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- PDB-7p3l: Isopenicillin N synthase in complex with Fe and the substrate ana... -

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Basic information

Entry
Database: PDB / ID: 7p3l
TitleIsopenicillin N synthase in complex with Fe and the substrate analogue AadCyshomoCys
ComponentsIsopenicillin N synthase
KeywordsOXIDOREDUCTASE / Isopenicillin N synthase / substrate analogues
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
CYSTEINE / : / D-homocysteine / 2-AMINOHEXANEDIOIC ACID / Isopenicillin N synthase
Similarity search - Component
Biological speciesEmericella nidulans FGSC A4 (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.32 Å
AuthorsRabe, P. / Clifton, I. / Schofield, C.J.
Funding support United Kingdom, 4items
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
CitationJournal: To Be Published
Title: Isopenicillin N synthase in complex with Fe and the substrate analogue AadCyshomoCys
Authors: Rabe, P. / Clifton, I. / Schofield, C.J.
History
DepositionJul 8, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 20, 2022Provider: repository / Type: Initial release
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id
Revision 2.1Jan 31, 2024Group: Refinement description / Category: 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)38,51010
Polymers37,5641
Non-polymers9469
Water7,728429
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1310 Å2
ΔGint-36 kcal/mol
Surface area14450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.980, 71.420, 101.080
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
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 FGSC A4 (mold) / 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 , 7 types, 438 molecules

#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-UN1 / 2-AMINOHEXANEDIOIC ACID


Type: L-peptide linking / Mass: 161.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H11NO4 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-CYS / CYSTEINE


Type: L-peptide linking / Mass: 121.158 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO2S / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-KCY / D-homocysteine


Type: D-peptide linking / Mass: 135.185 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H9NO2S / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 429 / 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: 2.26 Å3/Da / Density % sol: 45.51 % / Description: plate, 250 um length
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 1.8 M 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: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 27, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.32→58.33 Å / Num. obs: 80679 / % possible obs: 100 % / Redundancy: 12.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.167 / Rpim(I) all: 0.049 / Rrim(I) all: 0.175 / Net I/σ(I): 10.7
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
1.32-1.3412.82.355262840980.5070.6722.4461.299.8
7.11-58.3310.80.04166376150.9990.0120.0434099.9

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
xia2data reduction
Aimless0.7.4data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BLZ

1blz


Resolution: 1.32→58.33 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1732 1999 2.48 %
Rwork0.1513 78587 -
obs0.1519 80586 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 118.66 Å2 / Biso mean: 19.9576 Å2 / Biso min: 8.24 Å2
Refinement stepCycle: final / Resolution: 1.32→58.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2627 0 87 435 3149
Biso mean--39.07 30.06 -
Num. residues----329
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.32-1.350.31021400.304855345674
1.35-1.390.27561420.282255565698
1.39-1.430.28291410.265855305671
1.43-1.480.28361420.236455725714
1.48-1.530.25331410.207455465687
1.53-1.590.19071410.176455655706
1.59-1.660.19851430.155355845727
1.66-1.750.18041410.145955695710
1.75-1.860.19241430.141956015744
1.86-20.1621420.131656005742
2-2.210.16681440.121256335777
2.21-2.520.14461430.124856565799
2.53-3.180.16011460.138957125858
3.18-58.330.13711500.134559296079
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)
12.2457-0.5973-1.21742.4420.85893.4908-0.06320.1930.0279-0.0925-0.00890.0128-0.0146-0.2860.09070.1154-0.0025-0.03660.14450.00720.07754.978733.446-17.7598
20.98260.25550.30412.0258-0.77612.8653-0.0045-0.0124-0.05040.01070.04390.08540.1645-0.137-0.06760.0827-0.00290.00970.1295-0.00910.12324.301525.4849-0.0471
30.9304-0.3773-1.38180.67560.99032.86480.0031-0.16510.05570.05940.0334-0.04840.00560.1329-0.04410.11070.0063-0.01760.12060.00150.105217.090231.67215.4729
44.41463.0053-1.25693.8534-0.63031.46030.1109-0.24990.01930.2139-0.0899-0.03250.10890.18760.00170.12490.0239-0.02610.1491-0.01130.095723.732225.981610.8912
50.655-0.1620.28591.1725-1.06722.664-0.02820.10210.0017-0.1189-0.0008-0.04270.08320.11260.04150.09660.00840.00460.1064-0.00470.097318.699528.9962-8.588
60.79340.0788-0.27941.9427-0.58331.79170.0339-0.07730.1510.22990.02430.187-0.2297-0.1715-0.06690.11380.0135-0.00420.1231-0.02340.11180.281640.927810.8888
71.96680.0478-0.58641.04470.34031.46270.05670.10370.143-0.1059-0.04940.076-0.1542-0.1526-0.01650.11980.0231-0.01870.11290.00920.0995.76339.9185-5.4538
80.5401-0.0677-0.76560.7923-0.10881.6052-0.0003-0.00260.00840.0134-0.01890.1183-0.0046-0.09930.02150.0967-0.0052-0.01210.1187-0.01540.11752.330335.8595.0002
91.8181-0.2541.18944.1585-2.7977.01780.020.32550.344-0.2236-0.0959-0.1404-0.64090.33640.09460.2041-0.01150.04390.18380.02660.178923.130246.7582-13.629
104.9998-3.0155-5.55792.75233.20239.40490.0884-0.3280.34590.05730.1281-0.1996-0.24690.3172-0.26630.1848-0.0244-0.02590.1358-0.010.179817.917344.6745.4692
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 64 )A38 - 64
3X-RAY DIFFRACTION3chain 'A' and (resid 65 through 114 )A65 - 114
4X-RAY DIFFRACTION4chain 'A' and (resid 115 through 137 )A115 - 137
5X-RAY DIFFRACTION5chain 'A' and (resid 138 through 182 )A138 - 182
6X-RAY DIFFRACTION6chain 'A' and (resid 183 through 214 )A183 - 214
7X-RAY DIFFRACTION7chain 'A' and (resid 215 through 269 )A215 - 269
8X-RAY DIFFRACTION8chain 'A' and (resid 270 through 286 )A270 - 286
9X-RAY DIFFRACTION9chain 'A' and (resid 287 through 312 )A287 - 312
10X-RAY DIFFRACTION10chain 'A' and (resid 313 through 331 )A313 - 331

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