4J2F | pdb_00004j2f

Crystal structure of a glutathione transferase family member from Ricinus communis, target EFI-501866

PDB DOI: https://doi.org/10.2210/pdb4J2F/pdb

Classification: Lyase, Transferase
Organism(s): Ricinus communis
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2013-02-04 Released: 2013-02-27
Deposition Author(s): Kim, J., Toro, R., Bhosle, R., Al Obaidi, N.F., Morisco, L.L., Wasserman, S.R., Sojitra, S., Washington, E., Scott Glenn, A., Chowdhury, S., Evans, B., Hammonds, J., Hillerich, B., Love, J., Seidel, R.D., Imker, H.J., Armstrong, R.N., Gerlt, J.A., Almo, S.C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.248 (Depositor), 0.253 (DCC)
R-Value Work:
0.203 (Depositor)
R-Value Observed:
0.206 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of a glutathione transferase family member from Ricinus communis, target EFI-501866

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

To be published.

Macromolecule Content

Total Structure Weight: 25.7 kDa
Atom Count: 1,839
Modeled Residue Count: 218
Deposited Residue Count: 223
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutathione s-transferase	A	223	Ricinus communis	Mutation(s): 0 Gene Names: RCOM_1023660 EC: 4.4.1.5 (PDB Primary Data), 2.5.1.18 (UniProt)
UniProt
Find proteins for B9RWR5 (Ricinus communis) Explore B9RWR5 Go to UniProtKB: B9RWR5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B9RWR5
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 B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.248 (Depositor), 0.253 (DCC)
R-Value Work: 0.203 (Depositor)
R-Value Observed: 0.206 (Depositor)

Space Group: C 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.556	α = 90
b = 112.438	β = 90
c = 54.408	γ = 90

Software Package:

Software Name	Purpose
CBASS	data collection
MOLREP	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2013-02-27

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-02-27
Type: Initial release
Version 1.1: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description