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- PDB-8bb9: IPNS H270N variant in complex with Fe and ACV after O2 exposure -

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Basic information

Entry
Database: PDB / ID: 8bb9
TitleIPNS H270N variant in complex with Fe and ACV after O2 exposure
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: 1.68 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 H270N variant in complex with Fe and ACV after O2 exposure
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)38,1515
Polymers37,5401
Non-polymers6114
Water6,774376
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1330 Å2
ΔGint-38 kcal/mol
Surface area14090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.260, 74.390, 101.220
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: 37539.793 Da / Num. of mol.: 1 / Mutation: H270N
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_H270N / Details (production host): pCold / 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.: 2 / 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.: 376 / 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: 2.07 Å3/Da / Density % sol: 40.55 % / Description: needle morphology, 3 um x 3 um x 160 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: 0.9763 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: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.68→50.63 Å / Num. obs: 36404 / % possible obs: 100 % / Redundancy: 13.4 % / Biso Wilson estimate: 18.95 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.225 / Rpim(I) all: 0.066 / Rrim(I) all: 0.241 / Net I/σ(I): 8.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.68-1.7112.62.3130.717920.4980.6972.49199.7
4.56-50.6512.736.220020.0170.063100

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Processing

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

6zae


Resolution: 1.68→50.61 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2164 1797 4.95 %
Rwork0.1771 34505 -
obs0.1789 36302 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 78.29 Å2 / Biso mean: 23.6287 Å2 / Biso min: 10.48 Å2
Refinement stepCycle: final / Resolution: 1.68→50.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2604 0 59 377 3040
Biso mean--32.07 28.89 -
Num. residues----329
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.68-1.730.31221360.29142604274099
1.73-1.780.25681300.264526162746100
1.78-1.830.28271530.250125762729100
1.83-1.90.2561370.232326212758100
1.9-1.970.23671360.209526412777100
1.97-2.060.23251450.182826292774100
2.06-2.170.23631230.178726432766100
2.17-2.310.20661320.174926222754100
2.31-2.490.2521150.165126702785100
2.49-2.740.2111310.175126772808100
2.74-3.130.21141740.169326412815100
3.13-3.950.18071290.141727182847100
3.95-50.610.1911560.161128473003100
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)
10.9558-0.02240.56760.5785-0.16872.5380.0176-0.0465-0.0738-0.02170.00620.09520.08-0.19750.0040.1305-0.01430.00080.14320.00580.1614-39.4088-1.83237.274
20.74370.03540.21112.96912.08223.2952-0.05860.15790.0776-0.25920.06170.0228-0.25780.1227-0.0040.1193-0.01320.00260.12020.01560.1044-30.56196.7537-18.1676
30.5351-0.0336-0.13650.6209-0.49552.39240.03870.02520.0656-0.00680.01040.0087-0.25490.0675-0.04560.1318-0.00450.01040.0797-0.00310.1225-30.990811.4638-0.2341
41.2585-0.00850.82270.95140.20122.39630.05890.037-0.1493-0.0024-0.01570.01470.21480.0738-0.05070.11950.0050.01680.11610.01340.1433-33.0915-8.6897-3.9133
52.08860.02750.74721.65-0.8734.37980.0438-0.3244-0.0730.1164-0.1653-0.22130.16170.96390.15740.1868-0.0003-0.00720.43440.04170.2136-14.94851.68110.7118
61.74870.79940.86655.42884.29066.7772-0.20280.1323-0.2145-0.29060.3966-0.04570.24610.5933-0.15720.25110.02340.01720.29640.02930.2215-19.9904-1.1121-8.3483
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 286 )A183 - 286
5X-RAY DIFFRACTION5chain 'A' and (resid 287 through 312 )A287 - 312
6X-RAY DIFFRACTION6chain 'A' and (resid 313 through 331 )A313 - 331

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