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

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Basic information

Entry
Database: PDB / ID: 6zal
TitleRoom temperature XFEL Isopenicillin N synthase structure in complex with Fe and ACV after exposure to dioxygen for 500ms without glycerol.
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 / : / OXYGEN MOLECULE / Isopenicillin N synthase
Similarity search - Component
Biological speciesEmericella nidulans (mold)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 1.83 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)38,1115
Polymers37,5641
Non-polymers5474
Water2,720151
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1310 Å2
ΔGint-29 kcal/mol
Surface area14170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.922, 75.529, 102.137
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

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Protein , 1 types, 1 molecules A

#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

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Non-polymers , 5 types, 155 molecules

#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-OXY / OXYGEN MOLECULE / Oxygen


Mass: 31.999 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O2 / Feature type: SUBJECT OF INVESTIGATION
#5: 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
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 151 / 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: 2.15 Å3/Da / Density % sol: 42.85 % / Description: needles - size range 40-60um x 3 um x 3 um
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: 298 K / Ambient temp details: room temperatre / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: MFX / Wavelength: 1.31145 Å
DetectorType: RAYONIX MX170-HS / Detector: CCD / Date: May 16, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.31145 Å / Relative weight: 1
ReflectionResolution: 1.83→38.782 Å / Num. obs: 29482 / % possible obs: 99.98 % / Redundancy: 93.13 % / Biso Wilson estimate: 26.8165216571 Å2 / CC1/2: 0.959 / R split: 0.171 / Net I/σ(I): 61.274
Reflection shellResolution: 1.83→1.862 Å / Redundancy: 34.65 % / Mean I/σ(I) obs: 1.67 / Num. unique obs: 1423 / CC1/2: 0.264 / R split: 0.843 / % possible all: 99.09
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: 1.83→38.7819 Å / SU ML: 0.2122 / Cross valid method: THROUGHOUT / σ(F): 1.3268 / Phase error: 21.1437
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2091 1995 6.8052 %
Rwork0.168 27321 -
obs0.1708 29316 99.83313 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.421 Å2
Refinement stepCycle: LAST / Resolution: 1.83→38.7819 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2578 0 32 151 2761
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0038762741
X-RAY DIFFRACTIONf_angle_d0.6336273751
X-RAY DIFFRACTIONf_chiral_restr0.047768398
X-RAY DIFFRACTIONf_plane_restr0.004377498
X-RAY DIFFRACTIONf_dihedral_angle_d8.7226531614
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8301-1.87580.33631370.31041894X-RAY DIFFRACTION99.2184
1.8758-1.92650.31651400.27651916X-RAY DIFFRACTION99.3717
1.9265-1.98320.26581400.24561921X-RAY DIFFRACTION99.8547
1.9832-2.04720.27691390.23211918X-RAY DIFFRACTION99.9514
2.0472-2.12040.27581420.20971931X-RAY DIFFRACTION100
2.1204-2.20530.23671430.18921947X-RAY DIFFRACTION99.9522
2.2053-2.30560.21691400.17321922X-RAY DIFFRACTION100
2.3056-2.42710.23391400.17931933X-RAY DIFFRACTION99.9518
2.4271-2.57920.23391420.18361942X-RAY DIFFRACTION100
2.5792-2.77830.26341430.18411958X-RAY DIFFRACTION100
2.7783-3.05780.21871440.16371959X-RAY DIFFRACTION100
3.0578-3.50.19181440.15081987X-RAY DIFFRACTION100
3.5-4.40860.13381470.12371990X-RAY DIFFRACTION100
4.4086-38.78180.19421540.14722103X-RAY DIFFRACTION99.4273
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)
11.936632793830.06303563119491.238800549210.973676191241-0.1476890213774.77653569654-0.015482407702-0.004405562464050.01483768208260.03682158912750.04941221833050.121509683518-0.10597945724-0.289848530833-0.008309406373790.11086983108-0.02266068501930.01962967970210.1946694456750.01528945082330.1930404543912.47449262527-2.299029706878.57426312804
29.343757420271.70858092278-2.7726966274.661448219180.4751374037317.050211511660.2822069564320.3177156180490.198793331947-0.1190483916750.01510556142990.172783403388-0.333496237198-0.278466540537-0.2823589935020.2538378700210.0128540988347-0.02955189825550.2207647736220.04482140459670.1598346961858.30962988756.25160256622-24.0215597365
32.066261048780.9981061472210.5777423662596.223651329581.843865097063.58907743842-0.03683576472970.196924993194-0.0284735518778-0.3480637089460.105090785367-0.182834138987-0.3709973604390.073656198739-0.09477197982770.209694069012-0.007789463749040.02732894842240.2177424165720.04295523703230.1653674038510.90336124546.35756193926-15.2792778056
46.554381076671.453191348890.5993976032513.088592559450.2416890254643.50438883702-0.0556793622450.5437808800370.386762932531-0.06363136066250.1273953255620.0808750632056-0.9417036650980.09616393457970.01765488920860.420793369166-0.01218761124650.06250117503370.2304096372780.07744457240230.18773340500111.309161454715.4410422255-13.1518878547
50.934647639733-0.514854831530.5806128382882.13746994101-2.138112151387.329028323-0.00200029776188-0.1183186027650.153216549453-0.0278953538394-0.0226695071308-0.110066439818-0.627845400574-0.01700243451640.07452276548720.220116586948-0.003260159069850.03052202488580.125303067335-0.02807440969830.20846655630810.00150985399.551255327435.36696190668
61.46501286125-0.05558948131070.4099109591431.554274505960.1866937526242.679920997040.02006806478790.0133679736035-0.103964174918-0.05188930224690.00831516988657-0.05884606380370.0273014171520.197509329419-0.04102617212970.106405253347-0.01041627394590.01873446827190.1690187255770.01364193371480.16382774638512.0717453125-6.66438072402-1.31222962523
78.259390843786.461733960125.479600391249.267563991736.73527461065.06313607433-0.2971745975950.79307795992-0.228844731524-0.6867569756110.526108159095-0.300909141830.04149012198750.887794545883-0.1785317338390.339076393412-0.001784810734690.02321090826180.4772027178320.07465926535730.3145738253321.6805742857-1.09964336001-8.50034497629
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 62 )
2X-RAY DIFFRACTION2chain 'A' and (resid 63 through 82 )
3X-RAY DIFFRACTION3chain 'A' and (resid 83 through 114 )
4X-RAY DIFFRACTION4chain 'A' and (resid 115 through 137 )
5X-RAY DIFFRACTION5chain 'A' and (resid 138 through 182 )
6X-RAY DIFFRACTION6chain 'A' and (resid 183 through 312 )
7X-RAY DIFFRACTION7chain 'A' and (resid 313 through 331 )

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