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- PDB-8p7o: Isopenicillin N synthase in complex with Fe and Aad-Cys-[(S)-1-am... -

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Basic information

Entry
Database: PDB / ID: 8p7o
TitleIsopenicillin N synthase in complex with Fe and Aad-Cys-[(S)-1-amino-2-methylpropane-1-sulfonic acid]
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
: / : / Isopenicillin N synthase
Similarity search - Component
Biological speciesAspergillus nidulans FGSC A4 (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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: Isopenicillin N synthase in complex with Fe and Aad-Cys-[(S)-1-amino-2-methylpropane-1-sulfonic acid]
Authors: Rabe, P. / Schofield, C.J.
History
DepositionMay 30, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 12, 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)38,3076
Polymers37,5641
Non-polymers7445
Water6,810378
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area520 Å2
ΔGint-38 kcal/mol
Surface area14340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.259, 74.459, 100.994
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

#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 / 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.: 3 / Source method: obtained synthetically / Formula: SO4
#3: 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
#4: Chemical ChemComp-X5L / (2~{S})-2-azanyl-6-[[(2~{R})-1-[[(1~{S})-2-methyl-1-sulfo-propyl]amino]-1-oxidanylidene-3-sulfanyl-propan-2-yl]amino]-6-oxidanylidene-hexanoic acid


Mass: 399.484 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H25N3O7S2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 378 / 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: 2.07 Å3/Da / Density % sol: 40.64 % / Description: needle morphology, 4 um x 4 um x 180 um
Crystal growTemperature: 293 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 2, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.7→59.93 Å / Num. obs: 35099 / % possible obs: 100 % / Redundancy: 13.5 % / Biso Wilson estimate: 16.27 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.371 / Rpim(I) all: 0.104 / Rrim(I) all: 0.386 / Net I/σ(I): 5.5
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 13.9 % / Rmerge(I) obs: 3.208 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 1829 / CC1/2: 0.488 / Rpim(I) all: 0.887 / Rrim(I) all: 3.33 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→59.93 Å / SU ML: 0.196 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.1213
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2267 1759 5.03 %
Rwork0.1961 33245 -
obs0.1976 35004 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.96 Å2
Refinement stepCycle: LAST / Resolution: 1.7→59.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2605 0 41 378 3024
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00232966
X-RAY DIFFRACTIONf_angle_d0.52694064
X-RAY DIFFRACTIONf_chiral_restr0.0439427
X-RAY DIFFRACTIONf_plane_restr0.0041543
X-RAY DIFFRACTIONf_dihedral_angle_d11.8811060
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.750.37041270.31642506X-RAY DIFFRACTION99.81
1.75-1.80.33171720.29112482X-RAY DIFFRACTION99.81
1.8-1.860.311340.2782522X-RAY DIFFRACTION99.77
1.86-1.920.24391340.25392501X-RAY DIFFRACTION99.85
1.92-20.25081200.22832529X-RAY DIFFRACTION99.89
2-2.090.26681410.20612531X-RAY DIFFRACTION99.96
2.09-2.20.24821170.19872576X-RAY DIFFRACTION100
2.2-2.340.24621310.19742526X-RAY DIFFRACTION99.85
2.34-2.520.22341550.19642530X-RAY DIFFRACTION99.96
2.52-2.770.22511350.19272570X-RAY DIFFRACTION100
2.77-3.170.19261360.18682594X-RAY DIFFRACTION100
3.17-40.17741380.15242602X-RAY DIFFRACTION100
4-59.930.18051190.16722776X-RAY DIFFRACTION99.9
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)
11.51626942769-0.297289308481-0.006640582140461.900542747450.3633738028081.95197144771-0.0153968799758-0.106241321805-0.1194512168170.137183541877-0.00384395133290.0397264079430.109522871524-0.09837634360230.03035523946080.150593935785-0.01165874453690.01099625993770.156323419950.02734340253270.1271227962654.71390371353-4.5778886775314.5505801114
21.17653353675-0.310571606542-0.07876344469650.9227725238820.01747650326770.3503040500460.04800118625470.0317803191213-0.083876719725-0.1343767221730.02528329572590.2326839253050.0102387562324-0.085564962011-0.04796421238070.139791653103-0.00325036969317-0.02023406192050.147788774803-0.0144544748450.130320792238-2.388537531.7142128233-2.19988135804
35.277626569450.690476972749-1.819972142762.69328160889-0.4147517834932.513617453590.06206331581950.3727946028750.0606000022352-0.120411933064-0.03311717486150.314080361502-0.31108314087-0.0622551639524-0.05567562890550.2646305725570.00729857449351-0.01998852741810.138143510998-0.01555575226890.163916234157.260280928656.15678718365-23.3706592618
41.072593978470.2887059271410.2679779363451.827133178490.6486764057722.06356122376-0.1198653432590.1496441242490.0521649464099-0.3043492992580.09637034621740.0509028791716-0.2206914536250.1760049816670.00852984872720.124599791-0.002553388522770.005663822591590.112520664470.00966051918180.097462253763310.70083392776.45761813239-15.0269987414
52.604857325520.3493716700330.3239123792450.8940736129080.0007536573151771.75380344813-0.1108535486660.3791621660020.195315579652-0.05996580724820.07842203458360.0133163167247-0.3556198665050.09572857321730.0480904768660.240013442711-0.02227483035080.00574084514930.1279165081740.02597304443980.1155662669111.321244642715.4950121733-12.9274457789
61.12578771592-0.4604095845881.147357142930.985056777683-0.6391956976153.33387770223-0.0311767454928-0.04899906583480.136240179298-0.059069671204-0.04203622624120.0170284687229-0.181329136627-0.1940930070720.05389996022980.155835378894-0.002898975088780.01856336553450.10457133742-0.002295203062140.1347340708035.509301770749.050378183932.92715809014
70.61142578550.1700538456180.2664433469660.908857714504-1.55110937466.565340853630.0695562992636-0.06708082642660.03340863866590.0919047910268-0.0699711466256-0.0320693252373-0.5381412821060.4812058017880.04268804574660.155199004665-0.01926456646660.00250314200350.14046323988-0.007452424105190.14114280024915.852928743510.45874493189.5407141749
81.113537022520.08885029590590.5240481698831.106703464960.1286904267491.87043446880.0468497384434-0.0174081877391-0.0944841980775-0.0390603762196-0.03520578582780.05006655862270.117364071176-0.0474642587702-0.01941630561230.1203501832130.004971316763220.01189177316810.1244476822350.007257009208610.1332275501898.29228773802-8.52562031808-3.89821363542
91.22606562721-0.0644122365580.1254656759370.619435328605-0.2330186961971.421897891850.0471660136308-0.0934587062177-0.05953223902970.09070431035-0.187111307392-0.224025087330.04577256597870.7633517458380.1524910167460.218447549879-0.0278975687835-0.02302807447950.3532309020180.05662264384090.21122804014626.25019792972.1257854781710.3617021067
100.7004248275990.2629586924420.8963865408922.06928607162.436424556853.43190076791-0.1001252588050.0456247929265-0.115018164793-0.3419969337790.171618419684-0.0819293829109-0.04292700276810.305134890672-0.06157000294590.2392016678830.004840857706540.02336276485830.2374618596050.04092751964950.1808748405821.2196248288-1.02986850553-8.45361719333
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 2 through 37 )2 - 371 - 36
22chain 'A' and (resid 38 through 62 )38 - 6237 - 61
33chain 'A' and (resid 63 through 82 )63 - 8262 - 81
44chain 'A' and (resid 83 through 114 )83 - 11482 - 113
55chain 'A' and (resid 115 through 137 )115 - 137114 - 136
66chain 'A' and (resid 138 through 164 )138 - 164137 - 163
77chain 'A' and (resid 165 through 182 )165 - 182164 - 181
88chain 'A' and (resid 183 through 286 )183 - 286182 - 285
99chain 'A' and (resid 287 through 312 )287 - 312286 - 311
1010chain 'A' and (resid 313 through 331 )313 - 331312 - 330

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