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- PDB-6zan: Isopenicillin N synthase in complex with Fe, the oxygen surrogate... -

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Basic information

Entry
Database: PDB / ID: 6zan
TitleIsopenicillin N synthase in complex with Fe, the oxygen surrogate NO and ACV.
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
L-D-(A-AMINOADIPOYL)-L-CYSTEINYL-D-VALINE / : / NITRIC OXIDE / Isopenicillin N synthase
Similarity search - Component
Biological speciesEmericella nidulans (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 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)38,3978
Polymers37,5641
Non-polymers8347
Water5,711317
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1760 Å2
ΔGint-62 kcal/mol
Surface area14270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.236, 74.404, 101.114
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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Protein , 1 types, 1 molecules A

#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

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Non-polymers , 5 types, 324 molecules

#2: Chemical ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-ACV / L-D-(A-AMINOADIPOYL)-L-CYSTEINYL-D-VALINE


Mass: 363.430 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H25N3O6S / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-NO / NITRIC OXIDE / Nitrogen monoxide / Nitric oxide


Mass: 30.006 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 317 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.16 Å3/Da / Density % sol: 42.98 % / Description: needles
Crystal growTemperature: 298 K / Method: batch mode / pH: 8.5 / Details: 1.7 M Li2SO4, 0.1M TRIS pH8.5

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: cryo / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97933 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jun 26, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97933 Å / Relative weight: 1
ReflectionResolution: 1.349→74.45 Å / Num. obs: 69251 / % possible obs: 100 % / Redundancy: 13.1 % / Biso Wilson estimate: 14.82 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.163 / Rpim(I) all: 0.047 / Rrim(I) all: 0.169 / Net I/σ(I): 9.4
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
1.35-1.39134.1941.250330.5811.1894.361
6.04-74.4512.30.05130.98990.9990.0150.053

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
XDSdata reduction
Aimless0.7.4data scaling
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BLZ

1blz


Resolution: 1.35→59.928 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 19.51
RfactorNum. reflection% reflection
Rfree0.188 3389 4.9 %
Rwork0.166 --
obs0.1671 69105 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 86.1 Å2 / Biso mean: 22.4027 Å2 / Biso min: 9.42 Å2
Refinement stepCycle: final / Resolution: 1.35→59.928 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2612 0 69 324 3005
Biso mean--31.95 31.59 -
Num. residues----328
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063001
X-RAY DIFFRACTIONf_angle_d0.8664109
X-RAY DIFFRACTIONf_chiral_restr0.074427
X-RAY DIFFRACTIONf_plane_restr0.006550
X-RAY DIFFRACTIONf_dihedral_angle_d17.2481093
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.35-1.36870.29211380.3008261597
1.3687-1.38910.30551480.29012696100
1.3891-1.41080.2921380.29022688100
1.4108-1.4340.27321560.27292693100
1.434-1.45870.28161180.25492729100
1.4587-1.48520.28691340.2512726100
1.4852-1.51380.26431300.22182713100
1.5138-1.54470.2321420.21942694100
1.5447-1.57830.26381250.20792743100
1.5783-1.6150.22651700.20522671100
1.615-1.65540.22711340.19732730100
1.6554-1.70020.20941410.18862722100
1.7002-1.75020.23061450.17852693100
1.7502-1.80670.19031580.16942727100
1.8067-1.87130.17371400.16172731100
1.8713-1.94620.15721380.15292737100
1.9462-2.03480.16291610.14452732100
2.0348-2.1420.17811200.14182776100
2.142-2.27630.16081330.1412765100
2.2763-2.4520.15971260.14422764100
2.452-2.69880.16831370.14732771100
2.6988-3.08930.16161420.15852812100
3.0893-3.89210.18021460.13912832100
3.8921-59.9280.17641690.15872956100
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)
11.8662-0.49280.17044.6032.74945.5037-0.0578-0.0779-0.08010.1539-0.02920.29990.0853-0.28130.08010.0748-0.02050.01210.15620.03510.1247-18.7311-4.643211.9353
20.92420.04770.91070.41-0.01863.8341-0.0189-0.1042-0.03130.0433-0.00060.0031-0.0636-0.1537-0.0050.0644-0.01550.00860.10590.00870.0982-16.6496-1.741412.3704
32.5040.1373-1.73610.7434-0.19894.9560.01260.23160.0145-0.02270.04490.0936-0.2329-0.3491-0.05060.14080.0259-0.01990.0724-0.00360.128-17.93235.4375-16.3032
41.43660.55440.13971.5993-0.16262.2269-0.05390.10080.0476-0.05340.0554-0.0461-0.2770.02970.00250.1451-0.00160.01580.09940.02060.0808-10.506410.1586-14.0486
50.7775-0.67171.1871.6541-2.07085.3964-0.0119-0.10190.02310.02650.06490.0166-0.4241-0.099-0.01340.1382-0.00190.01230.0801-0.00610.1038-11.01869.51265.4156
60.9841-0.11750.71360.84170.03921.89240.05340.0354-0.1159-0.0667-0.00340.02110.10360.0177-0.06030.1074-0.00520.0110.11620.00190.1311-12.8149-8.5866-4.2928
72.1713-0.0150.75961.5573-0.87223.71420.0544-0.1527-0.08890.0888-0.1551-0.2475-0.02640.54660.11940.149-0.0493-0.01170.2430.01430.16055.96092.269710.2971
88.243.55153.43224.31693.8353.6261-0.1470.8733-0.5933-0.78670.3891-0.01580.00780.2973-0.220.3258-0.032-0.01990.2913-0.00880.230.929-0.3393-8.324
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 21 )A4 - 21
2X-RAY DIFFRACTION2chain 'A' and (resid 22 through 50 )A22 - 50
3X-RAY DIFFRACTION3chain 'A' and (resid 51 through 88 )A51 - 88
4X-RAY DIFFRACTION4chain 'A' and (resid 89 through 137 )A89 - 137
5X-RAY DIFFRACTION5chain 'A' and (resid 138 through 183 )A138 - 183
6X-RAY DIFFRACTION6chain 'A' and (resid 184 through 286 )A184 - 286
7X-RAY DIFFRACTION7chain 'A' and (resid 287 through 312 )A287 - 312
8X-RAY DIFFRACTION8chain 'A' and (resid 313 through 331 )A313 - 331

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