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- PDB-8a4g: IPNS H270E variant in complex with Cd and ACV -

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Basic information

Entry
Database: PDB / ID: 8a4g
TitleIPNS H270E variant in complex with Cd and ACV
ComponentsIsopenicillin N synthase
KeywordsOXIDOREDUCTASE / Isopenicillin N synthase / cadmium / 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: 1.97 Å
AuthorsRabe, P. / Schofield, C.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/V001892/1 United Kingdom
CitationJournal: To Be Published
Title: IPNS H270E variant in complex with Cd and ACV
Authors: Rabe, P. / Schofield, C.J.
History
DepositionJun 11, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 5, 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)38,5429
Polymers37,5551
Non-polymers9888
Water3,639202
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.080, 74.070, 101.270
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: 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

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Non-polymers , 6 types, 210 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-CD / CADMIUM ION


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


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#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: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 202 / 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: 2.03 Å3/Da / Density % sol: 39.33 % / Description: 4 um x 4 um x 130 um, needle morphology
Crystal growTemperature: 298 K / Method: microbatch / pH: 8.5 / Details: 1.7 M Li2SO4, 0.1 M Tris pH 8.3

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: May 19, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.97→41.8 Å / Num. obs: 22498 / % possible obs: 99.8 % / Redundancy: 12.9 % / Biso Wilson estimate: 29.65 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.277 / Rpim(I) all: 0.08 / Rrim(I) all: 0.289 / Net I/σ(I): 7.2 / Num. measured all: 289108
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
1.97-2.0212.12.5811931316020.4190.7592.693199.3
8.81-41.810.70.06333713150.9990.0190.06625.599.6

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
Aimless0.7.8data scaling
PDB_EXTRACT3.27data extraction
DIALSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7ZOE

7zoe


Resolution: 1.97→41.8 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2539 1124 5.01 %
Rwork0.2169 21322 -
obs0.2187 22446 99.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 80.73 Å2 / Biso mean: 33.0151 Å2 / Biso min: 18.38 Å2
Refinement stepCycle: final / Resolution: 1.97→41.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2616 0 52 203 2871
Biso mean--37.42 32.98 -
Num. residues----329
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.97-2.060.34441490.30622594274399
2.06-2.170.31421430.26952613275699
2.17-2.30.29921220.24842611273399
2.3-2.480.29911560.234126152771100
2.48-2.730.27481540.221326602814100
2.73-3.130.29371210.219926782799100
3.13-3.940.20931270.186627112838100
3.94-41.80.21981520.201528402992100
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)
11.0451-0.054-0.7061.35740.71373.67950.0317-0.0106-0.03780.10890.0656-0.11270.03180.1534-0.09370.17670.0565-0.04930.20020.02020.181-4.51380.97531.7603
20.8804-0.14430.33041.1914-0.04371.6807-0.0077-0.008-0.01210.12160.0067-0.0303-0.0393-0.00930.0060.1708-0.00110.00970.1792-0.0060.1637-8.93960.53214.0914
34.53520.29732.40623.87880.42456.34650.0412-0.03120.0340.1043-0.09320.06560.2642-0.4854-0.00390.2130.02640.04590.2638-0.02160.2241-24.33120.799-2.6726
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 88 )A3 - 88
2X-RAY DIFFRACTION2chain 'A' and (resid 89 through 286 )A89 - 286
3X-RAY DIFFRACTION3chain 'A' and (resid 287 through 331 )A287 - 331

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