5VKW | pdb_00005vkw

Crystal structure of adenylosuccinate lyase ADE13 from Candida albicans

PDB DOI: https://doi.org/10.2210/pdb5VKW/pdb

Classification: LYASE
Organism(s): Candida albicans SC5314
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2017-04-24 Released: 2017-05-24
Deposition Author(s): Stogios, P.J., Evdokimova, E., Di Leo, R., Savchenko, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.195 (Depositor), 0.192 (DCC)
R-Value Work:
0.154 (Depositor), 0.153 (DCC)
R-Value Observed:
0.155 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Crystal structure of adenylosuccinate lyase ADE13 from Candida albicans

Stogios, P.J.

To be published.

Macromolecule Content

Total Structure Weight: 109.77 kDa
Atom Count: 8,763
Modeled Residue Count: 939
Deposited Residue Count: 964
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Adenylosuccinate lyase	A, B	482	Candida albicans SC5314	Mutation(s): 0 Gene Names: ADE13, CAALFM_CR06150CA, orf19.3870 EC: 4.3.2.2
UniProt
Find proteins for A0A1D8PT56 (Candida albicans (strain SC5314 / ATCC MYA-2876)) Explore A0A1D8PT56 Go to UniProtKB: A0A1D8PT56
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A1D8PT56
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PGE Query on PGE Download:Ideal Coordinates CCD File SDF format, chain P [auth B] MOL2 format, chain P [auth B] mmCIF format, chain P [auth B]	P [auth B]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain P [auth B] Interactions & Density Focus chain P [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain M [auth B] SDF format, chain F [auth A] MOL2 format, chain M [auth B] MOL2 format, chain F [auth A] mmCIF format, chain M [auth B] mmCIF format, chain F [auth A]	F [auth A], M [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain M [auth B] Interactions & Density Focus chain F [auth A] Focus chain M [auth B]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain O [auth B] SDF format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain N [auth B]	N [auth B], O [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain N [auth B] Focus chain O [auth B] Interactions & Density Focus chain N [auth B] Focus chain O [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain K [auth B] SDF format, chain J [auth B] SDF format, chain I [auth B] SDF format, chain H [auth B] SDF format, chain E [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain L [auth B] MOL2 format, chain K [auth B] MOL2 format, chain J [auth B] MOL2 format, chain I [auth B] MOL2 format, chain H [auth B] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain L [auth B] mmCIF format, chain K [auth B] mmCIF format, chain J [auth B] mmCIF format, chain I [auth B] mmCIF format, chain H [auth B] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A] D [auth A] E [auth A] H [auth B] I [auth B] C [auth A], D [auth A], E [auth A], H [auth B], I [auth B], J [auth B], K [auth B], L [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain Q [auth B] SDF format, chain G [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain G [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain G [auth A]	G [auth A], Q [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain Q [auth B] Interactions & Density Focus chain G [auth A] Focus chain Q [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.195 (Depositor), 0.192 (DCC)
R-Value Work: 0.154 (Depositor), 0.153 (DCC)
R-Value Observed: 0.155 (Depositor)

Diffraction Data:

Space Group: F 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.03	α = 90
b = 157.845	β = 90
c = 374.554	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing
PHENIX	model building
Coot	model building

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2017-05-24

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	HHSCN27220120026C

Revision History (Full details and data files)

Version 1.0: 2017-05-24
Type: Initial release
Version 1.1: 2017-09-20
Changes: Author supporting evidence
Version 1.2: 2019-12-11
Changes: Author supporting evidence
Version 1.3: 2023-10-04
Changes: Data collection, Database references, Derived calculations, Refinement description