6B8V | pdb_00006b8v

Crystal structure of adenylyl-sulfate kinase from Cryptococcus neoformans

PDB DOI: https://doi.org/10.2210/pdb6B8V/pdb

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

Deposited: 2017-10-09 Released: 2017-11-01
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.55 Å
R-Value Free:
0.240 (Depositor), 0.242 (DCC)
R-Value Work:
0.184 (Depositor), 0.189 (DCC)
R-Value Observed:
0.188 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 6B8V

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

Literature

Crystal structure of adenylyl-sulfate kinase from Cryptococcus neoformans

Delker, S.L., Abendroth, J., Lorimer, D., Edwards, T.E.

To be published.

Macromolecule Content

Total Structure Weight: 70.08 kDa
Atom Count: 3,929
Modeled Residue Count: 492
Deposited Residue Count: 633
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Adenylylsulfate kinase	A, B, C	211	Cryptococcus neoformans	Mutation(s): 0 Gene Names: C362_03154 EC: 2.7.1.25
UniProt
Find proteins for J9VMZ3 (Cryptococcus neoformans (strain H99 / ATCC 208821 / CBS 10515 / FGSC 9487)) Explore J9VMZ3 Go to UniProtKB: J9VMZ3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	J9VMZ3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain E [auth C] SDF format, chain D [auth A] MOL2 format, chain E [auth C] MOL2 format, chain D [auth A] mmCIF format, chain E [auth C] mmCIF format, chain D [auth A]	D [auth A], E [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth C] Interactions & Density Focus chain D [auth A] Focus chain E [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.55 Å
R-Value Free: 0.240 (Depositor), 0.242 (DCC)
R-Value Work: 0.184 (Depositor), 0.189 (DCC)
R-Value Observed: 0.188 (Depositor)

Space Group: P 3₁ 1 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.68	α = 90
b = 87.68	β = 90
c = 173.64	γ = 120

Software Package:

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

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2017-11-01

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2017-11-01
Type: Initial release
Version 1.1: 2023-10-04
Changes: Data collection, Database references, Refinement description

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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.