6FKO | pdb_00006fko

Deoxyguanylosuccinate synthase (DgsS) quaternary structure with ATP, dGMP, hadacidin at 2.1 Angstrom resolution

PDB DOI: https://doi.org/10.2210/pdb6FKO/pdb
Entry: 6FKO supersedes: 6FJR

Classification: BIOSYNTHETIC PROTEIN
Organism(s): Vibrio phage phiVC8
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2018-01-24 Released: 2019-06-26
Deposition Author(s): Sleiman, D., Loc'h, J., Haouz, A., Kaminski, P.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.222 (Depositor), 0.223 (DCC)
R-Value Work:
0.189 (Depositor), 0.192 (DCC)
R-Value Observed:
0.191 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 6FKO

Ligand Structure Quality Assessment

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

Literature

Deoxyguanylosuccinate synthase (DgsS) quaternary structure with ATP, dGMP, HAdacidin at 2.1 Angstrom resolution

Sleiman, D., Loc'h, J., Haouz, A., Kaminski, P.A.

To be published.

Macromolecule Content

Total Structure Weight: 82.8 kDa
Atom Count: 5,928
Modeled Residue Count: 686
Deposited Residue Count: 726
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Adenylosuccinate synthetase	A, B	363	Vibrio phage phiVC8	Mutation(s): 0 Gene Names: phiVC8_p27 EC: 6.3.4.25
UniProt
Find proteins for G3FFN6 (Vibrio phage phiVC8) Explore G3FFN6 Go to UniProtKB: G3FFN6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	G3FFN6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ATP (Subject of Investigation/LOI) Query on ATP Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain F [auth A]	F [auth A], H [auth B]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Interactions & Density Focus chain F [auth A] Focus chain H [auth B]
DGP (Subject of Investigation/LOI) Query on DGP Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain D [auth A] MOL2 format, chain G [auth B] MOL2 format, chain D [auth A] mmCIF format, chain G [auth B] mmCIF format, chain D [auth A]	D [auth A], G [auth B]	2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE C₁₀ H₁₄ N₅ O₇ P LTFMZDNNPPEQNG-KVQBGUIXSA-N		Interactions Focus chain D [auth A] Focus chain G [auth B] Interactions & Density Focus chain D [auth A] Focus chain G [auth B]
FLC Query on FLC Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	CITRATE ANION C₆ H₅ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-K		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
HDA (Subject of Investigation/LOI) Query on HDA Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	HADACIDIN C₃ H₅ N O₄ URJHVPKUWOUENU-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.222 (Depositor), 0.223 (DCC)
R-Value Work: 0.189 (Depositor), 0.192 (DCC)
R-Value Observed: 0.191 (Depositor)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.97	α = 90
b = 91.97	β = 90
c = 192.75	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2019-06-26

Deposition Author(s):

This entry supersedes: 6FJR

Revision History (Full details and data files)

Version 1.0: 2019-06-26
Type: Initial release
Version 1.1: 2024-05-08
Changes: Data collection, Database references

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