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- PDB-6zao: Isopenicillin N synthase structure in complex with Fe and IPN exp... -

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Basic information

Entry
Database: PDB / ID: 6zao
TitleIsopenicillin N synthase structure in complex with Fe and IPN exposed to dioxygen.
ComponentsIsopenicillin N synthase
KeywordsOXIDOREDUCTASE / Isopenicillin N synthase / oxygen binding / XFEL / time-resolved crystallography
Function / homology
Function and homology information


isopenicillin-N synthase / isopenicillin-N synthase activity / penicillin biosynthetic process / L-ascorbic acid binding / iron ion binding / cytosol
Similarity search - Function
Isopenicillin N synthase signature 1. / Isopenicillin N synthase, conserved site / Isopenicillin N synthase signature 2. / Non-haem dioxygenase N-terminal domain / non-haem dioxygenase in morphine synthesis N-terminal / Isopenicillin N synthase-like, Fe(2+) 2OG dioxygenase domain / 2OG-Fe(II) oxygenase superfamily / Isopenicillin N synthase-like superfamily / Oxoglutarate/iron-dependent dioxygenase / Fe(2+) 2-oxoglutarate dioxygenase domain profile.
Similarity search - Domain/homology
: / ISOPENICILLIN N / Isopenicillin N synthase
Similarity search - Component
Biological speciesEmericella nidulans (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.66 Å
AuthorsRabe, P. / Kamps, J.J.A.G. / Sutherlin, K. / Pharm, C. / McDonough, M.A. / Leissing, T.M. / Aller, P. / Butryn, A. / Linyard, J. / Lang, P. ...Rabe, P. / Kamps, J.J.A.G. / Sutherlin, K. / Pharm, C. / McDonough, M.A. / Leissing, T.M. / Aller, P. / Butryn, A. / Linyard, J. / Lang, P. / Brem, J. / Fuller, F.D. / Batyuk, A. / Hunter, M.S. / Pettinati, I. / Clifton, I.J. / Alonso-Mori, R. / Gul, S. / Young, I. / Kim, I. / Bhowmick, A. / ORiordan, L. / Brewster, A.S. / Claridge, T.D.W. / Sauter, N.K. / Yachandra, V. / Yano, J. / Kern, J.F. / Orville, A.M. / Schofield, C.J.
Funding support United Kingdom, 7items
OrganizationGrant numberCountry
Wellcome Trust106244/Z/14/Z United Kingdom
Medical Research Council (United Kingdom)106244/Z/14/Z United Kingdom
Wellcome Trust210734/Z/18/Z United Kingdom
Royal SocietyRSWF/R2/182017 United Kingdom
Wellcome Trust102593 United Kingdom
Biotechnology and Biological Sciences Research Council102593 United Kingdom
Biotechnology and Biological Sciences Research CouncilBB/S50676X/1 United Kingdom
CitationJournal: Sci Adv / Year: 2021
Title: X-ray free-electron laser studies reveal correlated motion during isopenicillin N synthase catalysis.
Authors: Rabe, P. / Kamps, J.J.A.G. / Sutherlin, K.D. / Linyard, J.D.S. / Aller, P. / Pham, C.C. / Makita, H. / Clifton, I. / McDonough, M.A. / Leissing, T.M. / Shutin, D. / Lang, P.A. / Butryn, A. / ...Authors: Rabe, P. / Kamps, J.J.A.G. / Sutherlin, K.D. / Linyard, J.D.S. / Aller, P. / Pham, C.C. / Makita, H. / Clifton, I. / McDonough, M.A. / Leissing, T.M. / Shutin, D. / Lang, P.A. / Butryn, A. / Brem, J. / Gul, S. / Fuller, F.D. / Kim, I.S. / Cheah, M.H. / Fransson, T. / Bhowmick, A. / Young, I.D. / O'Riordan, L. / Brewster, A.S. / Pettinati, I. / Doyle, M. / Joti, Y. / Owada, S. / Tono, K. / Batyuk, A. / Hunter, M.S. / Alonso-Mori, R. / Bergmann, U. / Owen, R.L. / Sauter, N.K. / Claridge, T.D.W. / Robinson, C.V. / Yachandra, V.K. / Yano, J. / Kern, J.F. / Orville, A.M. / Schofield, C.J.
History
DepositionJun 5, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 9, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 1, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 24, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Isopenicillin N synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,2676
Polymers37,5641
Non-polymers7035
Water5,513306
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1420 Å2
ΔGint-46 kcal/mol
Surface area14210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.010, 74.530, 101.110
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Isopenicillin N synthase / IPNS


Mass: 37563.836 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Emericella nidulans (strain FGSC A4 / ATCC 38163 / CBS 112.46 / NRRL 194 / M139) (mold)
Strain: FGSC A4 / ATCC 38163 / CBS 112.46 / NRRL 194 / M139 / Gene: ipnA, ips, AN2622 / Production host: Escherichia coli (E. coli) / Strain (production host): NM554 / References: UniProt: P05326, isopenicillin-N synthase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#4: Chemical ChemComp-IP1 / ISOPENICILLIN N


Mass: 359.398 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H21N3O6S / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 306 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.06 Å3/Da / Density % sol: 42.92 % / Description: needles
Crystal growTemperature: 298 K / Method: batch mode / pH: 8.5 / Details: 1.7 M Li2SO4, 0.1 M TRIS pH8.5

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Data collection

DiffractionMean temperature: 298 K / Ambient temp details: room-temperature / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9159 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 14, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9159 Å / Relative weight: 1
ReflectionResolution: 1.66→33.7 Å / Num. obs: 37503 / % possible obs: 100 % / Redundancy: 12.9 % / Biso Wilson estimate: 19.4 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.208 / Rpim(I) all: 0.06 / Rrim(I) all: 0.217 / Net I/σ(I): 9.2 / Num. measured all: 484635
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.66-1.713.62.858127600.5930.7982.969100
7.42-33.711.60.04436.94990.9990.0130.04698.9

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BLZ

1blz


Resolution: 1.66→31.849 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 24.62
RfactorNum. reflection% reflection
Rfree0.2175 1880 5.02 %
Rwork0.1771 --
obs0.1792 37426 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 82.39 Å2 / Biso mean: 28.3343 Å2 / Biso min: 13.75 Å2
Refinement stepCycle: final / Resolution: 1.66→31.849 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2580 0 59 308 2947
Biso mean--55.49 32.45 -
Num. residues----328
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062740
X-RAY DIFFRACTIONf_angle_d0.7573753
X-RAY DIFFRACTIONf_chiral_restr0.052395
X-RAY DIFFRACTIONf_plane_restr0.005497
X-RAY DIFFRACTIONf_dihedral_angle_d11.1831609
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.66-1.70490.3671480.33152726
1.7049-1.75510.34681460.30052634
1.7551-1.81170.31591380.26612718
1.8117-1.87650.26841350.24612717
1.8765-1.95160.28211590.2192671
1.9516-2.04040.25791470.19862695
2.0404-2.14790.20041380.18472719
2.1479-2.28250.221540.16742719
2.2825-2.45860.20951380.16532713
2.4586-2.7060.22771280.16852756
2.706-3.09720.19491240.16872773
3.0972-3.90110.18531660.14572786
3.9011-31.8490.18581590.14862919
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)
10.56030.12940.22820.5831-0.41033.43520.02770.0270.037-0.01750.05910.06910.156-0.19-0.10980.18940.0210.00460.1325-0.01160.18644.584673.75820.0269
21.4698-0.9235-0.70661.04890.25922.5105-0.082-0.1397-0.02490.07760.1147-0.04260.25650.1037-0.0180.2368-0.0004-0.01220.16740.01360.147152.286864.147713.9409
31.28490.143-1.14080.8135-0.46882.9942-0.050.069-0.0811-0.01140.0042-0.00680.2811-0.04580.14930.25080.0041-0.00730.1446-0.01220.162250.763364.9496-5.4909
41.1766-0.1003-1.00780.5793-0.03022.20880.0781-0.07810.14010.01610.00560.015-0.22510.1012-0.13180.1939-0.0119-0.010.14920.00070.162549.134783.27883.8224
53.1812-0.029-0.85174.9772-1.44816.1625-0.04950.38330.0839-0.4131-0.2259-0.4822-0.11990.90830.26320.23060.00580.01210.36140.03040.188167.158872.4358-10.1284
68.8285-0.0777-3.49236.63932.47972.32850.1383-0.85690.7610.99620.33190.246-0.60180.6755-0.39340.4973-0.01840.02020.32710.00140.26362.421775.1558.1533
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 82 )A4 - 82
2X-RAY DIFFRACTION2chain 'A' and (resid 83 through 137 )A83 - 137
3X-RAY DIFFRACTION3chain 'A' and (resid 138 through 182 )A138 - 182
4X-RAY DIFFRACTION4chain 'A' and (resid 183 through 286 )A183 - 286
5X-RAY DIFFRACTION5chain 'A' and (resid 287 through 312 )A287 - 312
6X-RAY DIFFRACTION6chain 'A' and (resid 313 through 331 )A313 - 331

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