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- PDB-9ub9: Wild-type Bacillus megaterium Penicillin G Acylase -

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Basic information

Entry
Database: PDB / ID: 9ub9
TitleWild-type Bacillus megaterium Penicillin G Acylase
Components(Penicillin G ...) x 2
KeywordsSTRUCTURAL PROTEIN / N-terminal nucleophile hydrolase / Bacillus megaterium / penicillin acylase
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
DI(HYDROXYETHYL)ETHER / Penicillin G acylase
Similarity search - Component
Biological speciesPriestia megaterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 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 2, 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)87,27520
Polymers85,9282
Non-polymers1,34618
Water7,927440
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: This enzyme is initially expressed as a monomeric pro-enzyme, which becomes auto-activation into the intertwining heterodimeric active-form.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15980 Å2
ΔGint-90 kcal/mol
Surface area27550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.726, 77.475, 84.170
Angle α, β, γ (deg.)90.000, 100.630, 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: There are 2 subunits. The alpha subunit (chain A) consists of amino acid number 1 - 210.
Source: (gene. exp.) Priestia megaterium (bacteria) / Gene: pac, pga / Plasmid: pBA402 / Production host: Priestia megaterium (bacteria) / Strain (production host): UN-cat stain / 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
Details: The beta subunit (chain B) starts at the amino acid number 211 and continues to number 747.
Source: (gene. exp.) Priestia megaterium (bacteria) / Gene: pac, pga / Plasmid: pBA402 / Production host: Priestia megaterium (bacteria) / Strain (production host): UN-cat stain / References: UniProt: Q60136

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Non-polymers , 6 types, 458 molecules

#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 440 / 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: 2.15 Å3/Da / Density % sol: 42.82 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.125 M NaCl, 29% w/v PEG 4000, and 0.1 M HEPES (pH 7.5)
PH range: 7.0-8.0

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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 7, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 1.92→50 Å / Num. obs: 55806 / % possible obs: 96.6 % / Redundancy: 6.9 % / Biso Wilson estimate: 25.09 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 24.88
Reflection shellResolution: 1.92→1.99 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.381 / Num. unique obs: 4763 / % possible all: 85.9
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: 1.92→30.94 Å / SU ML: 0.1584 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.1575
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1928 2735 5.08 %
Rwork0.1557 51155 -
obs0.1577 53890 96.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.47 Å2
Refinement stepCycle: LAST / Resolution: 1.92→30.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5829 0 82 440 6351
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0116077
X-RAY DIFFRACTIONf_angle_d1.10298174
X-RAY DIFFRACTIONf_chiral_restr0.0667818
X-RAY DIFFRACTIONf_plane_restr0.0091056
X-RAY DIFFRACTIONf_dihedral_angle_d6.3389821
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.92-1.950.28211080.21112126X-RAY DIFFRACTION80.33
1.95-1.990.29591270.19572291X-RAY DIFFRACTION86.82
1.99-2.020.26771400.19372324X-RAY DIFFRACTION89.76
2.02-2.070.25561430.1832396X-RAY DIFFRACTION90
2.07-2.110.23981410.17472434X-RAY DIFFRACTION93.09
2.11-2.160.23091190.17032552X-RAY DIFFRACTION95.53
2.16-2.210.20361360.15722578X-RAY DIFFRACTION97.24
2.21-2.270.19291370.16052596X-RAY DIFFRACTION98.95
2.27-2.340.19731500.15292629X-RAY DIFFRACTION99.29
2.34-2.420.22681430.15752636X-RAY DIFFRACTION99.53
2.42-2.50.22611380.16072638X-RAY DIFFRACTION99.71
2.5-2.60.18561370.15172633X-RAY DIFFRACTION99.82
2.6-2.720.21461300.15392656X-RAY DIFFRACTION99.86
2.72-2.860.21161420.15152654X-RAY DIFFRACTION99.89
2.86-3.040.20711530.15952637X-RAY DIFFRACTION99.93
3.04-3.280.18331430.14912642X-RAY DIFFRACTION99.89
3.28-3.610.17631410.13932689X-RAY DIFFRACTION99.93
3.61-4.130.14681350.13592674X-RAY DIFFRACTION99.75
4.13-5.20.15881460.13412632X-RAY DIFFRACTION98.51
5.2-30.940.18661260.18452738X-RAY DIFFRACTION99.62
Refinement TLS params.Method: refined / Origin x: 15.1256978431 Å / Origin y: 0.928337349297 Å / Origin z: 22.3452517169 Å
111213212223313233
T0.159793039436 Å20.0135056376828 Å2-0.0232138952293 Å2-0.213729997004 Å2-0.00300149238607 Å2--0.132973304685 Å2
L0.447444561474 °20.0801259182903 °20.221751889289 °2-1.21293623171 °20.0154588364261 °2--0.657726904851 °2
S-0.0275624756993 Å °-0.0586035935441 Å °0.0424962019866 Å °0.143555232658 Å °-0.0115772649796 Å °-0.134619775066 Å °0.00339623483336 Å °0.0459783180366 Å °0.0386643671725 Å °
Refinement TLS groupSelection details: all

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