5IFI

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

PDB DOI: https://doi.org/10.2210/pdb5IFI/pdb

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

Deposited: 2016-02-26 Released: 2016-03-16
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID), SSGCID, Fox III, D., Edwards, T.E., Lorimer, D.D., Mutz, M.W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free:
0.213 (Depositor), 0.210 (DCC)
R-Value Work:
0.185 (Depositor), 0.180 (DCC)
R-Value Observed:
0.186 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Crystal structure of Acetyl-CoA Synthetase in complex with Adenosine-5'-propylphosphate from Cryptococcus neoformans H99

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

To be published.

Macromolecule Content

Total Structure Weight: 235.09 kDa
Atom Count: 15,384
Modelled Residue Count: 1,859
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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PRX Query on PRX Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain O [auth B] SDF format, chain Z [auth C] MOL2 format, chain D [auth A] MOL2 format, chain O [auth B] MOL2 format, chain Z [auth C] mmCIF format, chain D [auth A] mmCIF format, chain O [auth B] mmCIF format, chain Z [auth C]	D [auth A], O [auth B], Z [auth C]	ADENOSINE-5'-MONOPHOSPHATE-PROPYL ESTER C₁₃ H₂₀ N₅ O₇ P XAMXMSZRQHPMRX-QYVSTXNMSA-N		Interactions Focus chain D [auth A] Focus chain O [auth B] Focus chain Z [auth C] Interactions & Density Focus chain D [auth A] Focus chain O [auth B] Focus chain Z [auth C]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain S [auth B] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B]	P [auth B], Q [auth B], R [auth B], S [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Interactions & Density Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain BA [auth C] 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 L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain T [auth B] SDF format, chain U [auth B] SDF format, chain V [auth B] SDF format, chain W [auth B] SDF format, chain X [auth B] SDF format, chain Y [auth B] MOL2 format, chain AA [auth C] MOL2 format, chain BA [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 L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B] MOL2 format, chain Y [auth B] mmCIF format, chain AA [auth C] mmCIF format, chain BA [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 L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain T [auth B] mmCIF format, chain U [auth B] mmCIF format, chain V [auth B] mmCIF format, chain W [auth B] mmCIF format, chain X [auth B] mmCIF format, chain Y [auth B]	AA [auth C] BA [auth C] E [auth A] F [auth A] G [auth A] AA [auth C], BA [auth C], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], T [auth B], U [auth B], V [auth B], W [auth B], X [auth B], Y [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain BA [auth C] 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 L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Interactions & Density Focus chain AA [auth C] Focus chain BA [auth C] 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 L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.213 (Depositor), 0.210 (DCC)
R-Value Work: 0.185 (Depositor), 0.180 (DCC)
R-Value Observed: 0.186 (Depositor)

Diffraction Data: https://doi.org/10.18430/M35IFI

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.46	α = 90
b = 185.55	β = 93.67
c = 84.89	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2016-03-16

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2016-03-16
Type: Initial release
Version 1.1: 2016-04-06
Changes: Database references
Version 1.2: 2023-09-27
Changes: Data collection, Database references, Derived calculations, Refinement description