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- PDB-6y0o: isopenicillin N synthase in complex with ACV and Fe under anaerob... -

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Basic information

Entry
Database: PDB / ID: 6y0o
Titleisopenicillin N synthase in complex with ACV and Fe under anaerobic environment using FT-SSX methods
ComponentsAnaerobic Fixed Target Structure of Isopenicillin N synthase in complex with Fe and ACV
KeywordsOXIDOREDUCTASE / iron dependent oxygenase / penicillin biosynthesis / isopenicillin N
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: 2.2 Å
AuthorsRabe, P. / Beale, J.H. / Lang, P.A. / Dirr, A.S. / Leissing, T.M. / Butryn, A. / Aller, P. / Kamps, J.J.A.G. / Axford, D. / McDonough, M.A. ...Rabe, P. / Beale, J.H. / Lang, P.A. / Dirr, A.S. / Leissing, T.M. / Butryn, A. / Aller, P. / Kamps, J.J.A.G. / Axford, D. / McDonough, M.A. / Orville, A.M. / Owen, R. / Schofield, C.J.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Wellcome Trust106244/Z/14/Z United Kingdom
Medical Research Council (United Kingdom)MR/N002679/1 United Kingdom
Biotechnology and Biological Sciences Research CouncilBB/S50676X/1 United Kingdom
CitationJournal: Iucrj / Year: 2020
Title: Anaerobic fixed-target serial crystallography.
Authors: Rabe, P. / Beale, J.H. / Butryn, A. / Aller, P. / Dirr, A. / Lang, P.A. / Axford, D.N. / Carr, S.B. / Leissing, T.M. / McDonough, M.A. / Davy, B. / Ebrahim, A. / Orlans, J. / Storm, S.L.S. / ...Authors: Rabe, P. / Beale, J.H. / Butryn, A. / Aller, P. / Dirr, A. / Lang, P.A. / Axford, D.N. / Carr, S.B. / Leissing, T.M. / McDonough, M.A. / Davy, B. / Ebrahim, A. / Orlans, J. / Storm, S.L.S. / Orville, A.M. / Schofield, C.J. / Owen, R.L.
History
DepositionFeb 10, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 9, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 30, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Anaerobic Fixed Target Structure of Isopenicillin N synthase in complex with Fe and ACV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1755
Polymers37,5641
Non-polymers6114
Water2,000111
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1300 Å2
ΔGint-34 kcal/mol
Surface area14260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.889, 75.797, 102.034
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
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 Anaerobic Fixed Target Structure of Isopenicillin N synthase in complex with Fe and ACV


Mass: 37563.836 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus nidulans FGSC A4 (mold) / Gene: ipnA (ips) / Plasmid: PJB703 / Production host: Escherichia coli (E. coli) / Variant (production host): NM554 / 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: isolated from a natural source / Formula: Fe
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / 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: 2.16 Å3/Da / Density % sol: 42.98 % / Description: needles
Crystal growTemperature: 298 K / Method: batch mode / pH: 8.5 / Details: 1.7 M Li2SO4, 0.1 M TRIS pH8.5

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Data collection

DiffractionMean temperature: 293 K / Ambient temp details: room temperature / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96863 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 9, 2019
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96863 Å / Relative weight: 1
ReflectionResolution: 2.2→60.85 Å / Num. obs: 16880 / % possible obs: 97.71 % / Redundancy: 130.22 % / Biso Wilson estimate: 24.7373704023 Å2 / CC1/2: 0.959 / R split: 0.235 / Net I/σ(I): 15.02
Reflection shellResolution: 2.2→2.238 Å / Redundancy: 7.96 % / Mean I/σ(I) obs: 1.4 / Num. unique obs: 600 / CC1/2: 0.176 / R split: 1.004 / % possible all: 99.75
Serial crystallography measurementCollimation: KB mirrors / Source size: 49 µm2
Serial crystallography sample deliveryDescription: fixed target / Method: fixed target
Serial crystallography sample delivery fixed targetDescription: Anaerobic / Sample holding: thin film mylar sandwich

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
GDAdata collection
DIALS1.8data reduction
DIALS1.8data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1blz

1blz


Resolution: 2.2→60.85 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.18
RfactorNum. reflection% reflection
Rfree0.247 833 4.973 %
Rwork0.209 --
obs0.211 16749 97.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 32.67 Å2
Refinement stepCycle: LAST / Resolution: 2.2→60.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2584 0 35 112 2731
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00242724
X-RAY DIFFRACTIONf_angle_d0.4790950880913720
X-RAY DIFFRACTIONf_chiral_restr0.0424090301173392
X-RAY DIFFRACTIONf_plane_restr0.00289414633692491
X-RAY DIFFRACTIONf_dihedral_angle_d8.472338183241602
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.21-2.340.361200.322373X-RAY DIFFRACTION88.94
2.34-2.520.351360.312578X-RAY DIFFRACTION97.28
2.52-2.770.371410.282685X-RAY DIFFRACTION99.93
2.77-3.170.281420.232694X-RAY DIFFRACTION100
3.17-40.171430.172718X-RAY DIFFRACTION100
4-60.840.191510.142868X-RAY DIFFRACTION99.93
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)
13.020859056281.21016527881.199170773895.78800766854.805198862368.164688881770.00399149779435-0.1916088466550.04590513333830.3406050658860.05197204938790.00594515895930.066445936325-0.211059452933-0.01791891633290.145386680612-0.006745409317070.01847611501790.1769424547610.05395004749510.153115025385-16.0805085059-3.4929183705815.2441332072
22.0020927240.305929787965-1.294631616360.293289488495-0.8116000459015.278522022710.1462837192710.2353304911350.194024115539-0.2128196419730.07481616352480.151641335215-0.245076849751-0.397877541268-0.2091923569190.2615818009970.00627840322728-0.04521273836490.100797988144-0.01626323380640.212271391566-18.04150090962.93284671202-11.0099538336
31.703357646690.8250526405940.08821977412212.72444172953-0.04864695823882.49187421854-0.005944701164630.2855743763480.13320087127-0.2124851128310.0673777173652-0.0748943769975-0.5466507566330.0255980829102-0.01862996117150.268605135398-0.0126767266430.02800392403220.1977043754760.05405151720840.156590799051-9.6018257867510.1275415531-14.2855743029
41.32957609729-0.5760546428060.3647197290432.08586445101-1.901133229794.883912864480.0432453836866-0.04060055387430.06100659143450.04909858074540.08977384318290.0305073429262-0.6619484515770.129549143322-0.04176876030070.2716681195530.003849484582260.0235256062280.123712462792-0.01625614385950.1635070031-11.02424667419.569805281465.23634764395
51.66123695210.1995772963420.4067446129322.260641578860.5923762483973.41696280371-0.0108478084209-0.0292005754956-0.106416411901-0.03947911337970.03325010803870.0751099785540.0459585445813-0.00329068521137-0.02324060706640.113218744036-0.002161747006730.01316835746460.1450853205560.01733086197580.1329711102-11.4843033124-9.30939744241-3.32297550847
61.369804151470.6772093100760.5529984620152.914061738461.657585777553.79235611002-0.09734313693480.171834210884-0.0208186860448-0.09897178683820.008003376118290.2697022815590.161666855092-0.244073416050.1355087087750.1474321999510.01571466339880.006859041416120.1976016201690.008410713459050.166877240179-16.1561575555-7.54570603302-7.73901317199
71.577308171371.00391911797-2.23128405942.17788199945-1.85688699043.292163266750.173224593085-0.3384270452-0.08597182525310.445874533408-0.236135577117-0.158358440943-0.468264856311.639394090390.337912283320.330615740009-0.0939865889048-0.07315955008610.5162642224610.005469679995340.2156055270515.518570421452.683781771489.88738212503
85.207909955922.757721373133.754889639598.315462642235.781096805326.20831159152-0.3022610524190.4687030570640.191819150078-0.5218677326850.328835121687-0.180925374271-0.2776990983881.19722908921-0.09419023148750.164835322227-0.0281009773719-0.003888840969620.3208971136180.06785924446230.2015900688221.01089231755-0.991764614219-8.46146638686
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 37 )
2X-RAY DIFFRACTION2chain 'A' and (resid 38 through 82 )
3X-RAY DIFFRACTION3chain 'A' and (resid 83 through 137 )
4X-RAY DIFFRACTION4chain 'A' and (resid 138 through 182 )
5X-RAY DIFFRACTION5chain 'A' and (resid 183 through 269 )
6X-RAY DIFFRACTION6chain 'A' and (resid 270 through 286 )
7X-RAY DIFFRACTION7chain 'A' and (resid 287 through 312 )
8X-RAY DIFFRACTION8chain 'A' and (resid 313 through 331 )

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