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- PDB-6nvx: Crystal structure of penicillin G acylase from Bacillus sp. FJAT-27231 -

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Basic information

Entry
Database: PDB / ID: 6nvx
TitleCrystal structure of penicillin G acylase from Bacillus sp. FJAT-27231
Components(penicillin G acylase, ...) x 2
KeywordsHYDROLASE / penicillin / acylase
Function / homology
Function and homology information


hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides / antibiotic biosynthetic process / metal ion binding
Similarity search - Function
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 ...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 sp. FJAT-27231 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.36 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 1.3Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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, alpha-subunit
B: penicillin G acylase, beta-subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,71912
Polymers86,6092
Non-polymers1,10910
Water17,475970
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14520 Å2
ΔGint-83 kcal/mol
Surface area29210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.366, 77.686, 210.365
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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

#1: Protein penicillin G acylase, alpha-subunit


Mass: 24858.033 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus sp. FJAT-27231 (bacteria) / Gene: AC623_04440 / Production host: Bacillus megaterium (bacteria) / References: UniProt: A0A0K9H482
#2: Protein penicillin G acylase, beta-subunit


Mass: 61751.305 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus sp. FJAT-27231 (bacteria) / Gene: AC623_04440 / Production host: Bacillus megaterium (bacteria) / References: UniProt: A0A0K9H482

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Non-polymers , 4 types, 980 molecules

#3: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


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


Mass: 18.015 Da / Num. of mol.: 970 / 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: 2.71 Å3/Da / Density % sol: 54.55 %
Crystal growTemperature: 309 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 85 mM HEPES (pH 7.5), 8.5% (w/v) PEG 8000, 15% (v/v) glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.36→46.15 Å / Num. obs: 202143 / % possible obs: 100 % / Redundancy: 12.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.105 / Rpim(I) all: 0.031 / Rrim(I) all: 0.109 / Net I/σ(I): 14.3 / Num. measured all: 2500361 / Scaling rejects: 82
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.36-1.3810.91.66798650.5030.5211.749100
7.45-46.1512.60.03514220.9990.010.03699.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIXdev_3386refinement
XDSdata reduction
Aimless0.7.3data scaling
PHASERphasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1CP9

1cp9


Resolution: 1.36→46.148 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 15.99
RfactorNum. reflection% reflection
Rfree0.1674 9839 4.87 %
Rwork0.1488 --
obs0.1497 202003 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 113.92 Å2 / Biso mean: 24.2142 Å2 / Biso min: 7.98 Å2
Refinement stepCycle: final / Resolution: 1.36→46.148 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5951 0 147 970 7068
Biso mean--59.28 36.23 -
Num. residues----730
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.36-1.37550.28763280.271962846612
1.3755-1.39160.2753300.253363486678
1.3916-1.40860.25413380.247163226660
1.4086-1.42650.27683310.238363326663
1.4265-1.44520.2613340.235363326666
1.4452-1.4650.26663050.22264096714
1.465-1.4860.22913400.212463166656
1.486-1.50810.21163190.198763476666
1.5081-1.53170.21673260.194463426668
1.5317-1.55680.20343080.18264336741
1.5568-1.58370.19643460.17462696615
1.5837-1.61250.18613320.165563696701
1.6125-1.64350.17873120.155963816693
1.6435-1.6770.17463330.158663226655
1.677-1.71350.18152920.154964096701
1.7135-1.75340.1853010.148564326733
1.7534-1.79720.1683380.146963706708
1.7972-1.84580.16163170.14663826699
1.8458-1.90010.16293600.144763686728
1.9001-1.96140.17453440.149263206664
1.9614-2.03150.15623050.13264606765
2.0315-2.11290.14593260.127264076733
2.1129-2.2090.13723210.126164476768
2.209-2.32550.16023170.133664136730
2.3255-2.47120.1473680.126764406808
2.4712-2.6620.13283310.121564436774
2.662-2.92980.14543180.124664996817
2.9298-3.35370.15273260.128165396865
3.3537-4.22480.14153250.123765876912
4.2248-46.17430.17483680.173468427210
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)
12.594-2.1391.48482.7032-2.56242.8494-0.190.04280.74620.5453-0.2522-1.0285-0.56250.42120.38110.3163-0.0291-0.08770.16190.02950.312134.54243.081397.0367
23.0262-2.24571.58212.0407-1.95982.5995-0.132-0.02090.27070.25660.036-0.0967-0.22690.02120.06140.1358-0.012-0.01680.06410.00910.122930.202736.818997.249
31.5496-0.27690.13040.80270.72311.67330.00850.15290.1585-0.0776-0.0003-0.0884-0.14080.1421-0.03160.118-0.03690.00410.12040.05060.122134.504835.033282.2065
43.5440.39491.46140.51530.04912.69970.09330.7155-0.3875-0.060.1695-0.22060.26120.7659-0.13240.17460.0260.00630.425-0.07250.162640.183822.672565.675
51.8819-1.2145-0.05711.72151.15611.7932-0.00210.36240.208-0.1972-0.00540.0287-0.20950.01240.03370.1948-0.0294-0.00680.21260.08250.158624.906238.410666.5451
66.4278-0.46482.04042.20680.3123.1008-0.10270.17910.55470.0062-0.0442-0.0624-0.30460.15270.16990.1709-0.0508-0.01920.10880.08270.176133.187543.094780.5759
73.1410.62990.66543.39311.46823.0181-0.09680.1320.07130.0643-0.0366-0.21010.04980.3160.03940.1275-0.0373-0.00050.24730.07290.250.691631.720483.343
85.2804-0.3691-0.38031.11570.87510.7605-0.03390.53320.3494-0.172-0.0797-0.1414-0.20840.33710.18010.1797-0.0656-0.00820.28290.09760.164242.375437.272375.066
91.79320.67320.94061.83410.39560.7856-0.02690.1944-0.081-0.10810.062-0.1003-0.02680.0649-0.00090.1238-0.01740.01510.17170.0110.106826.877625.339172.0537
101.0269-1.5035-1.13968.43464.4293.13210.01590.13120.042-0.21670.0988-0.290.09120.1731-0.13070.1817-0.01130.00430.2205-0.02780.113721.16240.61858.8816
114.8948-0.2648-1.34757.32214.69667.1345-0.10660.4187-0.2146-0.3011-0.0960.22870.2504-0.13680.14530.1555-0.0213-0.00050.1767-0.02890.08512.8679-4.306561.1932
122.1352-0.5303-1.08053.51951.83842.70010.0310.2365-0.0484-0.0801-0.11640.2360.0757-0.35890.10990.0995-0.014-0.01840.14490.00710.10966.92436.703276.8014
137.1245-1.96383.53761.86950.85294.24730.24230.52970.1639-0.6655-0.27290.9047-0.2998-1.12050.11460.37790.05-0.0990.58380.02940.5987-6.05915.6380.4546
140.46930.1810.10780.4719-0.1280.8608-0.04890.17580.0353-0.1090.0483-0.00620.02570.0756-0.00660.0932-0.0089-0.00050.13130.02670.101422.441224.662272.5739
150.47040.0695-0.08650.39630.12941.1119-0.02250.15610.0543-0.10150.020.0891-0.0281-0.11920.00040.1002-0.0086-0.01970.15920.02340.12488.897216.65473.4292
160.5126-0.21550.07162.12350.17370.33910.0044-0.0188-0.11120.19670.0147-0.03930.1176-0.005-0.01920.1257-0.0026-0.00370.07780.01560.111719.0301-3.796994.3459
171.0129-0.62381.09851.7638-1.16922.63950.09210.1406-0.1483-0.2197-0.0513-0.09430.26980.1347-0.03620.15330.00790.01790.1223-0.04160.149621.2255-10.326777.3194
180.74320.50340.02022.3129-0.82690.87110.0270.0345-0.2074-0.0413-0.0807-0.36680.14430.12430.04880.12820.0338-0.00670.1304-0.01290.182136.65014.723589.1228
191.43260.38060.05650.7098-0.22780.54040.0211-0.02240.10250.0951-0.0052-0.0587-0.06260.0501-0.03090.09140.0021-0.01250.0720.01010.086930.030324.551198.0201
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 13 )A2 - 13
2X-RAY DIFFRACTION2chain 'A' and (resid 14 through 25 )A14 - 25
3X-RAY DIFFRACTION3chain 'A' and (resid 26 through 53 )A26 - 53
4X-RAY DIFFRACTION4chain 'A' and (resid 54 through 74 )A54 - 74
5X-RAY DIFFRACTION5chain 'A' and (resid 75 through 89 )A75 - 89
6X-RAY DIFFRACTION6chain 'A' and (resid 90 through 112 )A90 - 112
7X-RAY DIFFRACTION7chain 'A' and (resid 113 through 125 )A113 - 125
8X-RAY DIFFRACTION8chain 'A' and (resid 126 through 133 )A126 - 133
9X-RAY DIFFRACTION9chain 'A' and (resid 134 through 152 )A134 - 152
10X-RAY DIFFRACTION10chain 'A' and (resid 153 through 168 )A153 - 168
11X-RAY DIFFRACTION11chain 'A' and (resid 169 through 180 )A169 - 180
12X-RAY DIFFRACTION12chain 'A' and (resid 181 through 193 )A181 - 193
13X-RAY DIFFRACTION13chain 'A' and (resid 194 through 204 )A194 - 204
14X-RAY DIFFRACTION14chain 'B' and (resid 1 through 187 )B1 - 187
15X-RAY DIFFRACTION15chain 'B' and (resid 188 through 265 )B188 - 265
16X-RAY DIFFRACTION16chain 'B' and (resid 266 through 345 )B266 - 345
17X-RAY DIFFRACTION17chain 'B' and (resid 346 through 424 )B346 - 424
18X-RAY DIFFRACTION18chain 'B' and (resid 425 through 462 )B425 - 462
19X-RAY DIFFRACTION19chain 'B' and (resid 463 through 527 )B463 - 527

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