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- PDB-8p7p: Isopenicillin N synthase in complex with Fe and Aad-Val-[(R)-1-am... -

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Basic information

Entry
Database: PDB / ID: 8p7p
TitleIsopenicillin N synthase in complex with Fe and Aad-Val-[(R)-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: 1.8 Å
AuthorsRabe, P. / Schofield, C.J.
Funding support United Kingdom, United States, 3items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/V001892/1 United Kingdom
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 and Aad-Val-[(R)-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)38,2115
Polymers37,5641
Non-polymers6474
Water4,936274
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area410 Å2
ΔGint-29 kcal/mol
Surface area14170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.230, 74.490, 101.010
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-X2R / (2~{S})-2-azanyl-6-[[(2~{R})-1-[[(1~{R})-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
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#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.: 274 / 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: 40.63 % / Description: needle morphology, 4 um x 4 um x 160 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: 1.8→41.8 Å / Num. obs: 29676 / % possible obs: 100 % / Redundancy: 13.4 % / Biso Wilson estimate: 22.02 Å2 / CC1/2: 0.995 / R split: 0.095 / Rmerge(I) obs: 0.339 / Rrim(I) all: 0.353 / Net I/σ(I): 6.7
Reflection shellResolution: 1.8→1.84 Å / Rmerge(I) obs: 3.85 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 1728 / CC1/2: 0.496 / Rpim(I) all: 1.059 / Rrim(I) all: 3.996 / % 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: 1.8→41.8 Å / SU ML: 0.2539 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.7052
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2418 1480 5 %
Rwork0.2065 28117 -
obs0.2083 29597 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.51 Å2
Refinement stepCycle: LAST / Resolution: 1.8→41.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2599 0 36 274 2909
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00192741
X-RAY DIFFRACTIONf_angle_d0.48183751
X-RAY DIFFRACTIONf_chiral_restr0.0427397
X-RAY DIFFRACTIONf_plane_restr0.0042499
X-RAY DIFFRACTIONf_dihedral_angle_d11.5592976
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.860.34551250.33352525X-RAY DIFFRACTION99.66
1.86-1.920.31161260.29772510X-RAY DIFFRACTION99.81
1.92-20.34241290.28152517X-RAY DIFFRACTION100
2-2.090.26931360.24742519X-RAY DIFFRACTION99.96
2.09-2.20.2941530.23482510X-RAY DIFFRACTION99.96
2.2-2.340.28311180.22352523X-RAY DIFFRACTION99.89
2.34-2.520.25981380.21612548X-RAY DIFFRACTION99.96
2.52-2.780.28221360.21152561X-RAY DIFFRACTION100
2.78-3.180.21131280.20232582X-RAY DIFFRACTION99.96
3.18-40.19361500.16892581X-RAY DIFFRACTION100
4-41.80.20311410.16732741X-RAY DIFFRACTION99.97
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)
10.5836932259620.0001000923973090.3138794934270.659508255623-0.233952760772.277933396370.0109593393441-0.01999383537190.01694429010170.09812049912090.04618961769830.06537290655830.098856260852-0.104132615922-0.0590473785770.2061352810080.02233122422030.02525981413230.145130589277-0.01242968634510.18336883068246.171784030373.73384061581.48084589945
20.627369776971-0.149605922557-0.006255148634190.9679790577240.03394626350441.940165435340.01603531101930.0002017464317120.002094591795450.00796090773661-0.0131613104802-0.01572156492660.08468083664250.12250153611-0.008201870424440.138168799187-0.00566848347658-0.01125263961370.1244769802670.01736754492340.14163400126353.184592041474.14995474952.85176581687
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 88 )2 - 881 - 87
22chain 'A' and (resid 89 through 331 )89 - 33188 - 330

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