4NHZ | pdb_00004nhz

Crystal structure of glutathione transferase BBTA-3750 from Bradyrhizobium sp., Target EFI-507290, with one glutathione bound

PDB DOI: https://doi.org/10.2210/pdb4NHZ/pdb

Classification: TRANSFERASE
Organism(s): Bradyrhizobium sp. BTAi1
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2013-11-05 Released: 2013-11-20
Deposition Author(s): Patskovsky, Y., Vetting, M.W., Toro, R., Bhosle, R., Al Obaidi, N., Morisco, L.L., Wasserman, S.R., Sojitra, S., Stead, M., Washington, E., Scott Glenn, A., Chowdhury, S., Evans, B., Hammonds, J., Hillerich, B., Love, J., Seidel, R.D., Imker, H.J., Gerlt, J.A., Armstrong, R.N., Almo, S.C., Enzyme Function Initiative (EFI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.225 (Depositor), 0.236 (DCC)
R-Value Work:
0.186 (Depositor), 0.199 (DCC)
R-Value Observed:
0.187 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Crystal Structure of Glutathione Transferase Bbta-3750 from Bradyrhizobium Sp., Target Efi-507290

Patskovsky, Y., Vetting, M.W., Toro, R., Bhosle, R., Al Obaidi, N., Morisco, L.L., Wasserman, S.R., Sojitra, S., Stead, M., Washington, E., Scott Glenn, A., Chowdhury, S., Evans, B., Hammonds, J., Hillerich, B., Love, J., Seidel, R.D., Imker, H.J., Gerlt, J.A., Armstrong, R.N., Almo, S.C.

To be published.

Macromolecule Content

Total Structure Weight: 469.53 kDa
Atom Count: 32,619
Modeled Residue Count: 3,734
Deposited Residue Count: 4,096
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative glutathione S-transferase enzyme with thioredoxin-like domain	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P	256	Bradyrhizobium sp. BTAi1	Mutation(s): 0 Gene Names: BBta_3750

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GSH Query on GSH Download:Ideal Coordinates CCD File SDF format, chain Z [auth J] SDF format, chain Y [auth I] SDF format, chain X [auth H] SDF format, chain W [auth G] SDF format, chain V [auth F] SDF format, chain U [auth E] SDF format, chain T [auth D] SDF format, chain S [auth C] SDF format, chain R [auth B] SDF format, chain Q [auth A] SDF format, chain FA [auth P] SDF format, chain EA [auth O] SDF format, chain DA [auth N] SDF format, chain CA [auth M] SDF format, chain BA [auth L] SDF format, chain AA [auth K] MOL2 format, chain Z [auth J] MOL2 format, chain Y [auth I] MOL2 format, chain X [auth H] MOL2 format, chain W [auth G] MOL2 format, chain V [auth F] MOL2 format, chain U [auth E] MOL2 format, chain T [auth D] MOL2 format, chain S [auth C] MOL2 format, chain R [auth B] MOL2 format, chain Q [auth A] MOL2 format, chain FA [auth P] MOL2 format, chain EA [auth O] MOL2 format, chain DA [auth N] MOL2 format, chain CA [auth M] MOL2 format, chain BA [auth L] MOL2 format, chain AA [auth K] mmCIF format, chain Z [auth J] mmCIF format, chain Y [auth I] mmCIF format, chain X [auth H] mmCIF format, chain W [auth G] mmCIF format, chain V [auth F] mmCIF format, chain U [auth E] mmCIF format, chain T [auth D] mmCIF format, chain S [auth C] mmCIF format, chain R [auth B] mmCIF format, chain Q [auth A] mmCIF format, chain FA [auth P] mmCIF format, chain EA [auth O] mmCIF format, chain DA [auth N] mmCIF format, chain CA [auth M] mmCIF format, chain BA [auth L] mmCIF format, chain AA [auth K]	AA [auth K] BA [auth L] CA [auth M] DA [auth N] EA [auth O] AA [auth K], BA [auth L], CA [auth M], DA [auth N], EA [auth O], FA [auth P], Q [auth A], R [auth B], S [auth C], T [auth D], U [auth E], V [auth F], W [auth G], X [auth H], Y [auth I], Z [auth J]	Glutathione C₁₀ H₁₇ N₃ O₆ S RWSXRVCMGQZWBV-WDSKDSINSA-N		Interactions Focus chain AA [auth K] Focus chain BA [auth L] Focus chain CA [auth M] Focus chain DA [auth N] Focus chain EA [auth O] Focus chain FA [auth P] Focus chain Q [auth A] Focus chain R [auth B] Focus chain S [auth C] Focus chain T [auth D] Focus chain U [auth E] Focus chain V [auth F] Focus chain W [auth G] Focus chain X [auth H] Focus chain Y [auth I] Focus chain Z [auth J] Interactions & Density Focus chain AA [auth K] Focus chain BA [auth L] Focus chain CA [auth M] Focus chain DA [auth N] Focus chain EA [auth O] Focus chain FA [auth P] Focus chain Q [auth A] Focus chain R [auth B] Focus chain S [auth C] Focus chain T [auth D] Focus chain U [auth E] Focus chain V [auth F] Focus chain W [auth G] Focus chain X [auth H] Focus chain Y [auth I] Focus chain Z [auth J]

Biologically Interesting Molecules (External Reference)

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_002593 (GSH) Query on PRD_002593	AA [auth K] BA [auth L] CA [auth M] DA [auth N] EA [auth O] AA [auth K], BA [auth L], CA [auth M], DA [auth N], EA [auth O], FA [auth P], Q [auth A], R [auth B], S [auth C], T [auth D], U [auth E], V [auth F], W [auth G], X [auth H], Y [auth I], Z [auth J]	Glutathione	Peptide-like / Oxidation-reduction		Interactions Focus chain AA [auth K] Focus chain BA [auth L] Focus chain CA [auth M] Focus chain DA [auth N] Focus chain EA [auth O] Focus chain FA [auth P] Focus chain Q [auth A] Focus chain R [auth B] Focus chain S [auth C] Focus chain T [auth D] Focus chain U [auth E] Focus chain V [auth F] Focus chain W [auth G] Focus chain X [auth H] Focus chain Y [auth I] Focus chain Z [auth J] Interactions & Density Focus chain AA [auth K] Focus chain BA [auth L] Focus chain CA [auth M] Focus chain DA [auth N] Focus chain EA [auth O] Focus chain FA [auth P] Focus chain Q [auth A] Focus chain R [auth B] Focus chain S [auth C] Focus chain T [auth D] Focus chain U [auth E] Focus chain V [auth F] Focus chain W [auth G] Focus chain X [auth H] Focus chain Y [auth I] Focus chain Z [auth J]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.225 (Depositor), 0.236 (DCC)
R-Value Work: 0.186 (Depositor), 0.199 (DCC)
R-Value Observed: 0.187 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.998	α = 89.98
b = 99.359	β = 89.97
c = 108.734	γ = 89.99

Software Package:

Software Name	Purpose
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: 2013-11-20

Deposition Author(s):

Enzyme Function Initiative (EFI)

Revision History (Full details and data files)

Version 1.0: 2013-11-20
Type: Initial release
Version 1.1: 2018-01-24
Changes: Structure summary
Version 1.2: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description