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- PDB-6zam: Fluorine labeled IPNS S55C in complex with Fe and ACV under anaer... -

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Basic information

Entry
Database: PDB / ID: 6zam
TitleFluorine labeled IPNS S55C in complex with Fe and ACV under anaerobic conditions.
ComponentsIsopenicillin N synthase
KeywordsOXIDOREDUCTASE / Isopenicillin N synthase / oxygen binding / XFEL / time-resolved crystallography
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 / : / 1,1,1-tris(fluoranyl)propan-2-one / 1,1,1-tris(fluoranyl)propane-2,2-diol / Isopenicillin N synthase
Similarity search - Component
Biological speciesEmericella nidulans (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsRabe, P. / Kamps, J.J.A.G. / Sutherlin, K. / Pharm, C. / McDonough, M.A. / Leissing, T.M. / Aller, P. / Butryn, A. / Linyard, J. / Lang, P. ...Rabe, P. / Kamps, J.J.A.G. / Sutherlin, K. / Pharm, C. / McDonough, M.A. / Leissing, T.M. / Aller, P. / Butryn, A. / Linyard, J. / Lang, P. / Brem, J. / Fuller, F.D. / Batyuk, A. / Hunter, M.S. / Pettinati, I. / Clifton, I.J. / Alonso-Mori, R. / Gul, S. / Young, I. / Kim, I. / Bhowmick, A. / ORiordan, L. / Brewster, A.S. / Claridge, T.D.W. / Sauter, N.K. / Yachandra, V. / Yano, J. / Kern, J.F. / Orville, A.M. / Schofield, C.J.
Funding support United Kingdom, 7items
OrganizationGrant numberCountry
Wellcome Trust106244/Z/14/Z United Kingdom
Medical Research Council (MRC, United Kingdom)106244/Z/14/Z United Kingdom
Wellcome Trust210734/Z/18/Z United Kingdom
Royal SocietyRSWF/R2/182017 United Kingdom
Wellcome Trust102593 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)102593 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/S50676X/1 United Kingdom
CitationJournal: Sci Adv / Year: 2021
Title: X-ray free-electron laser studies reveal correlated motion during isopenicillin N synthase catalysis.
Authors: Rabe, P. / Kamps, J.J.A.G. / Sutherlin, K.D. / Linyard, J.D.S. / Aller, P. / Pham, C.C. / Makita, H. / Clifton, I. / McDonough, M.A. / Leissing, T.M. / Shutin, D. / Lang, P.A. / Butryn, A. / ...Authors: Rabe, P. / Kamps, J.J.A.G. / Sutherlin, K.D. / Linyard, J.D.S. / Aller, P. / Pham, C.C. / Makita, H. / Clifton, I. / McDonough, M.A. / Leissing, T.M. / Shutin, D. / Lang, P.A. / Butryn, A. / Brem, J. / Gul, S. / Fuller, F.D. / Kim, I.S. / Cheah, M.H. / Fransson, T. / Bhowmick, A. / Young, I.D. / O'Riordan, L. / Brewster, A.S. / Pettinati, I. / Doyle, M. / Joti, Y. / Owada, S. / Tono, K. / Batyuk, A. / Hunter, M.S. / Alonso-Mori, R. / Bergmann, U. / Owen, R.L. / Sauter, N.K. / Claridge, T.D.W. / Robinson, C.V. / Yachandra, V.K. / Yano, J. / Kern, J.F. / Orville, A.M. / Schofield, C.J.
History
DepositionJun 5, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 9, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 1, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 24, 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)38,3376
Polymers37,5801
Non-polymers7575
Water6,431357
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1170 Å2
ΔGint-29 kcal/mol
Surface area14160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.410, 70.810, 100.570
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

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Protein , 1 types, 1 molecules A

#1: Protein Isopenicillin N synthase / IPNS


Mass: 37579.902 Da / Num. of mol.: 1
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 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P05326, isopenicillin-N synthase

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Non-polymers , 6 types, 362 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: 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
#4: Chemical ChemComp-W6X / 1,1,1-tris(fluoranyl)propan-2-one


Mass: 112.051 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H3F3O / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-W6Z / 1,1,1-tris(fluoranyl)propane-2,2-diol


Mass: 130.066 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5F3O2 / Feature type: SUBJECT OF INVESTIGATION
#6: 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
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 357 / 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: 2.2 Å3/Da / Density % sol: 44.04 % / Description: plate
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 1.7 M Li2SO4, 0.1 M TRIS pH 8.0

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: cryo / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Dec 9, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.55→30.3 Å / Num. obs: 48642 / % possible obs: 99.5 % / Redundancy: 12.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.019 / Rrim(I) all: 0.067 / Net I/σ(I): 21.6 / Num. measured all: 605815
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.55-1.597.20.3924.433670.9440.1520.42295.3
6.93-30.311.40.04546.36320.9990.0130.04798.8

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BLZ

1blz


Resolution: 1.55→27.18 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 17.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1803 2377 4.89 %
Rwork0.1573 46190 -
obs0.1584 48567 99.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 77.63 Å2 / Biso mean: 21.1509 Å2 / Biso min: 9.2 Å2
Refinement stepCycle: final / Resolution: 1.55→27.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2597 0 75 371 3043
Biso mean--28.05 29.48 -
Num. residues----328
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.55-1.580.22381340.18472503263794
1.58-1.620.21221460.17272613275998
1.62-1.650.20661380.165827092847100
1.65-1.690.21951360.161126862822100
1.7-1.740.19131470.158326822829100
1.74-1.790.21391460.151227002846100
1.79-1.850.19471480.147826982846100
1.85-1.920.18951280.1527112839100
1.92-1.990.16891340.151226962830100
1.99-2.080.18011440.141227262870100
2.08-2.190.16891450.138927202865100
2.19-2.330.16831230.140527442867100
2.33-2.510.15391290.140527342863100
2.51-2.760.17031420.156827612903100
2.76-3.160.20951330.166227812914100
3.16-3.980.17931490.148528052954100
3.98-27.180.16511550.181529213076100

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