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- PDB-9ul0: Wild-type Bacillus megaterium Penicillin G Acylase with Covalentl... -

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Basic information

Entry
Database: PDB / ID: 9ul0
TitleWild-type Bacillus megaterium Penicillin G Acylase with Covalently Bound Phenylacetic Acid
Components(Penicillin G ...) x 2
KeywordsSTRUCTURAL PROTEIN / N-terminal nucleophile hydrolase / Bacillus megaterium / Penicillin acylase / Covalently bound PAA
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
PHENYLACETALDEHYDE / Penicillin G acylase
Similarity search - Component
Biological speciesPriestia megaterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.71 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 18, 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)86,2358
Polymers85,9282
Non-polymers3076
Water25,3471407
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12970 Å2
ΔGint-125 kcal/mol
Surface area28680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.811, 78.056, 85.347
Angle α, β, γ (deg.)90.000, 101.537, 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
Details: The protein is a heterodimer composed of two distinct subunits. The alpha subunit (chain A) encompasses residues G1 through S210, whereas the beta subunit (chain B) comprises residues S211 to K747.
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 , 4 types, 1413 molecules

#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-HY1 / PHENYLACETALDEHYDE


Mass: 120.149 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H8O / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 1407 / 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: 2.2 Å3/Da / Density % sol: 43.9 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1 mM Penicillin G, 0.150 M NaCl, 31% w/v PEG 4000, and 0.1 M imidazole (pH 6.5)
PH range: 6.0-7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 0.99998 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: 0.99998 Å / Relative weight: 1
ReflectionResolution: 1.71→30 Å / Num. obs: 80619 / % possible obs: 97.5 % / Redundancy: 3.5 % / Biso Wilson estimate: 15.95 Å2 / Rmerge(I) obs: 0.043 / Net I/σ(I): 23.45
Reflection shellResolution: 1.71→1.77 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.183 / Mean I/σ(I) obs: 5.66 / Num. unique obs: 6551 / % possible all: 81.8
Serial crystallography sample deliveryMethod: fixed target

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PNM

1pnm


Resolution: 1.71→28.67 Å / SU ML: 0.1228 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 15.0839
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1582 3947 5.03 %
Rwork0.1355 74600 -
obs0.1367 78547 97.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.72 Å2
Refinement stepCycle: LAST / Resolution: 1.71→28.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5889 0 14 1407 7310
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00686190
X-RAY DIFFRACTIONf_angle_d0.84188380
X-RAY DIFFRACTIONf_chiral_restr0.0507846
X-RAY DIFFRACTIONf_plane_restr0.00661092
X-RAY DIFFRACTIONf_dihedral_angle_d14.06352366
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.71-1.730.2045900.16921946X-RAY DIFFRACTION71.41
1.73-1.750.1889970.15522256X-RAY DIFFRACTION81.59
1.75-1.770.20591200.15612356X-RAY DIFFRACTION87
1.77-1.80.18611290.15282557X-RAY DIFFRACTION93.23
1.8-1.820.15651220.15382716X-RAY DIFFRACTION98.61
1.82-1.850.19551570.15092691X-RAY DIFFRACTION99.72
1.85-1.880.16661290.15192714X-RAY DIFFRACTION99.61
1.88-1.910.17331590.15352745X-RAY DIFFRACTION99.86
1.91-1.940.19131410.15372748X-RAY DIFFRACTION99.72
1.94-1.980.19921380.14892699X-RAY DIFFRACTION99.68
1.98-2.020.17881560.14152701X-RAY DIFFRACTION99.65
2.02-2.060.17381390.1352752X-RAY DIFFRACTION99.86
2.06-2.10.17241430.13382696X-RAY DIFFRACTION99.72
2.1-2.150.15431230.13452765X-RAY DIFFRACTION99.65
2.15-2.20.16481670.13342714X-RAY DIFFRACTION99.76
2.2-2.260.16521480.14142713X-RAY DIFFRACTION99.69
2.26-2.330.18961450.14242726X-RAY DIFFRACTION99.72
2.33-2.40.15561460.13952744X-RAY DIFFRACTION99.66
2.4-2.490.16731620.14312706X-RAY DIFFRACTION99.45
2.49-2.590.16731350.13722728X-RAY DIFFRACTION99.72
2.59-2.710.15141480.14352728X-RAY DIFFRACTION99.58
2.71-2.850.17191440.13752739X-RAY DIFFRACTION99.62
2.85-3.030.16641640.13882746X-RAY DIFFRACTION99.56
3.03-3.260.14671430.132719X-RAY DIFFRACTION99.83
3.26-3.590.1381390.12462762X-RAY DIFFRACTION99.79
3.59-4.110.11791370.11222757X-RAY DIFFRACTION99.52
4.11-5.170.12251520.11332695X-RAY DIFFRACTION97.33
5.17-28.670.16531740.14562781X-RAY DIFFRACTION99.36
Refinement TLS params.Method: refined / Origin x: 14.8542026283 Å / Origin y: 0.364144103219 Å / Origin z: 22.5958432987 Å
111213212223313233
T0.122149162531 Å20.0126858155753 Å2-0.0302305613587 Å2-0.124595080196 Å2-0.000372866825093 Å2--0.0915067504065 Å2
L0.257239285461 °20.0379898322549 °20.0660882337222 °2-0.763613138459 °20.0686013412155 °2--0.473812912001 °2
S-0.0206552785298 Å °-0.0163339117028 Å °0.0346445359788 Å °0.111437585542 Å °-0.00561925021487 Å °-0.126297803004 Å °-0.00152246917441 Å °0.0544729941122 Å °0.025320185192 Å °
Refinement TLS groupSelection details: all

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