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- PDB-8p48: IPNS variant N252D in complex with Fe and ACV under anaerobic con... -

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Basic information

Entry
Database: PDB / ID: 8p48
TitleIPNS variant N252D in complex with Fe and ACV under anaerobic conditions
ComponentsIsopenicillin N synthase
KeywordsOXIDOREDUCTASE / Isopenicillin N synthase / penicillins / biosynthesis / 2OG oxygenases / antibiotic
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: 1.63 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 variant N252D in complex with Fe and ACV under anaerobic conditions
Authors: Rabe, P. / Schofield, C.J.
History
DepositionMay 19, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 5, 2024Provider: repository / Type: Initial release

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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)38,2726
Polymers37,5651
Non-polymers7075
Water6,882382
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1390 Å2
ΔGint-43 kcal/mol
Surface area14220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.230, 74.830, 101.160
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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: 37564.820 Da / Num. of mol.: 1 / Mutation: N252D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus nidulans FGSC A4 (mold) / Gene: ipnA, ips, AN2622 / Plasmid: pCold / Details (production host): pCold_IPNS_N252D / 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.: 3 / 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.: 382 / 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: 2.09 Å3/Da / Density % sol: 41.08 % / Description: needle morphology, 4 um x 4 um x 160 um
Crystal growTemperature: 298 K / Method: batch mode / pH: 8.3 / Details: 1.7 M Li2SO4, 0.1 M Tris pH 8.3

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: cryogenic / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Mar 9, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.63→50.58 Å / Num. obs: 39910 / % possible obs: 99.9 % / Redundancy: 13.4 % / Biso Wilson estimate: 19.12 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.218 / Rpim(I) all: 0.061 / Rrim(I) all: 0.226 / Χ2: 0.99 / Net I/σ(I): 9.2
Reflection shellResolution: 1.63→1.67 Å / Redundancy: 13.3 % / Rmerge(I) obs: 3.233 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 2869 / CC1/2: 0.545 / Rpim(I) all: 0.902 / Rrim(I) all: 3.359 / Χ2: 0.9 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.63→50.58 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2037 1968 4.95 %
Rwork0.1797 --
obs0.181 39792 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.63→50.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2609 0 40 382 3031
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042780
X-RAY DIFFRACTIONf_angle_d0.6563802
X-RAY DIFFRACTIONf_dihedral_angle_d12.3151004
X-RAY DIFFRACTIONf_chiral_restr0.047397
X-RAY DIFFRACTIONf_plane_restr0.005507
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.63-1.670.30641220.3152611X-RAY DIFFRACTION98
1.67-1.720.31361440.2822675X-RAY DIFFRACTION100
1.72-1.770.32251430.26482650X-RAY DIFFRACTION100
1.77-1.820.29821320.24892680X-RAY DIFFRACTION100
1.82-1.890.26731420.232670X-RAY DIFFRACTION100
1.89-1.960.23861140.20362692X-RAY DIFFRACTION100
1.96-2.050.20571610.18482660X-RAY DIFFRACTION100
2.05-2.160.20171180.17322702X-RAY DIFFRACTION100
2.16-2.30.21381470.16862689X-RAY DIFFRACTION100
2.3-2.480.21991520.16272682X-RAY DIFFRACTION100
2.48-2.720.20051470.17042717X-RAY DIFFRACTION100
2.72-3.120.19781520.1812726X-RAY DIFFRACTION100
3.12-3.930.17271420.14912768X-RAY DIFFRACTION100
3.93-50.580.16011520.15962902X-RAY DIFFRACTION100
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)
10.42750.06-0.07510.5801-0.28292.11280.00140.030.0141-0.05330.03210.0732-0.1041-0.1597-0.03360.1417-0.0003-0.0010.14060.00250.1648-14.70042.1013-4.609
20.4757-0.00070.08630.4561-0.05511.54680.02020.03930.0234-0.05260.00350.0184-0.13190.0189-0.01250.16020.00210.01270.14710.01390.1606-11.17264.35-4.6449
31.30250.41010.20071.0874-0.0151.48320.0157-0.0697-0.04510.0214-0.0165-0.0814-0.00060.1133-0.01280.1690.01030.00960.16830.01340.1674-5.6079-4.34881.108
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 114 )
2X-RAY DIFFRACTION2chain 'A' and (resid 115 through 214 )
3X-RAY DIFFRACTION3chain 'A' and (resid 215 through 331 )

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