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- PDB-6zap: Isopenicillin N synthase in complex with Fe, O2 and ACV under cry... -

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Basic information

Entry
Database: PDB / ID: 6zap
TitleIsopenicillin N synthase in complex with Fe, O2 and ACV under cryo conditions.
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.36 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 (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 Council102593 United Kingdom
Biotechnology and Biological Sciences Research CouncilBB/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
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
Water7,008389
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1450 Å2
ΔGint-40 kcal/mol
Surface area14190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.518, 74.460, 101.082
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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, 394 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-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 389 / 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: 2.08 Å3/Da / Density % sol: 40.86 % / Description: needles
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: 100 K / Ambient temp details: cryo / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91587 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 14, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91587 Å / Relative weight: 1
ReflectionResolution: 1.36→74.47 Å / Num. obs: 68190 / % possible obs: 100 % / Redundancy: 12.8 % / Biso Wilson estimate: 13.02 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.159 / Rpim(I) all: 0.046 / Rrim(I) all: 0.166 / Net I/σ(I): 9.6 / Num. measured all: 871404 / Scaling rejects: 684
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.36-1.412.92.3816426849790.5260.6792.478199.9
6.08-74.4712.60.044111368860.9990.0120.04536.9100

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
XDSdata reduction
Aimless0.7.1data scaling
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BLZ

1blz


Resolution: 1.36→59.95 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.7
RfactorNum. reflection% reflection
Rfree0.193 3338 4.9 %
Rwork0.161 --
obs0.1626 68060 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 64.72 Å2 / Biso mean: 20.426 Å2 / Biso min: 7.05 Å2
Refinement stepCycle: final / Resolution: 1.36→59.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2615 0 69 401 3085
Biso mean--30.89 31.49 -
Num. residues----329
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072998
X-RAY DIFFRACTIONf_angle_d0.9694105
X-RAY DIFFRACTIONf_chiral_restr0.116429
X-RAY DIFFRACTIONf_plane_restr0.007549
X-RAY DIFFRACTIONf_dihedral_angle_d12.7481091
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.36-1.37930.33581490.305262898
1.3793-1.39990.3471270.29442629100
1.3999-1.42180.30871450.28422682100
1.4218-1.44510.28311510.27272636100
1.4451-1.470.29571160.26322691100
1.47-1.49680.27121230.25092667100
1.4968-1.52560.27561420.23092665100
1.5256-1.55670.21991420.21812656100
1.5567-1.59060.23371260.20452693100
1.5906-1.62760.23781640.19552625100
1.6276-1.66830.22941320.18172691100
1.6683-1.71340.23961380.17672670100
1.7134-1.76380.21251390.17042687100
1.7638-1.82070.19521580.16542673100
1.8207-1.88580.21511390.15282697100
1.8858-1.96130.18081380.14722687100
1.9613-2.05060.17521490.13572662100
2.0506-2.15870.1661250.13372721100
2.1587-2.2940.18111260.12992736100
2.294-2.47110.18161290.1342738100
2.4711-2.71980.17371270.13752743100
2.7198-3.11330.16651430.14352744100
3.1133-3.92230.15541450.13292796100
3.9223-59.950.16891650.15372905100
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)
11.38980.55710.69951.81991.35043.47930.0533-0.0739-0.04640.0317-0.05780.0390.052-0.19940.01810.10890.00360.01610.07530.02770.1041-15.9813-4.125914.83
20.98330.107-0.35610.04620.15463.25190.03480.0376-0.0206-0.00220.02620.0874-0.304-0.4442-0.06380.10790.031-0.00120.0898-0.00650.1235-23.32471.9026-2.3874
37.24361.4522-3.5183.0745-0.83444.08570.11940.24980.1611-0.03310.02420.229-0.4017-0.2207-0.10840.19540.0199-0.01960.0746-0.00740.11-13.46416.0751-23.2319
41.01090.630.0981.4428-0.32912.3172-0.04140.16220.0603-0.0990.1071-0.0493-0.5690.0957-0.01610.2317-0.01460.01660.07460.01910.1158-9.63279.976-14.1414
50.7244-0.94241.03931.2817-1.81653.82180.0179-0.03460.0958-0.02940.02210.0377-0.4534-0.2272-0.01960.21040.03580.00710.07160.0160.1349-15.04749.07633
6-0.0214-0.05840.00681.2937-2.52385.20490.0061-0.00440.02820.14920.0025-0.0864-0.93370.45590.04610.2246-0.04860.00330.1057-0.01320.1315-4.897710.27279.013
70.8088-0.17650.45140.65070.01881.80660.0270.0136-0.1052-0.08910.0080.02670.1171-0.0204-0.03620.1005-0.00390.01650.05120.00590.1217-12.6601-8.5926-3.9785
81.77850.7267-1.03452.427-0.90722.7520.0822-0.2224-0.16720.2869-0.2153-0.3237-0.15661.17210.16970.2007-0.0773-0.02890.37440.00940.18185.57292.188910.3623
96.18770.50492.23259.11174.88697.0612-0.05860.5328-0.5405-0.94780.29050.06330.0150.5669-0.24230.2799-0.01890.00120.25410.02480.23230.6488-1.0724-8.2825
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 62 )A38 - 62
3X-RAY DIFFRACTION3chain 'A' and (resid 63 through 82 )A63 - 82
4X-RAY DIFFRACTION4chain 'A' and (resid 83 through 137 )A83 - 137
5X-RAY DIFFRACTION5chain 'A' and (resid 138 through 164 )A138 - 164
6X-RAY DIFFRACTION6chain 'A' and (resid 165 through 183 )A165 - 183
7X-RAY DIFFRACTION7chain 'A' and (resid 184 through 286 )A184 - 286
8X-RAY DIFFRACTION8chain 'A' and (resid 287 through 312 )A287 - 312
9X-RAY DIFFRACTION9chain 'A' and (resid 313 through 331 )A313 - 331

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