3NZT | pdb_00003nzt

2.0 Angstrom Crystal structure of Glutamate--Cysteine Ligase (gshA) ftom Francisella tularensis in Complex with AMP

PDB DOI: https://doi.org/10.2210/pdb3NZT/pdb

Classification: LIGASE
Organism(s): Francisella tularensis subsp. tularensis
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2010-07-16 Released: 2010-07-28
Deposition Author(s): Minasov, G., Halavaty, A., Shuvalova, L., Dubrovska, I., Winsor, J., Papazisi, L., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.196 (Depositor), 0.204 (DCC)
R-Value Work:
0.164 (Depositor), 0.171 (DCC)
R-Value Observed:
0.165 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

2.0 Angstrom Crystal structure of Glutamate--Cysteine Ligase (gshA) ftom Francisella tularensis in Complex with AMP.

Minasov, G., Halavaty, A., Shuvalova, L., Dubrovska, I., Winsor, J., Papazisi, L., Anderson, W.F.

To be published.

Macromolecule Content

Total Structure Weight: 61.13 kDa
Atom Count: 4,530
Modeled Residue Count: 498
Deposited Residue Count: 525
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutamate--cysteine ligase	A	525	Francisella tularensis subsp. tularensis	Mutation(s): 0 Gene Names: FTT_0367c, gshA EC: 6.3.2.2
UniProt
Find proteins for Q5NHS8 (Francisella tularensis subsp. tularensis (strain SCHU S4 / Schu 4)) Explore Q5NHS8 Go to UniProtKB: Q5NHS8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5NHS8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AMP Query on AMP Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	ADENOSINE MONOPHOSPHATE C₁₀ H₁₄ N₅ O₇ P UDMBCSSLTHHNCD-KQYNXXCUSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] 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] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] 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] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] 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]	C [auth A] D [auth A] E [auth A] F [auth A] G [auth A] C [auth A], D [auth A], 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]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain D [auth A] 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] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] 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]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.196 (Depositor), 0.204 (DCC)
R-Value Work: 0.164 (Depositor), 0.171 (DCC)
R-Value Observed: 0.165 (Depositor)

Diffraction Data:

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.849	α = 90
b = 89.849	β = 90
c = 151.468	γ = 120

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2010-07-28

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2010-07-28
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-11-08
Changes: Advisory, Refinement description
Version 1.3: 2023-09-06
Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description
Version 1.4: 2024-11-20
Changes: Structure summary

3NZT | pdb_00003nzt

2.0 Angstrom Crystal structure of Glutamate--Cysteine Ligase (gshA) ftom Francisella tularensis in Complex with AMP

Literature

2.0 Angstrom Crystal structure of Glutamate--Cysteine Ligase (gshA) ftom Francisella tularensis in Complex with AMP.

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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