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- PDB-8alj: IPNS H270E variant in complex with Fe and ACV after 3 hours O2 ex... -

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Basic information

Entry
Database: PDB / ID: 8alj
TitleIPNS H270E variant in complex with Fe and ACV after 3 hours O2 exposure
ComponentsIsopenicillin N synthase
KeywordsOXIDOREDUCTASE / Isopenicillin N synthase / antibiotic production / O2 binding / reactive intermediate
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: 1.68 Å
AuthorsRabe, P. / Schfoeidl, 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 H270E variant in complex with Fe and ACV after 3 hours O2 exposure
Authors: Rabe, P. / Schfoeidl, C.J.
History
DepositionAug 1, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 16, 2023Provider: 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)38,2626
Polymers37,5551
Non-polymers7075
Water6,071337
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1440 Å2
ΔGint-45 kcal/mol
Surface area14200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.135, 74.490, 101.150
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Isopenicillin N synthase / IPNS


Mass: 37554.805 Da / Num. of mol.: 1 / Mutation: H270E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus nidulans FGSC A4 (mold) / Strain: FGSC A4 / ATCC 38163 / CBS 112.46 / NRRL 194 / M139 / Gene: ipnA, ips, AN2622 / Plasmid: pCold_IPNS / 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.: 3 / Source method: obtained synthetically / Formula: SO4
#3: 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
#4: 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 337 / 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: 2.06 Å3/Da / Density % sol: 40.39 % / Description: needle morphology, 4 um x 4 um x 150 um
Crystal growTemperature: 298 K / Method: batch mode / pH: 8.3 / Details: 1.7 M Li2SO4, 0.1 M Tris pH8.3

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: cryo / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: May 25, 2022
RadiationMonochromator: 0.9763 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.68→59.98 Å / Num. obs: 36274 / % possible obs: 100 % / Redundancy: 13.4 % / Biso Wilson estimate: 19.96 Å2 / CC1/2: 0.996 / Rpim(I) all: 0.075 / Rrim(I) all: 0.277 / Net I/σ(I): 7.6
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
1.68-1.7113.70.617880.4760.7912.936
4.56-6013.134.219950.0210.079

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Processing

Software
NameVersionClassification
xia2data scaling
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
DIALSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6ZAE

6zae


Resolution: 1.68→59.98 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2297 1790 4.95 %
Rwork0.1804 34406 -
obs0.1827 36196 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 78.55 Å2 / Biso mean: 25.6129 Å2 / Biso min: 11.96 Å2
Refinement stepCycle: final / Resolution: 1.68→59.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2605 0 64 337 3006
Biso mean--36.11 30.89 -
Num. residues----329
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.68-1.730.33461350.308125942729
1.73-1.780.28451320.274926162748
1.78-1.830.30541450.257125772722
1.83-1.90.28721400.237426142754
1.9-1.980.27641390.208426332772
1.98-2.070.23041440.182226062750
2.07-2.170.24091190.177226452764
2.17-2.310.22381320.175426192751
2.31-2.490.2411160.168126542770
2.49-2.740.22581310.174126762807
2.74-3.140.23271720.177626322804
3.14-3.950.18751310.146727082839
3.95-59.980.20521540.16528322986
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)
10.7981-0.0011-0.07280.42010.46553.2929-0.00220.0666-0.03510.10440.1209-0.1433-0.08070.3374-0.12610.15890.0204-0.01890.1905-0.01870.1964-1.7046-1.5475-7.2755
20.6480.1704-0.25160.9943-0.12022.3424-0.0451-0.15470.03550.18830.0637-0.0472-0.2818-0.1605-0.01890.17380.01520.00580.1688-0.00330.1546-10.65256.732718.197
30.8965-0.04630.28230.69450.06052.09390.0384-0.0383-0.04860.00410.017-0.005-0.0538-0.0482-0.05610.0808-0.00660.01540.1134-0.00440.1237-8.7423-0.67212.4842
43.94250.15150.28712.671.85093.78660.078-0.1102-0.14950.1936-0.11820.05010.2094-0.77220.00440.1703-0.00050.00770.30130.01170.1975-24.40020.809-2.9029
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 64 )A3 - 64
2X-RAY DIFFRACTION2chain 'A' and (resid 65 through 114 )A65 - 114
3X-RAY DIFFRACTION3chain 'A' and (resid 115 through 286 )A115 - 286
4X-RAY DIFFRACTION4chain 'A' and (resid 287 through 331 )A287 - 331

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