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- PDB-7psw: Spin labeled IPNS S55C variant in complex with Fe and ACV under a... -

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Basic information

Entry
Database: PDB / ID: 7psw
TitleSpin labeled IPNS S55C variant in complex with Fe and ACV under anaerobic conditions
ComponentsIsopenicillin N synthase
KeywordsOXIDOREDUCTASE / Isopenicillin N synthase / Oxidase / Penicillin biosynthesis / Spin labeled protein
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 speciesEmericella nidulans (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.21 Å
AuthorsRabe, P. / Clifton, I. / Walla, C. / Schofield, C.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/V003291/1 United Kingdom
CitationJournal: J.Biol.Chem. / Year: 2022
Title: Spectroscopic studies reveal details of substrate-induced conformational changes distant from the active site in isopenicillin N synthase.
Authors: Rabe, P. / Walla, C.C. / Goodyear, N.K. / Welsh, J. / Southwart, R. / Clifton, I. / Linyard, J.D.S. / Tumber, A. / Claridge, T.D.W. / Myers, W.K. / Schofield, C.J.
History
DepositionSep 24, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 20, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 27, 2022Group: Database references / Category: citation / citation_author
Item: _citation.page_last / _citation.pdbx_database_id_PubMed ..._citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Aug 31, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)38,3797
Polymers37,5801
Non-polymers8006
Water8,359464
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1640 Å2
ΔGint-47 kcal/mol
Surface area14430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.660, 71.444, 101.073
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Isopenicillin N synthase / IPNS


Mass: 37579.902 Da / Num. of mol.: 1 / Mutation: Ser55Cys
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Emericella nidulans (strain FGSC A4 / ATCC 38163 / CBS 112.46 / NRRL 194 / M139) (mold)
Strain: FGSC A4 / ATCC 38163 / CBS 112.46 / NRRL 194 / M139 / Gene: ipnA, ips, AN2622 / Plasmid: pCOLD_IPNS / Details (production host): pCOLD_IPNS_S55C / Production host: Escherichia coli (E. coli) / References: UniProt: P05326, isopenicillin-N synthase

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Non-polymers , 5 types, 470 molecules

#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-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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 464 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.24 Å3/Da / Density % sol: 45.12 % / Description: plate morphology, 50 x 200 um
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 1.7 M Li2SO4, 0.1 M Tris pH 8.5

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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: Jan 21, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.21→58.35 Å / Num. obs: 103529 / % possible obs: 99.9 % / Redundancy: 12.2 % / Biso Wilson estimate: 11.96 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.015 / Rrim(I) all: 0.052 / Net I/σ(I): 24.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.21-1.237.20.4431.650100.9220.1750.47897.2
3.28-58.4112.2116.654790.0070.02499.3

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Processing

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

6zae


Resolution: 1.21→41.26 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 15.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1627 5140 4.97 %
Rwork0.1433 98282 -
obs0.1443 103422 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 105.97 Å2 / Biso mean: 18.4682 Å2 / Biso min: 6.94 Å2
Refinement stepCycle: final / Resolution: 1.21→41.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2621 0 76 479 3176
Biso mean--27.95 31.92 -
Num. residues----330
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.21-1.220.23781780.24263100327895
1.22-1.240.22211450.22033227337299
1.24-1.250.22131760.209832173393100
1.25-1.270.23091610.195932423403100
1.27-1.290.21671640.191632593423100
1.29-1.30.18561530.189932733426100
1.3-1.320.20561570.180732633420100
1.32-1.340.20771920.183632253417100
1.34-1.360.2121800.172432423422100
1.36-1.380.17661770.170732433420100
1.38-1.410.17951710.166232683439100
1.41-1.430.19181540.171732563410100
1.43-1.460.19832020.171132613463100
1.46-1.490.19581650.166232553420100
1.49-1.520.18621510.159432873438100
1.52-1.560.17271620.158832593421100
1.56-1.60.16321750.147532723447100
1.6-1.640.17481770.143432523429100
1.64-1.690.17231740.13932563430100
1.69-1.740.16541580.146133333491100
1.74-1.810.14791510.139832853436100
1.81-1.880.15241770.143132763453100
1.88-1.960.15621790.135532963475100
1.97-2.070.14751780.12832873465100
2.07-2.20.13391530.127633213474100
2.2-2.370.14742000.125133063506100
2.37-2.610.142030.124332903493100
2.61-2.980.15591740.131533533527100
2.98-3.760.1661650.126134073572100
3.76-41.260.15061880.14143471365998
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)
10.730.0689-0.08550.8726-0.78832.4212-0.04760.0314-0.0209-0.0420.04640.0190.0434-0.19920.01950.0924-0.0095-0.0120.1164-0.00150.09474.555230.1244-10.0875
21.6724-0.4802-1.37240.75810.7062.9717-0.0424-0.18960.00120.07330.0215-0.01750.03580.09220.01450.08380.0012-0.0180.07870.00640.069716.384330.750715.555
35.45813.8048-2.00674.5725-1.4641.69920.0653-0.3193-0.07840.1652-0.1189-0.08780.05820.19480.06670.09530.0217-0.0240.11450.00390.068123.410225.549211.0402
40.6831-0.56780.94091.3382-2.0294.8273-0.03850.08280.0112-0.1224-0.0356-0.06840.14770.14910.08150.08290.00680.01040.0781-0.00480.081118.760829.2806-8.6252
50.91580.0165-0.78570.6932-0.15171.39150.05040.04260.06030.0006-0.00860.059-0.137-0.114-0.04650.09570.0122-0.01230.10280.00320.09443.481539.48641.0638
61.0206-0.88131.36054.4593-3.66166.11550.07150.25080.2233-0.1981-0.1914-0.2119-0.45460.29630.13230.1978-0.00510.04870.1430.02720.148622.812147.117-13.6384
74.7701-2.5207-5.39432.08282.60476.36150.1887-0.36720.410.15860.112-0.1715-0.29350.1468-0.27580.1785-0.017-0.02280.1382-0.01710.164517.554745.03035.775
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 62 )A2 - 62
2X-RAY DIFFRACTION2chain 'A' and (resid 63 through 114 )A63 - 114
3X-RAY DIFFRACTION3chain 'A' and (resid 115 through 137 )A115 - 137
4X-RAY DIFFRACTION4chain 'A' and (resid 138 through 183 )A138 - 183
5X-RAY DIFFRACTION5chain 'A' and (resid 184 through 286 )A184 - 286
6X-RAY DIFFRACTION6chain 'A' and (resid 287 through 312 )A287 - 312
7X-RAY DIFFRACTION7chain 'A' and (resid 313 through 331 )A313 - 331

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