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- PDB-8ptv: IPNS variant N252Q in complex with Fe and ACV under anaerobic con... -

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Basic information

Entry
Database: PDB / ID: 8ptv
TitleIPNS variant N252Q in complex with Fe and ACV under anaerobic conditions
ComponentsIsopenicillin N synthase
KeywordsOXIDOREDUCTASE / Isopenicillin N synthase / penicillins / biosynthesis / 2OG oxygenases / antibiotic
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: 1.6 Å
AuthorsRabe, P. / Schofield, C.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/V001892/1 United Kingdom
CitationJournal: To Be Published
Title: IPNS variant N252Q in complex with Fe and ACV under anaerobic conditions
Authors: Rabe, P. / Schofield, C.J.
History
DepositionJul 15, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 24, 2024Provider: 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)38,76611
Polymers37,5781
Non-polymers1,18810
Water5,477304
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.880, 74.280, 100.760
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
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: 37577.863 Da / Num. of mol.: 1 / Mutation: N252Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus nidulans FGSC A4 (mold) / Gene: ipnA, ips, AN2622 / Plasmid: pCold_IPNS_N252Q / Details (production host): pCold_IPNS_N252Q / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P05326, isopenicillin-N synthase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / 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-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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 304 / Source method: isolated from a natural source / Formula: H2O
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: 2.04 Å3/Da / Density % sol: 39.57 % / Description: needle morphology, 3 um x 3 um x 160 um
Crystal growTemperature: 293 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: I04 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jul 2, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.6→50.38 Å / Num. obs: 41326 / % possible obs: 99.9 % / Redundancy: 13.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.156 / Rpim(I) all: 0.044 / Rrim(I) all: 0.162 / Χ2: 1 / Net I/σ(I): 9.9 / Num. measured all: 547888
Reflection shellResolution: 1.6→1.64 Å / Redundancy: 12.6 % / Rmerge(I) obs: 3.277 / Mean I/σ(I) obs: 0.7 / Num. unique obs: 3001 / CC1/2: 0.535 / Rpim(I) all: 0.948 / Rrim(I) all: 3.415 / Χ2: 0.88 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→50.38 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2295 2098 5.09 %
Rwork0.1994 --
obs0.2009 41208 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.6→50.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2600 0 65 304 2969
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032749
X-RAY DIFFRACTIONf_angle_d0.5913756
X-RAY DIFFRACTIONf_dihedral_angle_d12.512980
X-RAY DIFFRACTIONf_chiral_restr0.048392
X-RAY DIFFRACTIONf_plane_restr0.005492
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.640.42981570.40682516X-RAY DIFFRACTION99
1.64-1.680.3811370.34722555X-RAY DIFFRACTION100
1.68-1.720.35361300.30972578X-RAY DIFFRACTION99
1.72-1.770.31781240.27752595X-RAY DIFFRACTION100
1.77-1.830.29561250.2622559X-RAY DIFFRACTION100
1.83-1.90.25381330.24522574X-RAY DIFFRACTION100
1.9-1.970.29081460.23852598X-RAY DIFFRACTION100
1.97-2.060.25861400.20112599X-RAY DIFFRACTION100
2.06-2.170.28691390.19942587X-RAY DIFFRACTION100
2.17-2.310.24351250.20032612X-RAY DIFFRACTION100
2.31-2.490.24911520.19672593X-RAY DIFFRACTION100
2.49-2.740.26321400.20272643X-RAY DIFFRACTION100
2.74-3.130.21931590.20082626X-RAY DIFFRACTION100
3.13-3.940.18481380.16912664X-RAY DIFFRACTION100
3.95-50.380.16351530.16032811X-RAY DIFFRACTION100

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