5K85 | pdb_00005k85

Crystal Structure of Acetyl-CoA Synthetase in Complex with Adenosine-5'-propylphosphate and Coenzyme A from Cryptococcus neoformans H99

PDB DOI: https://doi.org/10.2210/pdb5K85/pdb

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

Deposited: 2016-05-27 Released: 2016-08-17
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., SSGCID

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.217 (Depositor), 0.224 (DCC)
R-Value Work:
0.179 (Depositor), 0.189 (DCC)
R-Value Observed:
0.179 (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

CRYSTAL STRUCTURE OF ACETYL-COA SYNTHETASE IN COMPLEX WITH ADENOSINE-5'-PROPYLPHOSPHATE AND COENZYME A FROM CRYPTOCOCCUS NEOFORMANS H99

Seattle Structural Genomics Center for Infectious Disease (SSGCID), 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: 235.08 kDa
Atom Count: 15,536
Modeled Residue Count: 1,883
Deposited Residue Count: 2,082
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Acetyl-coenzyme A synthetase	A, B, C	694	Cryptococcus neoformans H99	Mutation(s): 0 Gene Names: CNAG_00797 EC: 6.2.1.1
UniProt
Find proteins for J9VFT1 (Cryptococcus neoformans (strain H99 / ATCC 208821 / CBS 10515 / FGSC 9487)) Explore J9VFT1 Go to UniProtKB: J9VFT1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	J9VFT1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
COA Query on COA Download:Ideal Coordinates CCD File SDF format, chain P [auth C] MOL2 format, chain P [auth C] mmCIF format, chain P [auth C]	P [auth C]	COENZYME A C₂₁ H₃₆ N₇ O₁₆ P₃ S RGJOEKWQDUBAIZ-IBOSZNHHSA-N		Interactions Focus chain P [auth C] Interactions & Density Focus chain P [auth C]
PRX Query on PRX Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain M [auth B] SDF format, chain Q [auth C] MOL2 format, chain D [auth A] MOL2 format, chain M [auth B] MOL2 format, chain Q [auth C] mmCIF format, chain D [auth A] mmCIF format, chain M [auth B] mmCIF format, chain Q [auth C]	D [auth A], M [auth B], Q [auth C]	ADENOSINE-5'-MONOPHOSPHATE-PROPYL ESTER C₁₃ H₂₀ N₅ O₇ P XAMXMSZRQHPMRX-QYVSTXNMSA-N		Interactions Focus chain D [auth A] Focus chain M [auth B] Focus chain Q [auth C] Interactions & Density Focus chain D [auth A] Focus chain M [auth B] Focus chain Q [auth C]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain L [auth B] MOL2 format, chain L [auth B] mmCIF format, chain L [auth B]	L [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain L [auth B] Interactions & Density Focus chain L [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain R [auth C] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain R [auth C] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain R [auth C]	E [auth A] F [auth A] G [auth A] H [auth A] I [auth A] E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], N [auth B], O [auth B], R [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain R [auth C] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain R [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.217 (Depositor), 0.224 (DCC)
R-Value Work: 0.179 (Depositor), 0.189 (DCC)
R-Value Observed: 0.179 (Depositor)

Diffraction Data:

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.8	α = 90
b = 186.09	β = 93.8
c = 85.32	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2016-08-17

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2016-08-17
Type: Initial release
Version 1.1: 2023-09-27
Changes: Data collection, Database references, Derived calculations, Refinement description