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- PDB-9uew: Wild-type Bacillus megaterium Penicillin G Acylase with Non-Coval... -

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Basic information

Entry
Database: PDB / ID: 9uew
TitleWild-type Bacillus megaterium Penicillin G Acylase with Non-Covalently Bound Phenylacetic Acid
Components(Penicillin G ...) x 2
KeywordsSTRUCTURAL PROTEIN / N-terminal nucleophile hydrolase / Bacillus megaterium / penicillin acylase / nob-covalently bound PAA / enzyme-product complex
Function / homology
Function and homology information


penicillin amidase activity / penicillin amidase / antibiotic biosynthetic process / response to antibiotic / extracellular region / metal ion binding
Similarity search - Function
Penicillin G acylase, C-terminal / Penicillin/GL-7-ACA/AHL acylase / Penicillin/GL-7-ACA/AHL/aculeacin-A acylase / Penicillin amidase type, domain 1 / Penicillin amidase type, N-terminal domain, B-knob / Penicillin amidase type, A-knob / Penicillin amidase / Nucleophile aminohydrolases, N-terminal
Similarity search - Domain/homology
2-PHENYLACETIC ACID / DI(HYDROXYETHYL)ETHER / PHOSPHATE ION / Penicillin G acylase
Similarity search - Component
Biological speciesPriestia megaterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å
AuthorsKaewsasan, C. / Rojviriya, C. / Yuvaniyama, J.
Funding support Thailand, 1items
OrganizationGrant numberCountry
Other government2561A11003259 Thailand
CitationJournal: Acs Catalysis / Year: 2026
Title: Capturing Catalysis: Structural Insights into the Acyl-Enzyme Intermediate of Priestia megaterium Penicillin G Acylase
Authors: Kaewsasan, C. / Rojviriya, C. / Oonanant, W. / Prathumrat, N. / Koinueng, W. / Yuvaniyama, J.
History
DepositionApr 9, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 18, 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: Penicillin G acylase
B: Penicillin G acylase subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,02833
Polymers85,9282
Non-polymers2,09931
Water9,098505
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18360 Å2
ΔGint-84 kcal/mol
Surface area28160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.995, 76.951, 82.216
Angle α, β, γ (deg.)90.000, 100.470, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Penicillin G ... , 2 types, 2 molecules AB

#1: Protein Penicillin G acylase / Penicillin G amidase / Penicillin G amidohydrolase


Mass: 24452.488 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Priestia megaterium (bacteria) / Gene: pac, pga / Plasmid: pBA402 / Production host: Priestia megaterium (bacteria) / Strain (production host): UN-cat / References: UniProt: Q60136, penicillin amidase
#2: Protein Penicillin G acylase subunit beta


Mass: 61475.883 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Priestia megaterium (bacteria) / Gene: pac, pga / Plasmid: pBA402 / Production host: Priestia megaterium (bacteria) / Strain (production host): UN-cat / References: UniProt: Q60136

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Non-polymers , 8 types, 536 molecules

#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical ChemComp-PAC / 2-PHENYLACETIC ACID


Mass: 136.148 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H8O2 / Feature type: SUBJECT OF INVESTIGATION
#9: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 505 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.1 Å3/Da / Density % sol: 41.6 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.175 M NaCl, 30.5% w/v PEG 4000, and 0.1 M imidazole (pH 6.0)
PH range: 6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 0.9999 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 10, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 1.96→50 Å / Num. obs: 50818 / % possible obs: 97.5 % / Redundancy: 3.8 % / Biso Wilson estimate: 19.7 Å2 / Rmerge(I) obs: 0.036 / Net I/σ(I): 35.49
Reflection shellResolution: 1.96→2.03 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.144 / Num. unique obs: 4774 / % possible all: 83.5
Serial crystallography sample deliveryMethod: fixed target

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PNM

1pnm


Resolution: 1.96→28.57 Å / SU ML: 0.167 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.9882
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1877 2512 5.07 %
Rwork0.1416 47021 -
obs0.144 49533 97.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.12 Å2
Refinement stepCycle: LAST / Resolution: 1.96→28.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5890 0 129 505 6524
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0146160
X-RAY DIFFRACTIONf_angle_d1.20458262
X-RAY DIFFRACTIONf_chiral_restr0.0767827
X-RAY DIFFRACTIONf_plane_restr0.00921064
X-RAY DIFFRACTIONf_dihedral_angle_d7.9376833
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.96-20.2355910.15591984X-RAY DIFFRACTION73.79
2-2.040.19841260.14482452X-RAY DIFFRACTION92.6
2.04-2.090.21771500.13322657X-RAY DIFFRACTION98.18
2.09-2.130.19541550.13332598X-RAY DIFFRACTION98.46
2.13-2.190.19531360.12922646X-RAY DIFFRACTION98.79
2.19-2.250.19751290.13642641X-RAY DIFFRACTION98.93
2.25-2.310.19971220.14032664X-RAY DIFFRACTION98.93
2.31-2.390.1731540.13732635X-RAY DIFFRACTION98.97
2.39-2.470.18781460.13782638X-RAY DIFFRACTION99
2.47-2.570.20551390.13412637X-RAY DIFFRACTION98.97
2.57-2.690.20671540.13072658X-RAY DIFFRACTION99.43
2.69-2.830.19771410.13892686X-RAY DIFFRACTION99.44
2.83-3.010.18481460.13512644X-RAY DIFFRACTION99.36
3.01-3.240.19251450.13192690X-RAY DIFFRACTION99.54
3.24-3.560.16351390.1322689X-RAY DIFFRACTION99.72
3.57-4.080.15821350.13382676X-RAY DIFFRACTION99.57
4.08-5.130.16441490.14252721X-RAY DIFFRACTION99.76
5.14-28.570.22151550.19022705X-RAY DIFFRACTION98.52
Refinement TLS params.Method: refined / Origin x: 15.4431315939 Å / Origin y: 1.14413763084 Å / Origin z: 21.8704776828 Å
111213212223313233
T0.100739046027 Å2-0.00661169489753 Å2-0.0227141648424 Å2-0.116590795334 Å20.00824952007781 Å2--0.095763599833 Å2
L0.341786167828 °20.0570720060872 °20.126187089542 °2-0.884055583815 °20.0522490189724 °2--0.613138813173 °2
S0.00188137485682 Å °-0.0492148946049 Å °0.00058063985707 Å °0.0864238635304 Å °-0.0200828451839 Å °-0.0096563323561 Å °0.0143740040011 Å °0.0153612967613 Å °0.0184976978395 Å °
Refinement TLS groupSelection details: all

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