6ZAK | pdb_00006zak

Room temperature XFEL Isopenicillin N synthase structure in complex with the Fe(IV)=O mimic VO and ACV.

PDB DOI: https://doi.org/10.2210/pdb6ZAK/pdb

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

Deposited: 2020-06-05 Released: 2022-01-12
Deposition Author(s): Rabe, P., Kamps, J.J.A.G., Sutherlin, K., Pharm, C., McDonough, M.A., Leissing, T.M., Aller, P., Butryn, A., Linyard, J., Lang, P., Brem, J., Fuller, F.D., Batyuk, A., Hunter, M.S., Pettinati, I., Clifton, I.J., Alonso-Mori, R., Gul, S., Young, I., Kim, I., Bhowmick, A., ORiordan, L., Brewster, A.S., Claridge, T.D.W., Sauter, N.K., Yachandra, V., Yano, J., Kern, J.F., Orville, A.M., Schofield, C.J.
Funding Organization(s): Wellcome Trust, Medical Research Council (MRC, United Kingdom), Royal Society, Biotechnology and Biological Sciences Research Council (BBSRC), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Department of Energy (DOE, United States)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.54 Å
R-Value Free:
0.226 (Depositor), 0.228 (DCC)
R-Value Work:
0.197 (Depositor), 0.198 (DCC)
R-Value Observed:
0.198 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Room temperature XFEL Isopenicillin N synthase structure in complex with the Fe(IV)=O mimic VO and ACV.

Rabe, P., Kamps, J.J.A.G., Sutherlin, K., Pharm, C., McDonough, M.A., Leissing, T.M., Aller, P., Butryn, A., Linyard, J., Lang, P., Brem, J., Fuller, F.D., Batyuk, A., Hunter, M.S., Pettinati, I., Clifton, I.J., Alonso-Mori, R., Gul, S., Young, I., Kim, I., Bhowmick, A., ORiordan, L., Brewster, A.S., Claridge, T.D.W., Sauter, N.K., Yachandra, V., Yano, J., Kern, J.F., Orville, A.M., Schofield, C.J.

To be published.

Macromolecule Content

Total Structure Weight: 38.09 kDa
Atom Count: 2,858
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 3 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 C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	L-D-(A-AMINOADIPOYL)-L-CYSTEINYL-D-VALINE C₁₄ H₂₅ N₃ O₆ S BYEIJZFKOAXBBV-ATZCPNFKSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
SO4 Query on SO4 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]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
VVO (Subject of Investigation/LOI) Query on VVO Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	oxovanadium(2+) O V MHHDXUNFNAZUGB-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.54 Å
R-Value Free: 0.226 (Depositor), 0.228 (DCC)
R-Value Work: 0.197 (Depositor), 0.198 (DCC)
R-Value Observed: 0.198 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.79	α = 90
b = 75.564	β = 90
c = 101.724	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2022-01-12

Deposition Author(s):

Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	106244/Z/14/Z
Medical Research Council (MRC, United Kingdom)	United Kingdom	106244/Z/14/Z
Wellcome Trust	United Kingdom	210734/Z/18/Z
Royal Society	United Kingdom	RSWF/R2/182017
Wellcome Trust	United Kingdom	102593
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	102593
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	BB/S50676X/1
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM133081
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	GM110501
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM126289
Department of Energy (DOE, United States)	United States	DOE BES DE-AC02-05CH11231
Department of Energy (DOE, United States)	United States	DOE BES DE-AC02-76SF00515