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- PDB-8bbb: IPNS H270A variant in complex with ACV exposed to O2 -

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Basic information

Entry
Database: PDB / ID: 8bbb
TitleIPNS H270A variant in complex with ACV exposed to O2
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: 1.57 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 H270A variant in complex with ACV exposed to O2
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)38,1485
Polymers37,4971
Non-polymers6524
Water7,062392
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1210 Å2
ΔGint-29 kcal/mol
Surface area14460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.300, 74.250, 101.010
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: 37496.770 Da / Num. of mol.: 1 / Mutation: H270A
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_H270A / 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.: 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 392 / 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: 40.44 % / Description: needle morphology, 4 um x 4 um x 220 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: 1.57→41.76 Å / Num. obs: 44249 / % possible obs: 100 % / Redundancy: 13.3 % / Biso Wilson estimate: 18.84 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.217 / Rpim(I) all: 0.062 / Rrim(I) all: 0.226 / Net I/σ(I): 8 / Num. measured all: 588792 / Scaling rejects: 4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.57-1.6112.23.4150.732130.5121.0083.56499.6
7.02-41.7611.90.0475880.9990.0140.04999.8

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Processing

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

6zae


Resolution: 1.57→41.76 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2053 2194 4.97 %
Rwork0.1785 41930 -
obs0.1798 44124 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 79.03 Å2 / Biso mean: 25.8314 Å2 / Biso min: 13.1 Å2
Refinement stepCycle: final / Resolution: 1.57→41.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2609 0 39 393 3041
Biso mean--33.88 33.54 -
Num. residues----331
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.57-1.60.44751460.35642559270599
1.6-1.640.34541450.329925402685100
1.64-1.680.29251370.307425822719100
1.68-1.730.33091240.279326062730100
1.73-1.780.28161270.259325882715100
1.78-1.840.281310.23725852716100
1.84-1.90.23891500.216125932743100
1.9-1.980.22811370.189426012738100
1.98-2.070.23161550.166926002755100
2.07-2.180.17591260.160726202746100
2.18-2.310.1941400.156525892729100
2.31-2.490.20171230.155726392762100
2.49-2.740.19941330.16126632796100
2.74-3.140.16731370.164926532790100
3.14-3.960.17711300.142426882818100
3.96-41.760.16761530.161728242977100
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)
11.54250.21180.30522.74530.54032.06050.0577-0.1094-0.07560.1241-0.02290.04870.0926-0.1525-0.01160.2163-0.02140.01220.21050.02840.1817-15.8746-4.603214.5957
21.806-0.54690.08451.1393-0.94563.78010.0417-0.0262-0.00640.00930.0680.1628-0.1256-0.3611-0.14220.1623-0.0305-0.01570.1681-0.02030.1988-22.46420.9605-2.2603
38.51480.7588-2.66173.84650.13013.26150.26120.26760.1415-0.196-0.12910.0347-0.2606-0.0408-0.12490.2691-0.00310.00030.1669-0.00870.1392-10.83276.7233-23.9203
41.11940.84420.74190.95370.53562.1339-0.09030.15220.0686-0.12170.1386-0.0661-0.20080.0864-0.04460.1907-0.0050.01810.16350.01930.1668-9.241710.2903-13.9128
51.0746-1.08221.81461.369-1.97555.33230.0154-0.04710.0284-0.0102-0.00870.0434-0.1575-0.09080.05980.181-0.00840.01330.15280.00420.1875-15.47399.51682.5286
60.74560.11270.0692.9042-3.04963.29840.0361-0.01590.10280.2660.0186-0.0447-0.5630.209-0.0520.2181-0.01810.01250.1947-0.01590.195-4.497110.31349.5039
71.02940.03460.73540.8340.18671.95620.0428-0.0003-0.1035-0.0032-0.01160.01650.19550.0486-0.04490.17330.00590.0120.15740.00570.1625-12.696-8.7308-4.0594
82.60450.1024-0.26672.7413-2.53816.33210.1125-0.3948-0.1070.2179-0.3244-0.31220.32331.05380.24630.27470.0085-0.01870.37980.01040.20435.68731.559310.5822
92.38790.83962.4455.49164.7828.8096-0.13150.1261-0.2084-0.38880.3071-0.10920.17480.4579-0.17080.27820.02950.02660.30120.03290.24250.7134-1.1563-8.3359
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 37 )A1 - 37
2X-RAY DIFFRACTION2chain 'A' and (resid 38 through 64 )A38 - 64
3X-RAY DIFFRACTION3chain 'A' and (resid 65 through 82 )A65 - 82
4X-RAY DIFFRACTION4chain 'A' and (resid 83 through 137 )A83 - 137
5X-RAY DIFFRACTION5chain 'A' and (resid 138 through 163 )A138 - 163
6X-RAY DIFFRACTION6chain 'A' and (resid 164 through 182 )A164 - 182
7X-RAY DIFFRACTION7chain 'A' and (resid 183 through 286 )A183 - 286
8X-RAY DIFFRACTION8chain 'A' and (resid 287 through 312 )A287 - 312
9X-RAY DIFFRACTION9chain 'A' and (resid 313 through 331 )A313 - 331

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