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- PDB-7zoe: IPNS H270E variant in complex with Fe and ACV under anaerobic con... -

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Basic information

Entry
Database: PDB / ID: 7zoe
TitleIPNS H270E variant in complex with Fe and ACV under anaerobic conditions
ComponentsIsopenicillin N synthase
KeywordsOXIDOREDUCTASE / Isopenicillin N synthase / Active site mutations / anaerobic conditions / antibiotic biosynthesis
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 speciesAspergillus nidulans FGSC A4 (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsRabe, P. / Schofield, C.J.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC) United Kingdom
Wellcome Trust106244/Z/14/Z United Kingdom
CitationJournal: To Be Published
Title: IPNS H270E variant in complex with Fe and ACV under anaerobic conditions
Authors: Rabe, P. / Schofield, C.J.
History
DepositionApr 25, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 10, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 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)38,1665
Polymers37,5551
Non-polymers6114
Water8,341463
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1310 Å2
ΔGint-38 kcal/mol
Surface area14220 Å2
Unit cell
Length a, b, c (Å)41.410, 74.732, 101.371
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

#1: Protein Isopenicillin N synthase / IPNS


Mass: 37554.805 Da / Num. of mol.: 1 / Mutation: H270E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus nidulans FGSC A4 (mold) / Strain: FGSC A4 / ATCC 38163 / CBS 112.46 / NRRL 194 / M139 / Gene: ipnA, ips, AN2622 / Plasmid: pCOLD_IPNS / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P05326, isopenicillin-N synthase
#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-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 463 / Source method: isolated from a natural source / Formula: H2O
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: 2.18 Å3/Da / Density % sol: 43.64 % / Description: needle, 4 um x 4 um x 120 um
Crystal growTemperature: 298 K / Method: batch mode / pH: 8 / Details: 1.7 M Li2SO4, 0.1 M Tris pH 8.0

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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 EIGER2 XE 16M / Detector: PIXEL / Date: Apr 14, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.5→60.15 Å / Num. obs: 51282 / % possible obs: 100 % / Redundancy: 13.4 % / Biso Wilson estimate: 14.62 Å2 / CC1/2: 0.998 / Rpim(I) all: 0.046 / Rrim(I) all: 0.171 / Net I/σ(I): 10.8 / Num. measured all: 687457
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.5-1.5313.71.23481425400.660.4191.57199.9
4.07-60.212.545.43476627920.0150.053100

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6ZAE

6zae


Resolution: 1.5→60.15 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 17.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1867 2550 4.98 %
Rwork0.1565 48658 -
obs0.158 51208 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 75.46 Å2 / Biso mean: 19.5166 Å2 / Biso min: 8 Å2
Refinement stepCycle: final / Resolution: 1.5→60.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2614 0 35 463 3112
Biso mean--19.78 29.26 -
Num. residues----329
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 18 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.5-1.530.24181330.253426852818
1.53-1.560.30611280.245126462774
1.56-1.590.24171520.221526772829
1.59-1.630.26141430.205326292772
1.63-1.670.2221510.195126612812
1.67-1.720.22071220.194126922814
1.72-1.770.22491410.183826762817
1.77-1.820.23041170.180927142831
1.82-1.890.21191390.169826732812
1.89-1.970.19371400.16526992839
1.97-2.050.1941470.143926482795
2.06-2.160.17041290.146327282857
2.16-2.30.181610.143126852846
2.3-2.480.17851530.135626982851
2.48-2.730.16791530.139627192872
2.73-3.120.16521490.144627272876
3.12-3.930.13991460.135727842930
3.93-60.150.1961460.149129173063
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)
11.1751-0.42940.65573.3098-2.43073.51040.06730.1206-0.0359-0.1934-0.1307-0.04670.14530.19930.05630.10720.00980.02430.1334-0.03880.098615.8544-4.0411-14.9589
22.00760.7631-0.18421.07090.46143.66970.03210.0163-0.0210.03850.0492-0.1183-0.09250.3745-0.09660.07660.041-0.01230.07230.01390.131322.67251.14031.669
36.6133-1.1-2.08846.2377-0.50215.42970.1567-0.14460.24710.1307-0.0862-0.0238-0.29130.0849-0.04890.1362-0.0008-0.0010.0741-0.00240.031910.9286.69523.9849
40.8209-0.46480.41052.4772-1.2891.9162-0.0878-0.10820.06880.25440.10010.0422-0.2393-0.1665-0.01920.1030.0080.01020.0983-0.01540.09489.40526.786614.707
55.3137-0.4750.99281.0944-0.07291.9349-0.0828-0.45570.22920.08590.1024-0.0233-0.3202-0.07970.01490.17070.00250.02150.0913-0.02940.08649.263415.440613.095
61.55591.43962.4561.86862.99847.8398-0.00530.06970.0383-0.02410.037-0.0131-0.28550.1853-0.03290.08920.0030.01570.0839-0.00060.099315.5319.5652-2.5329
70.32130.13880.63921.37792.46818.51530.00480.05840.067-0.1958-0.03250.0966-0.5476-0.3260.03750.10010.02420.00290.12450.0210.12764.66659.937-9.5017
81.06180.03150.43980.8416-0.20421.63140.02720.0206-0.10010.0191-0.0081-0.03690.1314-0.004-0.0290.0930.00030.01330.0893-0.01550.113712.5199-8.90123.9527
91.63670.41040.58371.56860.36612.45110.03140.4007-0.1373-0.2512-0.07180.20810.0808-0.54890.04590.15980.0132-0.03210.3426-0.04260.1778-6.01071.7254-10.6324
102.5401-2.86082.83956.4948-5.41764.6839-0.1336-0.1839-0.1020.20180.32460.3274-0.0087-0.4814-0.23010.1229-0.00690.02220.1705-0.010.1458-0.7193-1.27898.3743
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 82 )A65 - 82
4X-RAY DIFFRACTION4chain 'A' and (resid 83 through 114 )A83 - 114
5X-RAY DIFFRACTION5chain 'A' and (resid 115 through 137 )A115 - 137
6X-RAY DIFFRACTION6chain 'A' and (resid 138 through 163 )A138 - 163
7X-RAY DIFFRACTION7chain 'A' and (resid 164 through 183 )A164 - 183
8X-RAY DIFFRACTION8chain 'A' and (resid 184 through 286 )A184 - 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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