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- PDB-8pya: Isopenicillin N synthase in complex with Fe, O2, ACdV or thioalde... -

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Basic information

Entry
Database: PDB / ID: 8pya
TitleIsopenicillin N synthase in complex with Fe, O2, ACdV or thioaldehyde after 4s O2 exposure
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 / : / : / OXYGEN MOLECULE / Isopenicillin N synthase
Similarity search - Component
Biological speciesAspergillus nidulans FGSC A4 (mold)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsRabe, P. / Schofield, C.J.
Funding support United Kingdom, United States, 11items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/V001892/1 United Kingdom
Wellcome Trust210734/Z/18/Z United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/V001892/1 United Kingdom
Department of Energy (DOE, United States)DE- AC02-76SF00515 United States
Department of Energy (DOE, United States)DE-AC02- 05CH11231 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM117126 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM55302 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM110501 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM126289 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1P41GM139687 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)S10 OD023453 United States
CitationJournal: To Be Published
Title: Isopenicillin N synthase in complex with Fe, O2, ACdV or thioaldehyde after 4s O2 exposure
Authors: Rabe, P. / Schofield, C.J.
History
DepositionJul 25, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 7, 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)38,5697
Polymers37,5641
Non-polymers1,0056
Water3,387188
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2050 Å2
ΔGint-41 kcal/mol
Surface area13980 Å2
Unit cell
Length a, b, c (Å)41.701, 75.179, 101.711
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
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.) Aspergillus 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 , 6 types, 194 molecules

#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-OXY / OXYGEN MOLECULE


Mass: 31.999 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O2
#5: 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
#6: Chemical ChemComp-IO0 / (2S)-2-azanyl-6-[[(2R)-1-[[(2R)-3-methyl-1-oxidanyl-1-oxidanylidene-butan-2-yl]amino]-1-oxidanylidene-3-sulfanylidene-propan-2-yl]amino]-6-oxidanylidene-hexanoic acid / ACdV thioaldehyde


Mass: 361.414 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H23N3O6S / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 188 / 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: 2.12 Å3/Da / Density % sol: 42.04 % / Description: needle morphology, 3 um x 3 um x 60-80 um
Crystal growTemperature: 298 K / Method: batch mode / pH: 8.5 / Details: 1.7 M Li2SO4, 0.1 M tris pH 8.5

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Data collection

DiffractionMean temperature: 298 K / Ambient temp details: room temperature / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: MFX / Wavelength: 1.300289 Å
DetectorType: RAYONIX MX340-HS / Detector: CCD / Date: Mar 8, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.300289 Å / Relative weight: 1
ReflectionResolution: 1.5→22.48 Å / Num. obs: 52007 / % possible obs: 99.94 % / Redundancy: 161.62 % / Biso Wilson estimate: 19.82 Å2 / CC1/2: 0.996 / R split: 0.073 / Net I/σ(I): 5.986
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 12.63 % / Mean I/σ(I) obs: 0.578 / Num. unique obs: 2527 / CC1/2: 0.353 / R split: 0.866 / % possible all: 99.61
Serial crystallography measurementPulse duration: 35 fsec. / Pulse energy: 2.9 µJ / Pulse photon energy: 9.52 keV / XFEL pulse repetition rate: 30 Hz
Serial crystallography sample deliveryMethod: injection

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
cctbx.xfeldata reduction
cctbx.xfel.mergedata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→22.48 Å / SU ML: 0.2097 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.5031
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2069 2000 3.85 %
Rwork0.1808 49976 -
obs0.1818 51976 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.74 Å2
Refinement stepCycle: LAST / Resolution: 1.5→22.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2591 0 55 188 2834
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01412804
X-RAY DIFFRACTIONf_angle_d1.06383831
X-RAY DIFFRACTIONf_chiral_restr0.0725402
X-RAY DIFFRACTIONf_plane_restr0.0101510
X-RAY DIFFRACTIONf_dihedral_angle_d11.68831012
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.540.42721400.37253481X-RAY DIFFRACTION99.07
1.54-1.580.3141400.32083493X-RAY DIFFRACTION100
1.58-1.630.25511410.28223546X-RAY DIFFRACTION100
1.63-1.680.27811410.2493525X-RAY DIFFRACTION100
1.68-1.740.23931420.22943530X-RAY DIFFRACTION100
1.74-1.810.25331420.2213541X-RAY DIFFRACTION100
1.81-1.890.25441410.21433534X-RAY DIFFRACTION100
1.89-1.990.24721420.19873566X-RAY DIFFRACTION100
1.99-2.110.20151420.18153551X-RAY DIFFRACTION100
2.11-2.280.19981440.17433564X-RAY DIFFRACTION100
2.28-2.510.21171430.17683589X-RAY DIFFRACTION99.97
2.51-2.870.22881440.17943611X-RAY DIFFRACTION100
2.87-3.610.17161450.15673637X-RAY DIFFRACTION100
3.61-22.480.16811530.14353808X-RAY DIFFRACTION99.85
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)
13.074115592770.3474048760050.8862047754115.374176100763.139440170936.876937557740.0634731064472-0.232604500450.04723483746850.182336521523-0.1501355299820.1137639824720.0327779668031-0.3711771825820.1151329643280.0991172133095-0.02400753845490.02199768376240.1533944380.03827256930560.120005023635-16.1157585387-3.1106525078215.5412104309
22.55459125838-0.155605977035-0.280638597491.09642233509-0.4503636069813.2028232576-0.0162535987810.1916058521510.147100478721-0.09889850774240.1478964724910.246477053201-0.275953725625-0.530882291655-0.1061691626020.15588684967-0.00510323720378-0.032867870840.2085130319390.02277670376070.201267283576-22.61743373560.758976693154-2.35348847351
37.803064280.0144187147367-0.2216385517664.790788716151.299503236397.259565274110.03241612959810.1577495964670.0299164768761-0.1407266307970.04806829393840.235815673789-0.432862298664-0.216590704876-0.06546837664010.256561042362-0.0157097730244-0.0183537633670.1951529500540.02153099011080.157408252824-11.27140244796.6613865772-24.3684060293
42.432051185081.941590370380.2721403804936.4718581350.1198509099671.80398960759-0.1092353340.2676707375590.0571370294919-0.3093887066390.112813591420.0387065464885-0.3691096683680.17278314093-0.01818255537460.191875330385-0.005618130901270.01494794010240.1567739380540.03462223112780.126100100019-10.0050066016.35966803167-15.1181330849
54.926512883671.528524530070.1626618873183.031465447280.4092320007062.2989115958-0.1573469386570.4070378109370.33642580782-0.02515873318480.1267207330760.0482208188088-1.053515580670.06688500157260.04673955907730.436329326264-0.002899097903810.02274492806950.1973435496830.05755216559120.158645916415-9.4619731795715.4346688874-13.0366651601
63.01264485264-2.019942854113.13871387213.7998517543-3.898121519048.621284406230.0182211056668-0.06421267886520.176781226641-0.0498187230375-0.0009079874613370.0491775064528-0.550351717086-0.366881898642-0.008414974822370.2176810477250.02277979792280.03618791521670.112599158166-0.009564089965940.156436479186-15.17831840439.081350553862.92207802936
70.8532872591250.1018789077090.5472821099462.59290776288-2.84618071166.915280828510.00746923738285-0.1137840261780.1750015493780.283663274033-0.0488399576985-0.100549179661-1.125094152770.5778252207770.071579276460.262433261765-0.07075065384020.017953058890.192047480524-0.02211932350890.198866589498-5.0111944571610.4320094788.18208375054
81.38736343040.1073992732970.3131261944031.351465948370.1493922772622.553706520240.01999002034090.0300279318216-0.11239691626-0.1010323711390.0222260761710.0007331077807510.03310381205420.0870854299264-0.04209663770980.106591331611-0.01134799792320.01494239711210.1157211462040.006306608956780.144786117107-11.2244355706-7.09787605634-3.33988922492
95.324374998593.15065388641-3.47616897485.02598207196-1.536932218132.381718518430.209380414243-0.504527264505-0.3232256944230.293463659494-0.264469503443-0.2631903524950.1942403321261.561152839920.1002286405710.257626852968-0.0160617416446-0.0637407587560.5870981646950.05152612727770.3088368687577.34843564028-1.7486961885714.1523527183
105.082701691784.185914949124.770753966174.743203548075.275371654847.1955488054-0.1567848136080.712829542221-0.162463715547-0.6964664214080.292041793284-0.0372476092440.04394653126090.693533437092-0.1852454407170.325211413115-0.01296844661420.008495273491750.3929322571090.0451255600140.2708547553410.753557938682-1.05529194371-8.40312939228
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 4 through 37 )4 - 371 - 34
22chain 'A' and (resid 38 through 64 )38 - 6435 - 61
33chain 'A' and (resid 65 through 82 )65 - 8262 - 79
44chain 'A' and (resid 83 through 114 )83 - 11480 - 111
55chain 'A' and (resid 115 through 137 )115 - 137112 - 134
66chain 'A' and (resid 138 through 164 )138 - 164135 - 161
77chain 'A' and (resid 165 through 183 )165 - 183162 - 180
88chain 'A' and (resid 184 through 295 )184 - 295181 - 292
99chain 'A' and (resid 296 through 312 )296 - 312293 - 309
1010chain 'A' and (resid 313 through 331 )313 - 331310 - 328

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