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- PDB-8bbd: IPNS H270Q variant in complex with ACV after O2 exposure -

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Basic information

Entry
Database: PDB / ID: 8bbd
TitleIPNS H270Q variant in complex with ACV after O2 exposure
ComponentsIsopenicillin N synthase
KeywordsOXIDOREDUCTASE / Isopenicillin N synthase / antibiotic biosynthesis / anaerobic / penicillins
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: 1.81 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 H270Q variant in complex ACV after O2 exposure
Authors: Rabe, P. / Schofield, C.J.
History
DepositionOct 12, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 25, 2023Provider: 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)38,1094
Polymers37,5541
Non-polymers5563
Water4,738263
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1110 Å2
ΔGint-22 kcal/mol
Surface area14120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.070, 74.440, 100.800
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Isopenicillin N synthase / IPNS


Mass: 37553.820 Da / Num. of mol.: 1 / Mutation: H270Q
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_H270Q / Details (production host): pCold / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 263 / 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: 2.05 Å3/Da / Density % sol: 40.04 % / Description: needle morphology, 3 um x 3 um x 180 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: Sep 13, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.81→41.73 Å / Num. obs: 28255 / % possible obs: 97.4 % / Redundancy: 11.8 % / Biso Wilson estimate: 19.63 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.256 / Rpim(I) all: 0.079 / Rrim(I) all: 0.268 / Net I/σ(I): 8.3 / Num. measured all: 332734 / Scaling rejects: 42
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
1.81-1.8610.72.2162165320190.4340.6852.3241.196.3
8.09-41.7311.20.05844483960.9980.0170.0629.199.6

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Processing

Software
NameVersionClassification
Aimless0.7.9data scaling
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
DIALSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6ZAE

6zae


Resolution: 1.81→41.73 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 28.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.257 1335 4.79 %
Rwork0.2334 26537 -
obs0.2346 27872 96.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 64.63 Å2 / Biso mean: 23.0266 Å2 / Biso min: 12.61 Å2
Refinement stepCycle: final / Resolution: 1.81→41.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2607 0 34 264 2905
Biso mean--26.62 25.03 -
Num. residues----329
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.81-1.870.38781290.34422625275497
1.87-1.950.52291030.46262266236983
1.95-2.040.29741360.270527032839100
2.04-2.150.36361520.32732583273595
2.15-2.280.31051280.28872415254389
2.28-2.460.25031430.221127292872100
2.46-2.70.25341290.232427562885100
2.7-3.090.20811250.208827732898100
3.09-3.90.2461460.20072751289798
3.9-41.730.17661440.174629363080100
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)
10.6998-0.1257-0.21220.5222-0.46541.61020.01730.01710.05350.0428-0.0026-0.0126-0.15030.0729-0.00230.1675-0.0120.00640.1238-0.01010.1707-10.298211.5392-0.6353
21.10540.29320.8341.17630.16912.04130.0439-0.003-0.09260.0054-0.01280.03380.14070.0355-0.05040.13460.01930.0130.14010.00730.1384-12.2877-8.7309-3.7328
31.08130.3278-0.10450.8086-0.3022.19820.0565-0.1555-0.10810.05-0.1414-0.15350.32990.69050.06490.19650.0472-0.01350.33770.05050.21153.53030.45082.7092
41.47630.27380.3820.9288-0.10922.4460.0656-0.0854-0.1280.1603-0.04970.05790.1033-0.2105-0.0240.168-0.0262-0.00470.20610.01970.1509-16.8166-2.994113.1174
50.46570.33030.19271.19340.68641.8411-0.06010.0722-0.0196-0.15720.08910.047-0.105-0.0101-0.02530.181-0.0009-0.01050.1750.01380.1754-13.34326.2553-16.3671
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 115 through 182 )A115 - 182
2X-RAY DIFFRACTION2chain 'A' and (resid 183 through 286 )A183 - 286
3X-RAY DIFFRACTION3chain 'A' and (resid 287 through 331 )A287 - 331
4X-RAY DIFFRACTION4chain 'A' and (resid 3 through 50 )A3 - 50
5X-RAY DIFFRACTION5chain 'A' and (resid 51 through 114 )A51 - 114

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