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- PDB-6zw8: Isopenicillin N synthase in complex with Cd and ACV. -

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Basic information

Entry
Database: PDB / ID: 6zw8
TitleIsopenicillin N synthase in complex with Cd and ACV.
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 FGSC A4 (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.22 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, 7items
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
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
DepositionJul 27, 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 31, 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)38,70810
Polymers37,5641
Non-polymers1,1449
Water9,512528
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1950 Å2
ΔGint-64 kcal/mol
Surface area14600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.239, 101.239, 115.451
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-560-

HOH

21A-619-

HOH

31A-1016-

HOH

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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 FGSC A4 (mold) / Gene: ipnA, ips, AN2622 / Production host: Escherichia coli (E. coli) / Variant (production host): NM554 / References: UniProt: P05326, isopenicillin-N synthase

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Non-polymers , 5 types, 537 molecules

#2: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cd / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: 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
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 528 / 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: 4.55 Å3/Da / Density % sol: 72.95 % / Description: hexagonal - 300 x 450 um
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 1.7M Li2SO4, 0.1 M TRIS pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: cryo / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97951 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 12, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97951 Å / Relative weight: 1
ReflectionResolution: 1.22→69.82 Å / Num. obs: 202322 / % possible obs: 100 % / Redundancy: 19.1 % / CC1/2: 1 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.015 / Rrim(I) all: 0.068 / Net I/σ(I): 19.7 / Num. measured all: 3857331 / Scaling rejects: 3213
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs
1.22-1.2518.70.991276383148100.5630.2331.0182.1
5.46-69.8218.50.0474579324800.9990.0110.04875.4

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
Aimless0.6.2data scaling
PDB_EXTRACT3.25data extraction
PHASERphasing
DIALSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BLZ

1blz


Resolution: 1.22→69.82 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1765 10333 5.11 %
Rwork0.1683 191916 -
obs0.1687 202249 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 89.89 Å2 / Biso mean: 26.3488 Å2 / Biso min: 12.7 Å2
Refinement stepCycle: final / Resolution: 1.22→69.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2634 0 90 528 3252
Biso mean--32.39 38.39 -
Num. residues----329
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.22-1.230.3473370.342462936630
1.23-1.250.31513280.336663656693
1.25-1.260.3283650.329463096674
1.26-1.280.30463270.309764006727
1.28-1.30.29443510.304563226673
1.3-1.310.27353640.288163286692
1.31-1.330.26963030.265563836686
1.33-1.350.26783440.255863296673
1.35-1.370.25613120.241563856697
1.37-1.40.23133180.228763876705
1.4-1.420.22513410.224363686709
1.42-1.450.22753540.220463606714
1.45-1.470.22453190.222764036722
1.47-1.50.20363510.196863606711
1.5-1.540.18893500.189363846734
1.54-1.570.20593390.180763126651
1.57-1.610.19652970.177764556752
1.61-1.660.18873240.179163906714
1.66-1.70.19593500.175363756725
1.7-1.760.18093590.17963856744
1.76-1.820.19043760.17963906766
1.82-1.90.19153610.179363896750
1.9-1.980.17443320.169764056737
1.98-2.090.17483320.158464136745
2.09-2.220.16153940.152563976791
2.22-2.390.15763320.147364586790
2.39-2.630.14913540.154464486802
2.63-3.010.15783780.150764696847
3.01-3.790.14983390.136665336872
3.79-69.820.15714020.143367217123
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)
13.4076-0.5083-1.48532.89420.84092.4708-0.0208-0.0881-0.0190.38040.1776-0.45920.20030.1848-0.13720.24340.0975-0.06090.1522-0.01770.231825.508453.728124.1971
22.5731-1.60540.27093.689-0.25441.15610.12350.20160.31-0.2044-0.1268-0.3382-0.15870.10150.020.2050.02480.03450.1157-0.01930.116814.860477.783616.711
30.8419-0.52960.02051.88320.34980.84260.12190.155-0.008-0.2861-0.12760.0227-0.1016-0.0298-0.00250.18140.04930.00230.1305-0.00050.148110.923870.35714.0956
41.2382-0.2397-0.16382.04610.97821.47580.0041-0.0425-0.09090.26710.0179-0.06510.19780.0804-0.01240.19150.0479-0.00550.10920.00170.147914.563664.170626.8644
52.9105-2.84471.3967.2704-2.97753.66110.0089-0.0352-0.84420.01210.15820.77490.5086-0.4136-0.17230.3085-0.00730.02250.2002-0.0550.41055.256146.989815.6585
63.1348-3.6983-3.70946.45675.11227.19820.10550.2785-0.1388-0.0783-0.44060.6423-0.2325-0.66870.36180.19040.041-0.00380.2304-0.00140.3010.015265.809119.6726
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 37 )A3 - 37
2X-RAY DIFFRACTION2chain 'A' and (resid 38 through 82 )A38 - 82
3X-RAY DIFFRACTION3chain 'A' and (resid 83 through 214 )A83 - 214
4X-RAY DIFFRACTION4chain 'A' and (resid 215 through 286 )A215 - 286
5X-RAY DIFFRACTION5chain 'A' and (resid 287 through 312 )A287 - 312
6X-RAY DIFFRACTION6chain 'A' and (resid 313 through 331 )A313 - 331

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