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- PDB-8bbc: IPNS H270A variant in complex with Fe and ACV under anaerobic con... -

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Basic information

Entry
Database: PDB / ID: 8bbc
TitleIPNS H270A variant in complex with Fe and ACV under anaerobic conditions
ComponentsIsopenicillin N synthase
KeywordsOXIDOREDUCTASE / Isopenicillin N synthase / antibiotic biosynthesis / anaerobic / penicillins
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: 1.71 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 H270A variant in complex with Fe and ACV under anaerobic conditions
Authors: Rabe, P. / Schofield, C.J.
History
DepositionOct 12, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 25, 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)38,4929
Polymers37,4971
Non-polymers9968
Water5,314295
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1850 Å2
ΔGint-70 kcal/mol
Surface area14380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.930, 73.730, 100.830
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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: 37496.770 Da / Num. of mol.: 1 / Mutation: H270A
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_H270A / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P05326, isopenicillin-N synthase
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / 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 / Iron


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


Mass: 18.015 Da / Num. of mol.: 295 / 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: 2.03 Å3/Da / Density % sol: 39.37 % / 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: 0.97628 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Sep 13, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97628 Å / Relative weight: 1
ReflectionResolution: 1.71→41.62 Å / Num. obs: 33572 / % possible obs: 99.5 % / Redundancy: 13.5 % / Biso Wilson estimate: 21.01 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.21 / Rpim(I) all: 0.059 / Rrim(I) all: 0.219 / Net I/σ(I): 9.4 / Num. measured all: 454378
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.71-1.7514.12.7671.224250.4930.7542.86998.8
7.65-41.6211.30.0624570.9970.0190.06599.7

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6ZAE

6zae


Resolution: 1.71→41.62 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2268 1666 4.97 %
Rwork0.1826 31857 -
obs0.1848 33523 99.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 93.01 Å2 / Biso mean: 23.7125 Å2 / Biso min: 13.38 Å2
Refinement stepCycle: final / Resolution: 1.71→41.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2606 0 79 296 2981
Biso mean--35.37 29.16 -
Num. residues----329
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.71-1.760.32891220.27362595271799
1.76-1.820.28291170.25092596271399
1.82-1.880.26881150.22892633274899
1.88-1.960.23891180.19832643276199
1.96-2.050.20071470.18292614276199
2.05-2.150.23221490.17572609275899
2.15-2.290.22381480.16582626277499
2.29-2.470.22711460.17072624277099
2.47-2.710.24481420.178926782820100
2.71-3.110.23751460.184426742820100
3.11-3.910.1891600.160227052865100
3.91-41.620.22821560.18228603016100
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)
10.86790.16910.30220.9044-0.30152.53-0.0018-0.0360.0032-0.0130.00160.10660.0339-0.2410.00120.1059-0.01660.00430.1654-0.0030.14941.5389-1.59597.2078
20.9010.140.37632.76832.53793.7855-0.03220.13640.0371-0.28660.0036-0.0139-0.28070.00180.01460.1534-0.00740.00050.1310.020.118210.55756.9302-18.2335
30.51510.1443-0.27920.5614-0.33831.44140.0291-0.02430.0822-0.0189-0.00810.0661-0.10870.0115-0.00730.1688-0.0020.00250.1342-0.0030.18029.897611.4972-0.3011
41.03020.18020.64650.52610.19491.21240.0470.0073-0.0404-0.0246-0.0222-0.03690.0410.0837-0.03680.17060.01050.00790.15980.0070.171513.0035-5.7271-1.9972
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 182 )A115 - 182
4X-RAY DIFFRACTION4chain 'A' and (resid 183 through 331 )A183 - 331

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