5VPV | pdb_00005vpv

Crystal structure of Apo Cryptococcus neoformans H99 Acetyl-CoA Synthetase with an Acetylated Active Site Lysine

PDB DOI: https://doi.org/10.2210/pdb5VPV/pdb

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

Deposited: 2017-05-05 Released: 2017-05-17
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID), Fox III, D., Davies, D.R., Calhoun, B.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free:
0.216 (Depositor), 0.224 (DCC)
R-Value Work:
0.156 (Depositor)
R-Value Observed:
0.159 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 5VPV

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

Literature

Crystal structure of Apo Cryptococcus neoformans H99 Acetyl-CoA Synthetase with an Acetylated Active Site Lysine

Seattle Structural Genomics Center for Infectious Disease (SSGCID), Fox III, D., Davies, D.R., Calhoun, B., Edwards, T.E., Lorimer, D.D., Mutz, M.W., Krysan, D.J.

To be published.

Macromolecule Content

Total Structure Weight: 233.57 kDa
Atom Count: 14,915
Modeled Residue Count: 1,825
Deposited Residue Count: 2,082
Unique protein chains: 1

Macromolecules

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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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain N [auth C] SDF format, chain K [auth B] SDF format, chain H [auth A] MOL2 format, chain N [auth C] MOL2 format, chain K [auth B] MOL2 format, chain H [auth A] mmCIF format, chain N [auth C] mmCIF format, chain K [auth B] mmCIF format, chain H [auth A]	H [auth A], K [auth B], N [auth C]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain H [auth A] Focus chain K [auth B] Focus chain N [auth C] Interactions & Density Focus chain H [auth A] Focus chain K [auth B] Focus chain N [auth C]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain M [auth C] SDF format, chain L [auth C] SDF format, chain J [auth B] SDF format, chain I [auth B] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain M [auth C] MOL2 format, chain L [auth C] MOL2 format, chain J [auth B] MOL2 format, chain I [auth B] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain M [auth C] mmCIF format, chain L [auth C] mmCIF format, chain J [auth B] mmCIF format, chain I [auth B] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A] E [auth A] F [auth A] G [auth A] I [auth B] D [auth A], E [auth A], F [auth A], G [auth A], I [auth B], J [auth B], L [auth C], M [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain L [auth C] Focus chain M [auth C] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain L [auth C] Focus chain M [auth C]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
ALY Query on ALY	A, B, C	L-PEPTIDE LINKING	C₈ H₁₆ N₂ O₃		LYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.216 (Depositor), 0.224 (DCC)
R-Value Work: 0.156 (Depositor)
R-Value Observed: 0.159 (Depositor)

Diffraction Data:

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 176.98	α = 90
b = 176.98	β = 90
c = 159.92	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XSCALE	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2017-05-17

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2017-05-17
Type: Initial release
Version 1.1: 2024-11-20
Changes: Data collection, Database references, Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.