentsamidase
KeywordsHYDROLASE / inhibitor / 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 / phenylmethanesulfonic 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.
#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
DepositionMay 19, 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)106,45410
Polymers105,8122
Non-polymers6418
Water19,4741081
1
A: amidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,2275
Polymers52,9061
Non-polymers3214
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: amidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,2275
Polymers52,9061
Non-polymers3214
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.657, 66.414, 67.582
Angle α, β, γ (deg.)101.63, 88.82, 111.4
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: 52906.176 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: residues [1-20] part of cloning and purification strategy residues [4-9] His6tag residues [11-18] HRV 3C tag residues [1-16] removed by proteolytic digest actual protein starts from residue ...Details: residues [1-20] part of cloning and purification strategy residues [4-9] His6tag residues [11-18] HRV 3C tag residues [1-16] removed by proteolytic digest actual protein starts from residue 21 which is natively residue 2
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, 1089 molecules

#2: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH2O2
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-PMS / phenylmethanesulfonic acid


Mass: 172.202 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H8O3S / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1081 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.15 Å3/Da / Density % sol: 42.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 20% (w/v) PEG3350, 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: 0.82655 Å
DetectorType: DECTRIS EIGER2 X CdTe 16M / Detector: PIXEL / Date: Feb 4, 2026
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.82655 Å / Relative weight: 1
ReflectionResolution: 1.06→66.081 Å / Num. obs: 234949 / % possible obs: 93.1 % / Redundancy: 8.5 % / Biso Wilson estimate: 12.19 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.047 / Rpim(I) all: 0.017 / Rrim(I) all: 0.05 / Net I/σ(I): 17.3
Reflection shell

Num. unique obs: 11747 / Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsCC1/2Rpim(I) allRrim(I) all% possible all
3.436-66.0819.40.0351.80.9990.010.031100
1.06-1.1810.7441.60.6540.3920.84854.9

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Processing

Software
NameVersionClassification
BUSTER2.10.4refinement
autoPROC2025-04-07data reduction
XDS20250430data reduction
STARANISO3.0.6 (20250212)data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.2→17.54 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.971 / SU R Cruickshank DPI: 0.041 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.039 / SU Rfree Blow DPI: 0.042 / SU Rfree Cruickshank DPI: 0.041
RfactorNum. reflection% reflectionSelection details
Rfree0.1593 10966 -RANDOM
Rwork0.1349 ---
obs0.1361 218814 79.4 %-
Displacement parametersBiso mean: 17.12 Å2
Baniso -1Baniso -2Baniso -3
1--0.5255 Å20.1471 Å2-0.2349 Å2
2--0.3278 Å20.0101 Å2
3---0.1978 Å2
Refine analyzeLuzzati coordinate error obs: 0.11 Å
Refinement stepCycle: LAST / Resolution: 1.2→17.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7107 0 36 1081 8224
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.01415128HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.7727391HARMONIC8
X-RAY DIFFRACTIONt_dihedral_angle_d4456SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes2595HARMONIC5
X-RAY DIFFRACTIONt_it15085HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion979SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies49HARMONIC1
X-RAY DIFFRACTIONt_ideal_dist_contact16221SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion6.23
X-RAY DIFFRACTIONt_other_torsion14.7
LS refinement shellResolution: 1.2→1.22 Å
RfactorNum. reflection% reflection
Rfree0.2129 243 -
Rwork0.1887 --
obs0.19 4377 36.17 %

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