5K8F | pdb_00005k8f

Crystal structure of Acetyl-CoA Synthetase in complex with ATP and Acetyl-AMP from Cryptococcus neoformans H99

PDB DOI: https://doi.org/10.2210/pdb5K8F/pdb

Classification: LIGASE
Organism(s): Cryptococcus neoformans var. grubii H99
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2016-05-30 Released: 2016-07-13
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID), Fox III, D., Delker, S.L., Potts, K.T., Lorimer, D.D., Edwards, T.E., Mutz, M.W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.45 Å
R-Value Free:
0.224 (Depositor), 0.220 (DCC)
R-Value Work:
0.188 (Depositor), 0.190 (DCC)
R-Value Observed:
0.189 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Literature

Crystal structure of Acetyl-CoA Synthetase in complex with ATP and Acetyl-AMP from Cryptococcus neoformans H99

Seattle Structural Genomics Center for Infectious Disease (SSGCID), Fox III, D., Delker, S.L., Potts, K.T., Numa, M.M., Edwards, T.E., Lorimer, D.D., Mutz, M.W., Krysan, D.J.

To be published.

Macromolecule Content

Total Structure Weight: 235.87 kDa
Atom Count: 15,624
Modelled Residue Count: 1,962
Deposited Residue Count: 2,082
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Acetyl-coenzyme A synthetase	A, B, C	694	Cryptococcus neoformans var. grubii H99	Mutation(s): 0 Gene Names: CNAG_00797 EC: 6.2.1.1
UniProt
Find proteins for J9VFT1 (Cryptococcus neoformans var. grubii serotype A (strain H99 / ATCC 208821 / CBS 10515 / FGSC 9487)) Explore J9VFT1 Go to UniProtKB: J9VFT1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	J9VFT1
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ATP (Subject of Investigation/LOI) Query on ATP Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain K [auth B] SDF format, chain Q [auth C] MOL2 format, chain D [auth A] MOL2 format, chain K [auth B] MOL2 format, chain Q [auth C] mmCIF format, chain D [auth A] mmCIF format, chain K [auth B] mmCIF format, chain Q [auth C]	D [auth A], K [auth B], Q [auth C]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain D [auth A] Focus chain K [auth B] Focus chain Q [auth C] Interactions & Density Focus chain D [auth A] Focus chain K [auth B] Focus chain Q [auth C]
6R9 (Subject of Investigation/LOI) Query on 6R9 Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain L [auth B] SDF format, chain R [auth C] MOL2 format, chain E [auth A] MOL2 format, chain L [auth B] MOL2 format, chain R [auth C] mmCIF format, chain E [auth A] mmCIF format, chain L [auth B] mmCIF format, chain R [auth C]	E [auth A], L [auth B], R [auth C]	[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] ethanoate C₁₂ H₁₆ N₅ O₈ P UBPVOHPZRZIJHM-WOUKDFQISA-N		Interactions Focus chain E [auth A] Focus chain L [auth B] Focus chain R [auth C] Interactions & Density Focus chain E [auth A] Focus chain L [auth B] Focus chain R [auth C]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain W [auth C] MOL2 format, chain W [auth C] mmCIF format, chain W [auth C]	W [auth C]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain W [auth C] Interactions & Density Focus chain W [auth C]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain T [auth C] SDF format, chain U [auth C] SDF format, chain J [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain T [auth C] MOL2 format, chain U [auth C] MOL2 format, chain J [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain T [auth C] mmCIF format, chain U [auth C] mmCIF format, chain J [auth A]	G [auth A] H [auth A] I [auth A] J [auth A] N [auth B] G [auth A], H [auth A], I [auth A], J [auth A], N [auth B], O [auth B], P [auth B], T [auth C], U [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain T [auth C] Focus chain U [auth C] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain T [auth C] Focus chain U [auth C]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain S [auth C] SDF format, chain V [auth C] SDF format, chain M [auth B] MOL2 format, chain F [auth A] MOL2 format, chain S [auth C] MOL2 format, chain V [auth C] MOL2 format, chain M [auth B] mmCIF format, chain F [auth A] mmCIF format, chain S [auth C] mmCIF format, chain V [auth C] mmCIF format, chain M [auth B]	F [auth A], M [auth B], S [auth C], V [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain M [auth B] Focus chain S [auth C] Focus chain V [auth C] Interactions & Density Focus chain F [auth A] Focus chain M [auth B] Focus chain S [auth C] Focus chain V [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.45 Å
R-Value Free: 0.224 (Depositor), 0.220 (DCC)
R-Value Work: 0.188 (Depositor), 0.190 (DCC)
R-Value Observed: 0.189 (Depositor)

Diffraction Data: https://doi.org/10.18430/M35K8F

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.37	α = 110.06
b = 83.92	β = 105.24
c = 101.57	γ = 87.65

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2016-07-13

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2016-07-13
Type: Initial release
Version 2.0: 2021-04-28
Type: Coordinate replacement
Reason: Ligand identity
Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Database references, Derived calculations, Refinement description, Source and taxonomy, Structure summary
Version 2.1: 2023-09-27
Changes: Data collection, Database references, Refinement description