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- PDB-7poy: Spin labeled IPNS S55C variant in complex with Fe, ACV and NO -

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Basic information

Entry
Database: PDB / ID: 7poy
TitleSpin labeled IPNS S55C variant in complex with Fe, ACV and NO
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
Chem-81T / L-D-(A-AMINOADIPOYL)-L-CYSTEINYL-D-VALINE / : / NITRIC OXIDE / Isopenicillin N synthase
Similarity search - Component
Biological speciesEmericella nidulans (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsRabe, P. / Clifton, I. / Walla, C. / Schofield, C.J.
Funding support1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/V003291/1
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 10, 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)38,6149
Polymers37,5801
Non-polymers1,0348
Water5,621312
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1660 Å2
ΔGint-55 kcal/mol
Surface area14400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.374, 74.907, 101.048
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): Ser55Cys variant / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P05326, isopenicillin-N synthase

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Non-polymers , 6 types, 320 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-NO / NITRIC OXIDE / Nitrogen monoxide


Mass: 30.006 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-81T / ~{N}-[(3~{R})-2,2,5,5-tetramethyl-1-oxidanyl-pyrrolidin-3-yl]ethanamide


Mass: 200.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H20N2O2 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 312 / 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: 2.08 Å3/Da / Density % sol: 40.96 % / Description: needles, 4 um x 4 um x 120 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: 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 22, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.75→41.89 Å / Num. obs: 32521 / % possible obs: 100 % / Redundancy: 13.1 % / CC1/2: 0.997 / Rpim(I) all: 0.066 / Rrim(I) all: 0.24 / Net I/σ(I): 8.3
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
1.75-1.7813.30.615760.5850.7092.614
4.75-41.8912.837.517990.9990.0180.065

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
xia2data scaling
PDB_EXTRACT3.27data extraction
DIALSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6ZAM

6zam


Resolution: 1.75→41.88 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2169 1555 4.79 %
Rwork0.1806 30880 -
obs0.1824 32435 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 78.37 Å2 / Biso mean: 26.6751 Å2 / Biso min: 11.79 Å2
Refinement stepCycle: final / Resolution: 1.75→41.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2605 0 86 312 3003
Biso mean--35.9 32.44 -
Num. residues----328
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.75-1.810.37541340.330227452879
1.81-1.870.31711310.277527752906
1.87-1.950.27231450.241727522897
1.95-2.030.22671420.20927722914
2.03-2.140.25411330.193627842917
2.14-2.280.22031390.178727712910
2.28-2.450.20081220.168628292951
2.45-2.70.20011460.174727812927
2.7-3.090.22971310.169728452976
3.09-3.890.18971550.148328513006
3.89-41.890.19321770.167429753152
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)
10.35620.1025-0.61160.3903-0.51392.89770.01090.05470.023-0.05250.08830.0913-0.0242-0.346-0.10830.1385-0.0079-0.02620.17950.01040.1673-17.12880.384-0.7101
20.64280.00540.18180.7968-0.08951.6994-0.01140.03280.0071-0.04580.0301-0.0372-0.14680.0582-0.02110.10570.00350.02130.11640.00740.1142-9.55730.5711-3.0424
33.34825.28623.70438.85355.98034.1313-0.30420.8475-0.4268-0.94730.6186-0.2092-0.17280.6107-0.26320.3716-0.00510.04490.392-0.00240.30110.6632-0.8403-8.5481
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 82 )A4 - 82
2X-RAY DIFFRACTION2chain 'A' and (resid 83 through 312 )A83 - 312
3X-RAY DIFFRACTION3chain 'A' and (resid 313 through 331 )A313 - 331

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