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- PDB-9s1k: Isopenicillin N synthase S281A variant in complex with Fe and ACV... -

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Basic information

Entry
Database: PDB / ID: 9s1k
TitleIsopenicillin N synthase S281A variant in complex with Fe and ACV under anaerobic conditions.
ComponentsIsopenicillin N synthase
KeywordsOXIDOREDUCTASE / Isopenicillin N synthase / IPNS / penicillin / amtibiotic
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 / : / Isopenicillin N synthase
Similarity search - Component
Biological speciesAspergillus nidulans FGSC A4 (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.38 Å
AuthorsJabbary, M. / Rabe, P. / Schofield, C.J.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/V001892/1 United Kingdom
Wellcome Trust227298/Z/23/Z United Kingdom
CitationJournal: To Be Published
Title: Isopenicillin N synthase S281A variant in complex with Fe and ACV under anaerobic conditions.
Authors: Jabbary, M. / Rabe, P. / Schofield, C.J.
History
DepositionJul 18, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 29, 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)38,4438
Polymers37,5481
Non-polymers8967
Water7,206400
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1860 Å2
ΔGint-55 kcal/mol
Surface area14000 Å2
Unit cell
Length a, b, c (Å)41.120, 73.830, 100.520
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: 37547.836 Da / Num. of mol.: 1 / Mutation: S281A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus nidulans FGSC A4 (mold) / Gene: ipnA, ips, AN2622 / Plasmid: pCold_IPNS_S281A / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P05326, isopenicillin-N synthase

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Non-polymers , 5 types, 407 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION


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-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 400 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.03 Å3/Da / Density % sol: 39.46 % / Description: needle morphology, 4 um x 4um x 200 um
Crystal growTemperature: 293 K / Method: batch mode / pH: 8.3 / Details: 1.7 M Li2SO4, 0.1M Tris pH 8.3

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: cryogenic / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Nov 27, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.38→59.5 Å / Num. obs: 63582 / % possible obs: 99.7 % / Redundancy: 13.3 % / Biso Wilson estimate: 17.93 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.03 / Rrim(I) all: 0.081 / Net I/σ(I): 15.6
Reflection shellResolution: 1.38→1.4 Å / Redundancy: 13.5 % / Rmerge(I) obs: 2.452 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 3025 / CC1/2: 0.595 / Rpim(I) all: 0.99 / Rrim(I) all: 2.647 / % possible all: 97.9

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.38→59.5 Å / SU ML: 0.168 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 21.8686
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1892 3782 3.12 %
Rwork0.1645 117349 -
obs0.1653 63582 99.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.5 Å2
Refinement stepCycle: LAST / Resolution: 1.38→59.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2552 0 51 400 3003
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00822753
X-RAY DIFFRACTIONf_angle_d0.94493767
X-RAY DIFFRACTIONf_chiral_restr0.0838391
X-RAY DIFFRACTIONf_plane_restr0.0077503
X-RAY DIFFRACTIONf_dihedral_angle_d12.8665987
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.38-1.40.32041390.34154266X-RAY DIFFRACTION97.39
1.4-1.420.34521350.32584295X-RAY DIFFRACTION98.25
1.42-1.440.28981360.30944285X-RAY DIFFRACTION99.01
1.44-1.460.2771340.29554326X-RAY DIFFRACTION99.29
1.46-1.480.31231420.27444380X-RAY DIFFRACTION99.34
1.48-1.50.23381420.25364260X-RAY DIFFRACTION99.41
1.5-1.530.2921420.24584430X-RAY DIFFRACTION99.56
1.53-1.550.23781410.22454296X-RAY DIFFRACTION99.57
1.55-1.580.22051460.21824390X-RAY DIFFRACTION99.69
1.58-1.610.24311390.21374284X-RAY DIFFRACTION99.68
1.61-1.640.2511430.20884419X-RAY DIFFRACTION99.69
1.64-1.680.20741400.19434279X-RAY DIFFRACTION99.73
1.68-1.720.25251440.19184393X-RAY DIFFRACTION99.85
1.72-1.760.19171380.18024340X-RAY DIFFRACTION99.96
1.76-1.810.19531420.16914352X-RAY DIFFRACTION99.89
1.81-1.860.20141410.16214363X-RAY DIFFRACTION99.93
1.86-1.920.20861380.15454334X-RAY DIFFRACTION99.96
1.92-1.990.18981440.15454403X-RAY DIFFRACTION100
1.99-2.070.19931450.14464346X-RAY DIFFRACTION100
2.07-2.160.18931370.14784416X-RAY DIFFRACTION100
2.16-2.280.20611370.14234317X-RAY DIFFRACTION99.87
2.28-2.420.18411420.15284354X-RAY DIFFRACTION99.98
2.42-2.610.1841370.15314359X-RAY DIFFRACTION99.98
2.61-2.870.18031440.16724364X-RAY DIFFRACTION100
2.87-3.290.20561380.15734359X-RAY DIFFRACTION100
3.29-4.140.14341350.13544387X-RAY DIFFRACTION100
4.14-59.50.14261410.14364352X-RAY DIFFRACTION99.98
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)
11.125086294520.2287109886230.3170032474550.982103288967-0.0135455742472.70366719407-0.0182521176641-0.0090301587658-0.0277215876638-0.02997007282990.02533840621940.121332616342-0.0790168901015-0.2848614027610.0006933858699120.106318456648-0.004159597771760.005396937826690.1339675286570.003165929742240.1329824498741.49563293098-1.835453949267.26048550827
20.9692098565680.0161741825984-0.06260384319762.17018420120.6790636079492.89949143838-0.0300319112560.08851539815540.0177330183749-0.1565040725360.0269549604343-0.0215193285144-0.2859210416860.1207304240620.004699563089420.170629886683-0.0117010646624-0.001871422178140.1131154738960.004731279320920.10777725436110.45701071356.83319406464-18.0243718919
32.051756410350.972449106525-0.2241238427461.41206848303-0.1785873272572.43568469159-0.1916496432080.2285769690380.1840089496670.01156557456450.115627936988-0.00373170832004-0.5730701272780.05768406433790.08144989191490.268026031987-0.0167517951039-0.0009727352543140.1159144566130.01718294693950.13324780419210.884903034715.4293102303-12.8043601556
40.502241362006-0.4340986913680.4514350484640.994433265079-0.8618332077653.45991125415-0.02334660520650.002004336167410.07632551707220.01344880608870.004426467785470.0173058981914-0.4884171027110.004026781957180.05422136266110.201880930759-0.003257980122870.003237756179040.117600302112-0.004250861521870.1473305638079.422417531099.621566382345.87284197853
50.6287214159740.1654608259350.5454681125120.6574993296970.3627433390532.097068244890.01919197068730.00317325018509-0.119371015803-0.05656605200250.038308885851-0.01040335607120.114459965429-0.01442284693-0.05789390495310.131158158061-0.00679523616953-0.0006485530758690.1227802571320.0004977131849030.1678621837747.51697029588-8.5861295717-3.68751915051
61.963724277560.145493896590.1316637177641.89425192473-1.017647240164.459778887610.0914257781090.0424075457275-0.13898648688-0.0179147787935-0.157505280762-0.2877302908480.02915786863080.80828775130.04905359004570.176371636154-0.027920887125-0.01380933447990.270419993643-0.000544137344760.21854141269524.97342118062.579662356935.66415942464
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 3 through 64 )3 - 641 - 62
22chain 'A' and (resid 65 through 114 )65 - 11463 - 112
33chain 'A' and (resid 115 through 137 )115 - 137113 - 135
44chain 'A' and (resid 138 through 182 )138 - 182136 - 180
55chain 'A' and (resid 183 through 286 )183 - 286181 - 284
66chain 'A' and (resid 287 through 324 )287 - 324285 - 322

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