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- PDB-9i3d: Isopenicillin N synthase co-crystallised with Fe and ACdV after 1... -

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Basic information

Entry
Database: PDB / ID: 9i3d
TitleIsopenicillin N synthase co-crystallised with Fe and ACdV after 10s O2 exposure
ComponentsIsopenicillin N synthase
KeywordsOXIDOREDUCTASE / Isopenicillin N synthase / antiobiotic / O2 exposure / time-resolved crystallography / XFEL
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 / OXYGEN MOLECULE / Isopenicillin N synthase
Similarity search - Component
Biological speciesAspergillus nidulans FGSC A4 (mold)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 1.68 Å
AuthorsRabe, P. / Schofield, C.J.
Funding support United Kingdom, United States, Korea, Republic Of, 12items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/V001892/1 United Kingdom
Wellcome Trust210734/Z/18/Z United Kingdom
Wellcome Trust227298/Z/23/Z United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/V001892/1 United Kingdom
Department of Energy (DOE, United States)DE- AC02-76SF00515 United States
Department of Energy (DOE, United States)DE-AC02- 05CH11231 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM117126 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM55302 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM126289 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1P41GM139687 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)OD023453 United States
National Research Foundation (NRF, Korea)NRF-2017M3A9F6029733 Korea, Republic Of
CitationJournal: To Be Published
Title: Isopenicillin N synthase co-crystallised with Fe and ACdV after 10s O2 exposure
Authors: Rabe, P. / Schofield, C.J.
History
DepositionJan 22, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 12, 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: Isopenicillin N synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,09410
Polymers37,5641
Non-polymers1,5309
Water3,729207
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1180 Å2
ΔGint-43 kcal/mol
Surface area14320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.492, 74.806, 101.383
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
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

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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.) Aspergillus nidulans FGSC A4 (mold) / Gene: ipnA, ips, AN2622 / Plasmid: pCold_IPNS / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P05326, isopenicillin-N synthase

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Non-polymers , 8 types, 216 molecules

#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 / Feature type: SUBJECT OF INVESTIGATION
#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: Chemical ChemComp-A1I0E / oxidanylideneiron(4+)


Mass: 71.844 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: FeO / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-A1IZG / (2S)-2-azanyl-6-[[(3R,4R)-1-[(2R)-3-methyl-1-oxidanyl-1-oxidanylidene-butan-2-yl]-2-oxidanylidene-4-sulfanyl-azetidin-3-yl]amino]-6-oxidanylidene-hexanoic acid / 2-amino-6-{[1-(1-carboxy-2-methylpropyl)-2-oxo-4-sulfanylazetidin-3-yl]amino}-6-oxohexanoic acid


Mass: 361.414 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H23N3O6S
#7: Chemical ChemComp-IO0 / (2S)-2-azanyl-6-[[(2R)-1-[[(2R)-3-methyl-1-oxidanyl-1-oxidanylidene-butan-2-yl]amino]-1-oxidanylidene-3-sulfanylidene-propan-2-yl]amino]-6-oxidanylidene-hexanoic acid / ACdV thioaldehyde


Mass: 361.414 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H23N3O6S / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-OXY / OXYGEN MOLECULE


Mass: 31.999 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O2 / Feature type: SUBJECT OF INVESTIGATION
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 207 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.09 Å3/Da / Density % sol: 41.27 % / Description: needle morphology, 3 um x 3 um x 60 im
Crystal growTemperature: 293 K / Method: batch mode / pH: 8.5 / Details: 1.7M Li2SO4, 0.1 M TRIS pH 8.5

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Data collection

DiffractionMean temperature: 293 K / Ambient temp details: room temperature / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: PAL-XFEL / Beamline: NCI / Wavelength: 1.318066 Å
DetectorType: RAYONIX MX225-HS / Detector: CCD / Date: Oct 15, 2019
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.318066 Å / Relative weight: 1
ReflectionResolution: 1.68→27.78 Å / Num. obs: 36772 / % possible obs: 99.95 % / Redundancy: 93.75 % / Biso Wilson estimate: 21.82 Å2 / CC1/2: 0.984 / R split: 1.15 / Net I/σ(I): 3.921
Reflection shellResolution: 1.68→1.71 Å / Redundancy: 11.04 % / Mean I/σ(I) obs: 0.61 / Num. unique obs: 1807 / CC1/2: 0.096 / R split: 0.173 / % possible all: 99.72
Serial crystallography sample deliveryMethod: injection

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
cctbx.xfeldata reduction
cctbx.xfel.mergedata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.68→27.78 Å / SU ML: 0.2655 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.8162
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2586 2000 5.47 %
Rwork0.2107 34585 -
obs0.2133 36585 99.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.22 Å2
Refinement stepCycle: LAST / Resolution: 1.68→27.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2574 0 89 208 2871
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00562771
X-RAY DIFFRACTIONf_angle_d0.74123790
X-RAY DIFFRACTIONf_chiral_restr0.0516398
X-RAY DIFFRACTIONf_plane_restr0.0072503
X-RAY DIFFRACTIONf_dihedral_angle_d13.6072998
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.68-1.720.38961370.35732357X-RAY DIFFRACTION95.85
1.72-1.770.40611390.33352416X-RAY DIFFRACTION99.38
1.77-1.820.35951410.29772442X-RAY DIFFRACTION99.61
1.82-1.880.32741410.28292434X-RAY DIFFRACTION99.92
1.88-1.950.31341420.24622447X-RAY DIFFRACTION99.92
1.95-2.020.29551410.22982452X-RAY DIFFRACTION99.92
2.02-2.120.29131430.22272460X-RAY DIFFRACTION100
2.12-2.230.26771410.21242453X-RAY DIFFRACTION100
2.23-2.370.28541440.20792476X-RAY DIFFRACTION99.92
2.37-2.550.31511430.25662477X-RAY DIFFRACTION99.47
2.55-2.810.36071430.28062467X-RAY DIFFRACTION99.28
2.81-3.210.28981440.20022512X-RAY DIFFRACTION100
3.21-4.040.1751470.1592529X-RAY DIFFRACTION99.59
4.05-27.780.17271540.15962663X-RAY DIFFRACTION99.86
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)
11.98552651295-0.266426068281-1.09252855741.039582230620.3154625434534.31713718919-0.008228294582240.107166445288-0.00375943932349-0.0943301605502-0.0226043351670.08851991872720.0833341287262-0.2964208825640.08121458094350.1052469913510.0162622972984-0.03266609377590.1372728904740.01690893730310.15371773064243.511273591176.222443725-8.28569188847
25.97625387797-0.2541151429073.737461473795.890668299221.223450967976.08353577270.142308262484-0.207963993648-0.03638296987050.0579619149140.004031498672650.2431465215440.386562657986-0.074378527397-0.1446415389820.2805494316160.01818667950670.02561359352150.179276699150.02734392139050.12913348199349.910890487368.507087919623.6801244909
31.55156250602-0.794434749268-0.2927821468572.66464658784-0.3028619545122.9438608712-0.126036570188-0.166728843919-0.132550949320.2004273018320.132715469536-0.02303478305890.5410453619870.1549825331330.007838981497950.2582329581660.00101958494672-0.0208374575680.168529288310.02535338884040.1335083950552.771480660864.47096940714.0519530862
40.7375218465570.6753109534820.1359457558252.07217192009-1.402147448013.137225498290.08753425876020.0440501513436-0.151237023723-0.106417132414-0.114214614201-0.05604141330210.6298565340590.1440702793450.06170958204080.2444402536530.0454576274606-0.02505758068120.122893834728-0.008766883250720.17490138369851.325257591265.2761907037-5.21852933162
51.548059091620.104381752851-0.6753051943761.651144282350.2451024343343.121156850390.0495152957487-0.01477187552510.1413784142760.1581384526780.01242102167420.0228547073815-0.112514322220.0491344673483-0.06916765200310.1160259921850.0104663382826-0.02315211184220.1117164061770.008158303009860.13293999675749.857398750383.64986057033.90857332883
63.30785964296-1.131326610181.693612335532.50909906042-1.168445270222.478186503230.008201956371840.2958681447090.116242702384-0.290537001759-0.405364852351-0.5051597608220.2715701217451.187927016670.4279095376060.2280057683460.07938458314030.01120175291730.4218379176710.01693582627910.23453270633667.838393883972.1120735373-10.0904701575
74.17572566118-0.406320314078-3.279780375489.010532270735.473895238478.883910008920.120360651416-0.6700548648770.3699208152770.8923605328310.08023977215970.160425406259-0.364816749430.780627555756-0.1302566656710.389807482639-0.01221371296660.01201735986690.397885259990.03549138039610.29563914388463.251198935275.31914530388.20092528107
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 4 through 62 )4 - 621 - 59
22chain 'A' and (resid 63 through 82 )63 - 8260 - 79
33chain 'A' and (resid 83 through 137 )83 - 13780 - 134
44chain 'A' and (resid 138 through 183 )138 - 183135 - 180
55chain 'A' and (resid 184 through 286 )184 - 286181 - 283
66chain 'A' and (resid 287 through 312 )287 - 312284 - 309
77chain 'A' and (resid 313 through 331 )313 - 331310 - 328

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