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

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Basic information

Entry
Database: PDB / ID: 6zaj
TitleRoom temperature XFEL Isopenicillin N synthase structure in complex with Fe, O2 and ACV after exposure to dioxygen for 3000ms.
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: 1.5301 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
Water2,936163
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1260 Å2
ΔGint-26 kcal/mol
Surface area14050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.885, 75.639, 101.897
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): NM 554 / References: UniProt: P05326, isopenicillin-N synthase

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Non-polymers , 5 types, 167 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION


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


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.: 163 / 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: 42.75 % / 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, 0.1 M 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: 1.30179 Å
DetectorType: RAYONIX MX340-HS / Detector: CCD / Date: Oct 9, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.30179 Å / Relative weight: 1
ReflectionResolution: 1.53→21.13 Å / Num. obs: 49972 / % possible obs: 99.94 % / Redundancy: 90.71 % / Biso Wilson estimate: 22.1870954592 Å2 / CC1/2: 0.975 / R split: 0.16 / Net I/σ(I): 31.16
Reflection shellResolution: 1.53→1.556 Å / Redundancy: 22.48 % / Mean I/σ(I) obs: 0.679 / Num. unique obs: 2491 / CC1/2: 0.102 / R split: 1.113 / % possible all: 100
Serial crystallography sample deliveryDescription: acoustic droplet tape drive / Method: injection
Serial crystallography sample delivery injectionDescription: acoustic droplet tape drive

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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: 1.5301→21.1283 Å / SU ML: 0.2187 / Cross valid method: THROUGHOUT / σ(F): 1.3317 / Phase error: 24.1983
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1981 1999 4.0265 %
Rwork0.178 47647 -
obs0.1788 49646 99.9195 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.7271 Å2
Refinement stepCycle: LAST / Resolution: 1.5301→21.1283 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2581 0 29 163 2773
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009072753
X-RAY DIFFRACTIONf_angle_d0.931523764
X-RAY DIFFRACTIONf_chiral_restr0.05975396
X-RAY DIFFRACTIONf_plane_restr0.00664501
X-RAY DIFFRACTIONf_dihedral_angle_d9.233861622
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5301-1.56830.37831420.36723367X-RAY DIFFRACTION99.5461
1.5683-1.61060.35361410.3483356X-RAY DIFFRACTION99.9428
1.6106-1.6580.3321390.32033318X-RAY DIFFRACTION99.9133
1.658-1.71150.27741390.30393350X-RAY DIFFRACTION99.9141
1.7115-1.77270.28941420.27673358X-RAY DIFFRACTION99.9144
1.7727-1.84360.27381420.25643393X-RAY DIFFRACTION99.887
1.8436-1.92740.26511430.22033381X-RAY DIFFRACTION99.9149
1.9274-2.0290.2181400.19173373X-RAY DIFFRACTION100
2.029-2.1560.19751430.17323398X-RAY DIFFRACTION100
2.156-2.32230.19221430.16093385X-RAY DIFFRACTION100
2.3223-2.55560.21561420.17423416X-RAY DIFFRACTION99.9719
2.5556-2.92460.20671450.17233448X-RAY DIFFRACTION100
2.9246-3.68150.18361450.14993463X-RAY DIFFRACTION100
3.6815-21.12830.13761530.13863641X-RAY DIFFRACTION99.8947
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)
12.93287041935-0.06059679137810.965685379497.477607872715.758041435368.88857362770.0242671843621-0.2368447525770.09905480484320.247441627686-0.08553316923050.05068219665270.021564994914-0.2996732459380.1081388699210.139650094381-0.03258898136640.03989273540330.2172959888390.05393801122150.149290344263-16.2461412522-2.6677423279715.7237765266
21.012757439440.596074762099-1.601774887390.88521320676-0.3804045024313.63788277916-0.003501854319660.2069904811950.167502687766-0.1696593136060.1697463414680.235732062179-0.256446362308-0.760802428268-0.2126447294140.181573254838-0.00526510380689-0.05319451728720.3081231795350.01669208384240.22891141301-22.69667135550.530494060007-1.92723534832
36.802348241880.469111904155-3.565807667634.698690890553.374942610357.595894619050.1266019995710.2633988360.36477021527-0.06882205754070.05378823685950.0431588483648-0.356092340090.0306240420883-0.1405724239630.267292757641-0.011274920309-0.02021984673690.2129265566760.04711808020670.165248398574-11.09767969526.60377025626-24.3679259555
41.991236032612.032914094870.5674561527537.471522849032.012402490313.70472199376-0.08734158785010.2252809711910.0497447319459-0.2881545496570.143587613918-0.0221180501805-0.3410902231320.170787442576-0.06104844249780.207101344846-0.001211611692820.009828134772250.2112395360920.0347909286650.163114093727-9.862631149526.40958174976-14.9517326913
57.032357249271.357327797920.7854012890133.103690591390.2257691285283.48663368129-0.01138928643880.5214061922670.140183499138-0.01824310986670.1101641480360.100023516842-0.9242784899540.0234945853008-0.01861118191660.424328026534-0.0006650484836080.04283277395540.2111766452870.06819462991760.182798623066-9.6076785905815.3982475336-13.1348615898
61.51630016202-1.30585954871.216880930123.29593571478-3.023936796567.380756069590.0224561565909-0.11097557270.1099779239540.0199750679150.0519066658252-0.058961870126-0.727990563416-0.0282125578903-0.03063090643560.249251864067-0.003999563072120.03574610729280.137822946896-0.02660096938820.180616260347-11.29705686199.660646748685.11434369121
71.21452719693-0.05436847114850.4298253001351.290024534630.0462425309822.3739833050.02345231051830.0403050306297-0.11258234041-0.08582013522190.0223508898380.02121550606130.06439715148330.0658790738608-0.04715466532020.122138742952-0.006440090676330.01061915224960.1578378177520.00881608684050.156379660264-11.2127694115-7.2661817372-3.34907260562
89.251296213985.79311568885-7.886744746328.01088495404-4.241251059136.975750701090.119966449678-0.689152832233-0.3345186291380.256881108691-0.2289466453740.02553278772840.3406178513321.860997313870.1522857488880.243871130608-0.00739516941666-0.05391005938580.5843944992290.01996947397990.3209221680737.25182551303-1.7131270030713.9697864397
98.220516757365.406147936.063273004594.90133968055.581772282357.34144249938-0.2608501807290.806435985336-0.427955456287-0.8868170515210.472035544029-0.1464092894020.05217861633210.803395635776-0.2441229363860.442346637956-0.00942562589690.02377394487210.4604222357270.0298430224460.3430809527790.692316177114-0.891453191898-8.52144587083
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 114 )
5X-RAY DIFFRACTION5chain 'A' and (resid 115 through 137 )
6X-RAY DIFFRACTION6chain 'A' and (resid 138 through 182 )
7X-RAY DIFFRACTION7chain 'A' and (resid 183 through 295 )
8X-RAY DIFFRACTION8chain 'A' and (resid 296 through 312 )
9X-RAY DIFFRACTION9chain 'A' and (resid 313 through 331 )

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