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- PDB-6zah: Room temperature XFEL Isopenicillin N synthase structure in compl... -

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Basic information

Entry
Database: PDB / ID: 6zah
TitleRoom temperature XFEL Isopenicillin N synthase structure in complex with Fe and ACV after exposure to dioxygen for 800ms.
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 / : / Isopenicillin N synthase
Similarity search - Component
Biological speciesEmericella nidulans (mold)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 1.43 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, United States, 13items
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
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM133081 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM117126 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM110501 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM126289 United States
Department of Energy (DOE, United States)DOE BES DE-AC02-05CH11231 United States
Department of Energy (DOE, United States)DOE BES DE-AC02-76SF00515 United States
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)38,0794
Polymers37,5641
Non-polymers5153
Water3,459192
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1190 Å2
ΔGint-29 kcal/mol
Surface area14200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.918, 75.895, 101.923
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 Isopenicillin N synthase / / IPNS


Mass: 37563.836 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 / Production host: Escherichia coli (E. coli) / Strain (production host): NM554 / References: UniProt: P05326, isopenicillin-N synthase
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / 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-FE2 / FE (II) 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 / Water


Mass: 18.015 Da / Num. of mol.: 192 / 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: 43 % / Description: needles - size range 40-60um x 3 um x 3 um
Crystal growTemperature: 298 K / Method: batch mode / pH: 8.5 / Details: 1.7M Li2SO4, 0.1M TRIS pH 8.5

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Data collection

DiffractionMean temperature: 298 K / Ambient temp details: room temperature / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: MFX / Wavelength: 1.30178
DetectorType: RAYONIX MX340-HS / Detector: CCD / Date: Dec 10, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.30178 Å / Relative weight: 1
ReflectionResolution: 1.43→21.19 Å / Num. obs: 61018 / % possible obs: 99.96 % / Redundancy: 85.25 % / Biso Wilson estimate: 20.2994804644 Å2 / CC1/2: 0.977 / R split: 0.162 / Net I/σ(I): 28.131
Reflection shellResolution: 1.43→1.455 Å / Redundancy: 19.57 % / Mean I/σ(I) obs: 0.312 / Num. unique obs: 3049 / CC1/2: 0.06 / R split: 1.286 / % possible all: 100
Serial crystallography sample deliveryMethod: injection

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
cctbx.xfeldata reduction
PHASERphasing
cxi.mergedata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BLZ

1blz


Resolution: 1.43→20.9293 Å / SU ML: 0.2087 / Cross valid method: THROUGHOUT / σ(F): 1.3258 / Phase error: 24.4773
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2021 1961 3.2878 %
Rwork0.1645 57684 -
obs0.1657 59645 97.9264 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.0191 Å2
Refinement stepCycle: LAST / Resolution: 1.43→20.9293 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2598 0 30 192 2820
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005172782
X-RAY DIFFRACTIONf_angle_d0.714053807
X-RAY DIFFRACTIONf_chiral_restr0.0724399
X-RAY DIFFRACTIONf_plane_restr0.00438509
X-RAY DIFFRACTIONf_dihedral_angle_d11.405081005
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4301-1.46580.41771030.42162978X-RAY DIFFRACTION72.0702
1.4658-1.50540.37121390.36034095X-RAY DIFFRACTION98.9021
1.5054-1.54970.33751420.33714189X-RAY DIFFRACTION99.7926
1.5497-1.59970.31611410.30244126X-RAY DIFFRACTION99.9532
1.5997-1.65680.27421400.27574146X-RAY DIFFRACTION99.9534
1.6568-1.72310.27541420.25844170X-RAY DIFFRACTION99.9536
1.7231-1.80150.26331410.22464172X-RAY DIFFRACTION99.9768
1.8015-1.89640.22581430.20624197X-RAY DIFFRACTION99.977
1.8964-2.01510.19491420.17614181X-RAY DIFFRACTION99.9538
2.0151-2.17060.20561430.15234199X-RAY DIFFRACTION100
2.1706-2.38870.17371440.14354218X-RAY DIFFRACTION100
2.3887-2.73380.21521430.15864250X-RAY DIFFRACTION100
2.7338-3.44180.18681460.13684299X-RAY DIFFRACTION100
3.4418-20.92930.15031520.11984464X-RAY DIFFRACTION99.9567
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)
13.22834304250.4359590505770.9844372758167.239419891514.636197026176.962213908450.0708292347697-0.1960406679390.08560188647840.1740566528-0.09290117971580.006005209168030.0979750079766-0.2644528797430.07881988335790.142804091896-0.02701016740050.03328431474480.1994391245390.04889645021580.129431580898-16.1287190633-3.7127795208614.9651460151
22.130223706990.0747721964766-1.338497119691.15948689894-0.703850096325.530570327790.01914131128830.08709947758720.0776724580327-0.08319849253040.1675972502120.197965619752-0.312983138989-0.66962895971-0.2253285407620.150386464744-0.0347026300803-0.02233837584560.174392882507-0.004591717308750.196430356422-22.65833847810.504316426158-1.9653091379
39.73174064761.03489940724-0.3125634365277.25148015812.627711199365.494728435520.003772246080320.08467042317860.285310458484-0.2066185573730.008081322283750.0670815844356-0.347854334837-0.0578989462494-0.01060091625530.287731594509-0.0180504360963-0.003865480744120.2294524832160.03219387669160.127020480212-11.16545309826.4975753852-24.4335548509
41.498210300190.7760675822980.5703439576812.559346997150.5062950332943.14789200804-0.05565173287120.1623172550560.138768518111-0.187421697630.0837327635499-0.0788905963747-0.5797852268290.119616038148-0.0160310883780.284435785457-0.0167234632240.02027317272050.187618564950.03834595966380.164227497479-9.6814945185310.3830980523-14.2940054114
54.26380917305-3.563179905244.309285266244.72515695276-4.73010560165.160204565860.0428865057088-0.04761280920930.134569512486-0.105117613828-0.00191374011760.0775230355111-0.336910338217-0.141900087396-0.02547770051580.2119692485980.01633888991880.01683835396860.14153741841-0.01276083327670.148267364979-15.35171592539.067727715152.49366917079
60.9020880692480.2445763166781.294222674881.02194273432-0.1249582102075.66653054109-0.02812284130530.01070765416470.08610033969030.03543699448640.021630562307-0.0712042527653-0.6265709829360.3286753386850.03803170266780.162148751613-0.01022464289770.02720470307750.156135274811-0.02493542014320.175533411322-7.89369372657.200580589723.54731446353
76.61921161356-4.214390399751.705387749445.56346727668-1.620963542068.660301481060.4987549463510.570331900927-0.475766754542-0.654312724602-0.2452069667520.1472228635790.905420155190.192221043087-0.3407881570470.281874236295-0.0317537031873-0.03010918390980.167833883322-0.04988143879050.216869637949-15.0258218336-16.9932595583-16.6172511863
81.2085646187-0.02505343638650.2358808678761.325991647260.2385445116112.17510549717-0.0194146851065-0.0190531569246-0.0303049950152-0.01565392986370.02362653418110.012377320968-0.05136707772980.0932892828506-0.01019330714860.101115599862-0.01085309554870.0120441404380.1243262300240.005322340461520.120728237741-9.71926844477-5.94205340647-0.0388273478711
95.724126678434.18233464321-6.671148528516.08035563005-4.483949754587.860376432430.127424052773-0.605534654849-0.2872951721680.312972828053-0.359090697272-0.2409149866510.218830809072.081750413010.356024919320.284981349929-0.0372897521064-0.08445664106350.5932030925920.02939353580640.2900133957587.52594034151-1.7089691895313.8949283551
105.129491714945.172241289484.487477050129.328594573437.105162723466.04073969602-0.1659002864190.364598647427-0.100150224196-0.4972673807410.163393212162-0.217929567726-0.02647194194320.444118064077-0.006529772927370.265354274429-0.007408451077970.01451781272690.3562073717040.06236985615470.2527719873070.667819241524-1.21938985725-8.58708214725
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 64 )
3X-RAY DIFFRACTION3chain 'A' and (resid 65 through 82 )
4X-RAY DIFFRACTION4chain 'A' and (resid 83 through 137 )
5X-RAY DIFFRACTION5chain 'A' and (resid 138 through 163 )
6X-RAY DIFFRACTION6chain 'A' and (resid 164 through 189 )
7X-RAY DIFFRACTION7chain 'A' and (resid 190 through 209 )
8X-RAY DIFFRACTION8chain 'A' and (resid 210 through 295 )
9X-RAY DIFFRACTION9chain 'A' and (resid 296 through 312 )
10X-RAY DIFFRACTION10chain 'A' and (resid 313 through 331 )

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