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- PDB-9hwf: Isopenicillin N synthase N252E variant in complex with Fe and IPN... -

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Basic information

Entry
Database: PDB / ID: 9hwf
TitleIsopenicillin N synthase N252E variant in complex with Fe and IPN after 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 / Isopenicillin N synthase
Similarity search - Component
Biological speciesAspergillus nidulans FGSC A4 (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsRabe, P. / Schofield, C.J. / Stead, A.
Funding support United Kingdom, 3items
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
CitationJournal: To Be Published
Title: Isopenicillin N synthase N252E variant in complex with Fe and IPN after O2 exposure
Authors: Rabe, P. / Schofield, C.J. / Stead, A.
History
DepositionJan 3, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 14, 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)38,2666
Polymers37,5631
Non-polymers7035
Water7,855436
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1370 Å2
ΔGint-42 kcal/mol
Surface area14350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.339, 74.398, 101.283
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

#1: Protein Isopenicillin N synthase / IPNS


Mass: 37562.742 Da / Num. of mol.: 1 / Mutation: N252E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus nidulans FGSC A4 (mold) / Gene: ipnA, ips, AN2622 / Plasmid: pCold_IPNS / Details (production host): PCold_IPNS_N252E / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P05326, isopenicillin-N synthase
#2: 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
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#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.: 436 / Source method: isolated from a natural source / Formula: H2O
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: 2.07 Å3/Da / Density % sol: 40.67 % / Description: needle morphology, 4 um x 4 um x 200 um
Crystal growTemperature: 298 K / Method: batch mode / pH: 8.3 / Details: 1.7 M Li2SO4, 0.1 M 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: 0.9762 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Feb 22, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.4→41.87 Å / Num. obs: 61769 / % possible obs: 99.9 % / Redundancy: 13.6 % / Biso Wilson estimate: 14.86 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.144 / Rpim(I) all: 0.04 / Net I/σ(I): 11.6
Reflection shellResolution: 1.4→1.42 Å / Redundancy: 13.8 % / Rmerge(I) obs: 2.153 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 3024 / CC1/2: 0.569 / Rpim(I) all: 0.592 / % possible all: 97.8

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→41.86 Å / SU ML: 0.1688 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.7856
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2026 2055 3.33 %
Rwork0.1681 59640 -
obs0.1693 61695 98.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.45 Å2
Refinement stepCycle: LAST / Resolution: 1.4→41.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2619 0 40 438 3097
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00342827
X-RAY DIFFRACTIONf_angle_d0.62123877
X-RAY DIFFRACTIONf_chiral_restr0.0722401
X-RAY DIFFRACTIONf_plane_restr0.0052522
X-RAY DIFFRACTIONf_dihedral_angle_d12.39351026
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.430.33831260.31133890X-RAY DIFFRACTION97.4
1.43-1.470.29781250.28293889X-RAY DIFFRACTION97.83
1.47-1.510.28621530.24373845X-RAY DIFFRACTION98.28
1.51-1.550.25271400.22383924X-RAY DIFFRACTION98.52
1.55-1.60.23541150.20553938X-RAY DIFFRACTION98.47
1.6-1.660.24181470.19823871X-RAY DIFFRACTION97.43
1.66-1.730.23681410.19353935X-RAY DIFFRACTION98.93
1.73-1.80.21981290.18873952X-RAY DIFFRACTION99.17
1.8-1.90.24951410.16863975X-RAY DIFFRACTION99.3
1.9-2.020.21611270.15413985X-RAY DIFFRACTION99.47
2.02-2.170.18691410.14864027X-RAY DIFFRACTION99.67
2.17-2.390.16921390.14953966X-RAY DIFFRACTION99.06
2.39-2.740.19191370.15874084X-RAY DIFFRACTION99.88
2.74-3.450.20311320.1574103X-RAY DIFFRACTION100
3.45-41.860.16451620.14574256X-RAY DIFFRACTION99.71
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)
11.695753469180.07405812439290.1644028908493.1625550950.8463254286011.783099758690.0971005849937-0.0704616027031-0.1469934923450.00626403914158-0.09782417490060.003219956603720.164994981675-0.1411836860510.01494724881670.109368688917-0.007725388860560.005467756067580.09316127272970.03552046485170.08283181105075.12015558209-5.7044656959314.1139927115
21.09150141380.109950081817-1.392832009510.393829349911-0.3967150209014.2821991550.07513624938730.1073381280550.0212268786941-0.03792442361660.006335906433120.0759260443535-0.112299475296-0.283970574876-0.09195282134590.101004547726-0.00384814377957-0.02026774387290.0601336645072-0.01918438775620.1142098851672.647347366863.41004154682-10.6030795355
31.145620688960.5734666454310.3459109262141.161423736890.2314931238911.78520518816-0.04644095927560.1332646693890.079433117927-0.0868857141640.0832888946066-0.0545869878152-0.2014550385760.0605061144687-0.02982811268290.0870612871653-0.0026005747480.007558245031320.07889790575660.01733863050750.08410900553111.36182427310.302158127-13.9669315633
40.614792670828-0.5688886075470.6757234267290.977410837232-1.035151587663.2411059559-0.0118675887659-0.06007138345960.05337430087180.02593417104850.00968665354206-0.0120913909558-0.2409695917430.0105216254450.02377989427790.0934994642461-0.01491048028510.008827260626870.0581592997605-0.007889956912130.08690773293539.763161654019.705032444775.60801915588
50.8322235201910.09742806288480.5580619548670.8437354728870.2158077042421.493880538140.0337726201098-0.00294219168108-0.12798662396-0.01506968140250.00210358196184-0.00655095069990.1482058615110.0353800034034-0.04728857718740.089713817530.002171616700270.008915008274590.07956809401450.004592367469680.1095710694418.19395427631-8.69858264242-3.73930999814
60.881820302722-0.380277707930.6068965625951.57481761603-0.7728701872383.154804700430.108616057725-0.349177788147-0.1278587563190.144970806683-0.185754455576-0.2826576012010.2320481189260.8273517658090.06629135683130.185574764210.00329292680557-0.02877323418540.388742637860.06712055843360.19785271131926.42529546341.4220112357510.4617615118
72.386779313611.169426841922.046927352683.616950346043.876064262246.28334745928-0.0589202555840.08714730225-0.146822320085-0.272423245880.18504615013-0.1424350315860.1047312691440.309526296439-0.1195146867180.1848659655770.03166402488520.02617266125720.2017487543730.03538414801970.17429840805621.2390959495-1.39522091911-8.36890788682
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 1 through 37 )1 - 371 - 37
22chain 'A' and (resid 38 through 82 )38 - 8238 - 82
33chain 'A' and (resid 83 through 137 )83 - 13783 - 137
44chain 'A' and (resid 138 through 182 )138 - 182138 - 182
55chain 'A' and (resid 183 through 286 )183 - 286183 - 286
66chain 'A' and (resid 287 through 312 )287 - 312287 - 312
77chain 'A' and (resid 313 through 331 )313 - 331313 - 331

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