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- PDB-6nvw: Crystal structure of penicillin G acylase from Bacillus megaterium -

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Basic information

Entry
Database: PDB / ID: 6nvw
TitleCrystal structure of penicillin G acylase from Bacillus megaterium
Components(Penicillin G acylase) x 2
KeywordsHYDROLASE / 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 G acylase, beta-roll domain / Aminohydrolase, N-terminal nucleophile (Ntn) domain, beta-sheet knob region / 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 / Aminohydrolase, N-terminal nucleophile (Ntn) domain ...Penicillin G acylase, C-terminal / Penicillin G acylase, beta-roll domain / Aminohydrolase, N-terminal nucleophile (Ntn) domain, beta-sheet knob region / 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 / Aminohydrolase, N-terminal nucleophile (Ntn) domain / Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 / Nucleophile aminohydrolases, N-terminal / 4-Layer Sandwich / Roll / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Penicillin G acylase
Similarity search - Component
Biological speciesBacillus megaterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.203 Å
AuthorsBlankenfeldt, W.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationSPP1934 Germany
CitationJournal: Appl.Microbiol.Biotechnol. / Year: 2019
Title: Crystal structures and protein engineering of three different penicillin G acylases from Gram-positive bacteria with different thermostability.
Authors: Mayer, J. / Pippel, J. / Gunther, G. / Muller, C. / Lauermann, A. / Knuuti, T. / Blankenfeldt, W. / Jahn, D. / Biedendieck, R.
History
DepositionFeb 5, 2019Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 3, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 11, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Nov 20, 2019Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.process_site
Revision 1.3May 15, 2024Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,0094
Polymers85,9282
Non-polymers802
Water4,612256
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11800 Å2
ΔGint-100 kcal/mol
Surface area27970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.238, 77.961, 84.086
Angle α, β, γ (deg.)90.000, 101.670, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#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.) Bacillus megaterium (bacteria) / Gene: pac, pga / Production host: Bacillus megaterium (bacteria) / References: UniProt: Q60136, penicillin amidase
#2: Protein Penicillin G acylase / Penicillin G amidase / Penicillin G amidohydrolase


Mass: 61475.883 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus megaterium (bacteria) / Gene: pac, pga / Production host: Bacillus megaterium (bacteria) / References: UniProt: Q60136, penicillin amidase
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 256 / Source method: isolated from a natural source / Formula: H2O

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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: 2.18 Å3/Da / Density % sol: 43.46 %
Crystal growTemperature: 309 K / Method: vapor diffusion, sitting drop / Details: 200 mM MgCl2, 20% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.0003 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 12, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0003 Å / Relative weight: 1
ReflectionResolution: 2.2→46.032 Å / Num. obs: 25584 / % possible obs: 68.4 % / Redundancy: 6.6 % / Net I/σ(I): 9
Reflection shellResolution: 2.2→2.38 Å

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
PHASERphasing
PHENIXdev_3386refinement
PDB_EXTRACT3.24data extraction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.203→46.032 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 31.55
RfactorNum. reflection% reflection
Rfree0.2747 1210 4.79 %
Rwork0.2146 --
obs0.2175 25271 67.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 137.03 Å2 / Biso mean: 42.0979 Å2 / Biso min: 4.06 Å2
Refinement stepCycle: final / Resolution: 2.203→46.032 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5791 0 2 256 6049
Biso mean--40.08 23.63 -
Num. residues----719
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2034-2.29160.854590.40021531624
2.2916-2.39590.312640.28681218128231
2.3959-2.52220.37291060.29211928203449
2.5222-2.68020.29141350.28162526266164
2.6802-2.88710.34931680.27023037320577
2.8871-3.17760.32351780.25333510368889
3.1776-3.63720.26191690.22313775394495
3.6372-4.58190.26891800.18373869404997
4.5819-46.04170.20332010.161640454246100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.38472.27640.76963.71221.49373.4562-0.2773-0.22090.4076-0.2272-0.2389-0.193-0.58580.46360.30080.2934-0.0126-0.10340.26890.03710.42229.880324.4189-34.8126
21.0871-0.319-0.75770.946-0.36051.4487-0.26710.02640.1681-0.0847-0.03440.02520.0603-0.09050.0327-0.0438-0.0393-0.25590.1072-0.05640.2802-10.026223.1509-22.4397
33.74340.8359-0.4860.97070.6631.6770.0631-0.3716-0.01420.0396-0.05580.0045-0.120.629-0.00590.4257-0.0121-0.16820.2866-0.00970.2775-2.922826.9541-7.4878
42.70580.3750.24682.8680.01462.3076-0.2733-0.15780.77090.1261-0.1462-0.1599-0.48320.34970.29790.1812-0.1155-0.20930.17930.00130.40031.730531.4719-24.3822
57.291-3.84172.50834.4086-0.3354.95340.23570.70430.1947-0.1571-0.1457-0.03610.07960.30270.1480.3130.0408-0.19870.1111-0.00510.3962-14.021629.0335-37.0525
61.2101-1.60170.36143.3603-1.01060.8953-0.1075-0.11290.24560.24-0.02890.3431-0.1192-0.1770.02670.23910.0491-0.09050.14420.0360.531-13.164230.4368-26.1474
71.05251.3017-0.89252.7559-1.46070.95330.0422-0.0496-0.1263-0.19390.03770.34810.03130.01770.02070.1610.0061-0.09840.1268-0.12940.2236-6.815716.3816-14.1001
81.55070.18690.13161.44370.32240.259-0.1162-0.30360.03030.52160.01130.3888-0.1315-0.3437-0.04270.26050.0032-0.02730.23730.02670.2458-20.0505-8.1180.524
92.0279-1.1332-1.67086.00670.2046.2549-0.4905-0.3893-0.3663-0.3875-0.33970.15390.35710.34170.37370.10610.0523-0.05150.19020.03210.20530.6153-10.3104-7.3094
100.5116-0.1333-0.3020.67330.1550.9727-0.0705-0.10110.08920.1068-0.0391-0.1543-0.14950.03360.08720.1501-0.0193-0.14470.1632-0.0190.2835-3.514213.3096-11.6238
110.33730.036-0.15890.84760.08330.4239-0.0217-0.01-0.02150.0376-0.0593-0.12050.11710.11470.06920.1870.0464-0.10960.16680.05150.2973-1.4977-9.439-17.289
121.5793-1.2283-0.50511.57461.35251.7206-0.0708-0.1477-0.34060.096-0.08090.22620.1156-0.28150.13320.3108-0.0523-0.10590.11270.01760.2918-17.0646-17.1919-13.3434
130.9830.4885-0.06991.55190.09760.34680.2335-0.0958-0.00320.0332-0.20760.11150.11890.06790.02380.2005-0.0193-0.06210.05650.01520.2265-13.4687-7.993-30.2365
140.9192-0.19820.15771.46330.37581.0143-0.03180.24230.2418-0.5845-0.0091-0.2827-0.11220.16760.03420.2359-0.0385-0.02050.11620.06520.2641.768111.4008-38.7143
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 24 )A3 - 24
2X-RAY DIFFRACTION2chain 'A' and (resid 25 through 72 )A25 - 72
3X-RAY DIFFRACTION3chain 'A' and (resid 73 through 88 )A73 - 88
4X-RAY DIFFRACTION4chain 'A' and (resid 89 through 111 )A89 - 111
5X-RAY DIFFRACTION5chain 'A' and (resid 112 through 123 )A112 - 123
6X-RAY DIFFRACTION6chain 'A' and (resid 124 through 132 )A124 - 132
7X-RAY DIFFRACTION7chain 'A' and (resid 133 through 151 )A133 - 151
8X-RAY DIFFRACTION8chain 'A' and (resid 152 through 179 )A152 - 179
9X-RAY DIFFRACTION9chain 'A' and (resid 180 through 194 )A180 - 194
10X-RAY DIFFRACTION10chain 'B' and (resid 1 through 187 )B1 - 187
11X-RAY DIFFRACTION11chain 'B' and (resid 188 through 345 )B188 - 345
12X-RAY DIFFRACTION12chain 'B' and (resid 346 through 404 )B346 - 404
13X-RAY DIFFRACTION13chain 'B' and (resid 405 through 473 )B405 - 473
14X-RAY DIFFRACTION14chain 'B' and (resid 474 through 527 )B474 - 527

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