8PY8 | pdb_00008py8

Isopenicillin N synthase in complex with Fe, ACdV and O2 after 2s O2 exposure

PDB DOI: https://doi.org/10.2210/pdb8PY8/pdb

Classification: OXIDOREDUCTASE
Organism(s): Aspergillus nidulans FGSC A4
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2023-07-25 Released: 2024-08-07
Deposition Author(s): Rabe, P., Schofield, C.J.
Funding Organization(s): Biotechnology and Biological Sciences Research Council (BBSRC), Wellcome Trust, Department of Energy (DOE, United States), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.46 Å
R-Value Free:
0.191 (Depositor), 0.190 (DCC)
R-Value Work:
0.165 (Depositor), 0.165 (DCC)
R-Value Observed:
0.166 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Isopenicillin N synthase in complex with Fe, ACdV and O2 after 2s O2 exposure

Rabe, P., Schofield, C.J.

To be published.

Macromolecule Content

Total Structure Weight: 38.57 kDa
Atom Count: 2,898
Modeled Residue Count: 328
Deposited Residue Count: 331
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Isopenicillin N synthase	A	331	Aspergillus nidulans FGSC A4	Mutation(s): 0 Gene Names: ipnA, ips, AN2622 EC: 1.21.3.1
UniProt
Find proteins for P05326 (Emericella nidulans (strain FGSC A4 / ATCC 38163 / CBS 112.46 / NRRL 194 / M139)) Explore P05326 Go to UniProtKB: P05326
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P05326
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ACV (Subject of Investigation/LOI) Query on ACV Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	L-D-(A-AMINOADIPOYL)-L-CYSTEINYL-D-VALINE C₁₄ H₂₅ N₃ O₆ S BYEIJZFKOAXBBV-ATZCPNFKSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
IO0 (Subject of Investigation/LOI) Query on IO0 Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	(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 C₁₄ H₂₃ N₃ O₆ S NKCVUNAEQXDNRK-ATZCPNFKSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A]	C [auth A], D [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A]
FE (Subject of Investigation/LOI) Query on FE Download:Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
OXY (Subject of Investigation/LOI) Query on OXY Download:Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	OXYGEN MOLECULE O₂ MYMOFIZGZYHOMD-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.46 Å
R-Value Free: 0.191 (Depositor), 0.190 (DCC)
R-Value Work: 0.165 (Depositor), 0.165 (DCC)
R-Value Observed: 0.166 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.721	α = 90
b = 75.241	β = 90
c = 101.732	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
cctbx.xfel	data reduction
cctbx.xfel.merge	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2024-08-07

Deposition Author(s):

Rabe, P.

Schofield, C.J.

Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	BB/V001892/1
Wellcome Trust	United Kingdom	210734/Z/18/Z
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	BB/V001892/1
Department of Energy (DOE, United States)	United States	DE- AC02-76SF00515
Department of Energy (DOE, United States)	United States	DE-AC02- 05CH11231
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM117126
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM55302
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM110501
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM126289
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	1P41GM139687
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	S10 OD023453