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

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Basic information

Entry
Database: PDB / ID: 6zai
TitleRoom temperature XFEL Isopenicillin N synthase structure in complex with Fe, O2 and ACV after exposure to dioxygen for 1600ms.
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: 1.5501 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)38,2076
Polymers37,5641
Non-polymers6435
Water2,990166
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1420 Å2
ΔGint-34 kcal/mol
Surface area14240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.918, 75.798, 101.848
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, 171 molecules

#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-OXY / OXYGEN MOLECULE


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: isolated from a natural source / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 166 / 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: 42.89 % / 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 pH8.5

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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: 1.30454 Å
DetectorType: RAYONIX MX340-HS / Detector: CCD / Date: Dec 10, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.30454 Å / Relative weight: 1
ReflectionResolution: 1.55→20.27 Å / Num. obs: 48052 / % possible obs: 99.94 % / Redundancy: 78.04 % / Biso Wilson estimate: 22.4944852641 Å2 / CC1/2: 0.959 / R split: 0.161 / Net I/σ(I): 32.663
Reflection shellResolution: 1.55→1.577 Å / Redundancy: 24.1 % / Mean I/σ(I) obs: 0.855 / Num. unique obs: 2343 / CC1/2: 0.114 / R split: 1.109 / % 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: 1.5501→20.2688 Å / SU ML: 0.183 / Cross valid method: FREE R-VALUE / σ(F): 1.3267 / Phase error: 21.973
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1861 1999 4.1774 %
Rwork0.165 45853 -
obs0.1659 47852 99.9415 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.5574 Å2
Refinement stepCycle: LAST / Resolution: 1.5501→20.2688 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2591 0 37 166 2794
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009442764
X-RAY DIFFRACTIONf_angle_d0.923613781
X-RAY DIFFRACTIONf_chiral_restr0.06071399
X-RAY DIFFRACTIONf_plane_restr0.00661503
X-RAY DIFFRACTIONf_dihedral_angle_d9.280461632
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5501-1.58880.34251390.334563192X-RAY DIFFRACTION99.7305
1.5888-1.63170.32551420.31423223X-RAY DIFFRACTION99.822
1.6317-1.67970.32441400.28443223X-RAY DIFFRACTION99.9406
1.6797-1.73390.32241410.27263233X-RAY DIFFRACTION99.9408
1.7339-1.79580.27151410.24093226X-RAY DIFFRACTION99.8813
1.7958-1.86770.2811410.22343230X-RAY DIFFRACTION99.9407
1.8677-1.95260.24551420.19213258X-RAY DIFFRACTION99.9706
1.9526-2.05540.17961420.16533281X-RAY DIFFRACTION99.9708
2.0554-2.18410.1681430.15613257X-RAY DIFFRACTION100
2.1841-2.35250.1921430.1483286X-RAY DIFFRACTION100
2.3525-2.58880.16431410.1563274X-RAY DIFFRACTION99.9707
2.5888-2.96240.18181460.16013325X-RAY DIFFRACTION100
2.9624-3.72850.17041450.14133341X-RAY DIFFRACTION100
3.7285-20.26880.14191530.13743504X-RAY DIFFRACTION100
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)
12.63740261931-0.3406921189750.5970285292948.286922141375.727774243658.391108291090.0432591471355-0.2450291455850.1450336759860.245144557197-0.1391830740450.07722830614520.0340519570166-0.3377485403930.1043576461410.148088678572-0.01901082408610.03466524191410.2178666898240.04086215628030.135809576119-16.1903887341-2.669344833915.6442489246
21.275865779890.563411933022-1.828153747860.673353310201-0.7761563550225.365389345350.02434962070320.1954633902070.119775663224-0.1408993271280.2063466093950.210684881639-0.282777860272-0.794061394581-0.2413119198160.182250177475-0.0253940700253-0.04744598991840.2585895229860.01504179363340.211516462018-22.64789145080.46705569918-1.92212392075
32.514061006870.600537135145-2.743904898817.30410648699-0.6594382153193.146435080640.09657941575250.1571509255420.00657270569412-0.134298920494-0.00846987282346-0.0462231948688-0.397593880199-0.0401934567096-0.09393249083840.290415618786-0.0152275620547-0.005739384730460.2720709023230.01614472293480.147565475883-11.0401954366.53849085372-24.3649092129
41.649360247250.8052357977570.2294779135772.560900091560.3439782188793.588499414930.006145316255530.2102008276180.116084139694-0.1403641534940.0419770101013-0.0601517203503-0.5628595578180.0475411306789-0.02708763953950.2876344256250.002337161210780.01472911219450.2016072783720.04683050934530.177534039517-9.7258708259210.0899164969-14.3516023781
50.747901719381-0.3939664067520.4512331307941.92732186532-1.662934495936.181251896950.0441504742432-0.08307594643740.11314158411-0.007677517411110.0110538550953-0.0260346262363-0.6432627168230.04352833869520.009744454451970.24266672954-0.01247447018670.02919887997360.141923846858-0.02247783632730.178219819119-11.28342813419.628031220475.03835212755
61.43223393594-0.1211305437050.4858742274411.313649178550.1290178492832.292092915430.02926354215840.0225804145133-0.138162770415-0.1137217191220.01667101909510.03935230970250.1060076276420.0125891012738-0.05232555238120.16796331631-0.01021219325040.01476988861880.1786825244370.004809751004790.186633058542-12.2700736677-8.96687056146-4.0377309269
73.307033251151.52151112259-1.515926495632.37035230434-1.081545022093.370327628420.0813153244244-0.257757813959-0.09513631888520.349298011937-0.285725717233-0.226367143171-0.2823712756171.17448601890.2580331289760.231154883374-0.0713192818177-0.02446422428480.4182104213-0.01941645907580.2190938947985.561543620872.6271347967410.0418442549
88.196441527566.058823610986.602471615828.281749241767.626651979729.63887944152-0.2133061695090.731158797897-0.244415345166-0.6496017727560.426153787438-0.1486630470650.1545040425660.744994122591-0.2302829531510.369654877101-0.01323735108720.01781993633370.4570771744860.06989564750650.3012827770890.726931068779-1.11065088031-8.54439988912
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 4 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 182 )
6X-RAY DIFFRACTION6chain 'A' and (resid 183 through 286 )
7X-RAY DIFFRACTION7chain 'A' and (resid 287 through 312 )
8X-RAY DIFFRACTION8chain 'A' and (resid 313 through 331 )

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