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- PDB-9qpj: Isopenicillin N synthase in complex with Fe and IPN using tr-SSX -

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Basic information

Entry
Database: PDB / ID: 9qpj
TitleIsopenicillin N synthase in complex with Fe and IPN using tr-SSX
ComponentsIsopenicillin N synthase
KeywordsOXIDOREDUCTASE / Isopenicillin N synthase / IPNS / tr-SFX / XFEL / time-resolved crystallography / ADE tape drive
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: 1.9 Å
AuthorsRabe, P. / Schofield, C.J. / Stead, A.
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 in complex with Fe and IPN using tr-SSX
Authors: Rabe, P. / Schofield, C.J. / Stead, A.
History
DepositionMar 27, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 8, 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)38,0754
Polymers37,5641
Non-polymers5113
Water1,72996
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1160 Å2
ΔGint-27 kcal/mol
Surface area14240 Å2
Unit cell
Length a, b, c (Å)41.915, 75.236, 101.841
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: 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 (E. coli) / Strain (production host): BL12 (DE3) / 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.: 1 / 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.: 96 / 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: 2.14 Å3/Da / Density % sol: 42.46 % / Description: Needle morphology, 3 um x 3 um x 60 - 80 um
Crystal growTemperature: 293 K / Method: batch mode / pH: 8.5 / Details: 1.7 M Li2SO4, 0.1 M Tris pH 8.5

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Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.99985 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 3, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99985 Å / Relative weight: 1
ReflectionResolution: 1.9→60.51 Å / Num. obs: 26112 / % possible obs: 99.96 % / Redundancy: 31.61 % / Biso Wilson estimate: 29.96 Å2 / CC1/2: 0.931322 / R split: 0.261 / Net I/σ(I): 2.003
Reflection shellResolution: 1.9→1.9328 Å / Redundancy: 22.78 % / Mean I/σ(I) obs: 0.572 / Num. unique obs: 1258 / CC1/2: 0.24242 / R split: 0.957 / % possible all: 100
Serial crystallography measurementSource distance: 320 m / Source size: 7 µm2
Serial crystallography sample deliveryMethod: fixed target
Serial crystallography data reductionFrames total: 25600

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
PHENIX1.20.1_4487refinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→60.51 Å / SU ML: 0.3031 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.7248
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2379 2000 7.79 %
Rwork0.2036 23671 -
obs0.2064 25671 98.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.05 Å2
Refinement stepCycle: LAST / Resolution: 1.9→60.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2584 0 30 96 2710
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00222742
X-RAY DIFFRACTIONf_angle_d0.4923753
X-RAY DIFFRACTIONf_chiral_restr0.0437395
X-RAY DIFFRACTIONf_plane_restr0.004498
X-RAY DIFFRACTIONf_dihedral_angle_d12.1743987
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.950.36971270.34111509X-RAY DIFFRACTION90.69
1.95-20.37931380.33371628X-RAY DIFFRACTION95.05
2-2.060.32851340.30681586X-RAY DIFFRACTION95.4
2.06-2.130.37281400.29551662X-RAY DIFFRACTION97.25
2.13-2.20.31651430.27281695X-RAY DIFFRACTION99.08
2.2-2.290.30051410.25351660X-RAY DIFFRACTION99.34
2.29-2.390.26791440.2491705X-RAY DIFFRACTION99.68
2.39-2.520.28991430.24291694X-RAY DIFFRACTION99.67
2.52-2.680.30361450.23631710X-RAY DIFFRACTION99.95
2.68-2.880.25771450.22591730X-RAY DIFFRACTION99.89
2.88-3.170.25951460.20851730X-RAY DIFFRACTION100
3.18-3.630.19481480.17421734X-RAY DIFFRACTION100
3.63-4.580.16321480.14051765X-RAY DIFFRACTION100
4.58-60.510.1891580.15811863X-RAY DIFFRACTION99.95
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)
11.022949365150.3995990327350.2768762363370.807594588280.6062220667065.038322389910.06151875982530.08206374821840.00706142035137-0.0721393891090.107567480367-0.09030550058440.149117678830.281813520937-0.1420919976890.1842437282550.02285174543680.01431695085430.177250743716-0.005009726666180.23860297270515.7908228233-0.550354811296-3.2713681989
21.488162195510.144969038047-0.334110241811.142051892890.001084482969414.044713467120.02549516353120.168268006472-0.163904750218-0.1379538190730.005580830790140.009368810351770.54919783071-0.0665013988134-0.03309667280390.2562855214730.0157820608162-0.02105436336710.202915524394-0.03402154446220.22372160029411.2785017345-5.63350748756-5.02771033104
32.10100903630.276456171181-0.4821232538412.330452144580.03677301432394.0096032652-0.00896687115393-0.04546659955970.1159562536410.109288872820.06175321206530.05271614687130.0195236170438-0.331970516688-0.07478535441720.157537509962-0.00339081035731-0.02675073823970.1628074263020.002456946046710.1585619328347.555618599195.07864102442.65387303717
44.17267149077-2.244862862710.3054961997013.000451459982.918817588685.35027230689-0.2310461130390.5557629589770.5825754371-1.20559769384-0.130986915606-0.221174184171-0.846754213547-1.003099581310.2896645108570.5744930977640.0102118930331-0.06945219373130.5048505447080.04658441459630.369277432861-0.8381972739480.856707515203-8.4029961941
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 100 )3 - 1001 - 98
22chain 'A' and (resid 101 through 214 )101 - 21499 - 212
33chain 'A' and (resid 215 through 312 )215 - 312213 - 310
44chain 'A' and (resid 313 through 331 )313 - 331311 - 329

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